[med-svn] [lambda-align] 14/15: Imported Upstream version 1.0.0
Sascha Steinbiss
satta at debian.org
Fri Aug 19 16:10:06 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository lambda-align.
commit 3c989ef370c752c9dc19a5136bae33ea8dc77acc
Author: Sascha Steinbiss <satta at debian.org>
Date: Fri Aug 19 15:32:41 2016 +0000
Imported Upstream version 1.0.0
---
CMakeLists.txt | 4 +-
LICENSE-AGPL3.rst | 671 -------------------------------
LICENSE-GPL3.rst | 704 +++++++++++++++++++++++++++++++++
LICENSE.rst | 8 +-
src/CMakeLists.txt | 6 +-
src/holders.hpp | 79 +---
src/lambda.cpp | 103 ++---
src/lambda.hpp | 1033 ++++++++++--------------------------------------
src/lambda_indexer.cpp | 30 +-
src/lambda_indexer.hpp | 263 ++++++------
src/match.hpp | 32 +-
src/misc.hpp | 35 --
src/options.hpp | 276 +++----------
src/output.hpp | 25 +-
14 files changed, 1215 insertions(+), 2054 deletions(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 49bcb36..58969a9 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -37,5 +37,5 @@ add_subdirectory(src)
# Add Tests
# ----------------------------------------------------------------------------
-# message ("\n${ColourBold}Setting up unit tests${ColourReset}")
-# add_subdirectory(tests)
+message ("\n${ColourBold}Setting up unit tests${ColourReset}")
+add_subdirectory(tests)
diff --git a/LICENSE-AGPL3.rst b/LICENSE-AGPL3.rst
deleted file mode 100644
index 980af45..0000000
--- a/LICENSE-AGPL3.rst
+++ /dev/null
@@ -1,671 +0,0 @@
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-to choose that version for the Program.
-
-Later license versions may give you additional or different
-permissions. However, no additional obligations are imposed on any
-author or copyright holder as a result of your choosing to follow a
-later version.
-
-15. Disclaimer of Warranty
-~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
-APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
-HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
-OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
-THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
-IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
-ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
-
-16. Limitation of Liability
-~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
-THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
-GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
-USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
-DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
-PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
-EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
-SUCH DAMAGES.
-
-17. Interpretation of Sections 15 and 16
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-If the disclaimer of warranty and limitation of liability provided
-above cannot be given local legal effect according to their terms,
-reviewing courts shall apply local law that most closely approximates
-an absolute waiver of all civil liability in connection with the
-Program, unless a warranty or assumption of liability accompanies a
-copy of the Program in return for a fee.
-
-*END OF TERMS AND CONDITIONS*
-
-How to Apply These Terms to Your New Programs
----------------------------------------------
-
-If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-
-To do so, attach the following notices to the program. It is safest
-to attach them to the start of each source file to most effectively
-state the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
-| <one line to give the program's name and a brief idea of what it does.>
-| Copyright (C) <year> <name of author>
-|
-| This program is free software: you can redistribute it and/or modify
-| it under the terms of the GNU Affero General Public License as published by
-| the Free Software Foundation, either version 3 of the License, or
-| (at your option) any later version.
-|
-| This program is distributed in the hope that it will be useful,
-| but WITHOUT ANY WARRANTY; without even the implied warranty of
-| MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-| GNU Affero General Public License for more details.
-|
-| You should have received a copy of the GNU Affero General Public License
-| along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-Also add information on how to contact you by electronic and paper mail.
-
-If your software can interact with users remotely through a computer
-network, you should also make sure that it provides a way for users to
-get its source. For example, if your program is a web application, its
-interface could display a "Source" link that leads users to an archive
-of the code. There are many ways you could offer source, and different
-solutions will be better for different programs; see section 13 for the
-specific requirements.
-
-You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU AGPL, see
-<http://www.gnu.org/licenses/>.
diff --git a/LICENSE-GPL3.rst b/LICENSE-GPL3.rst
new file mode 100644
index 0000000..b2cade9
--- /dev/null
+++ b/LICENSE-GPL3.rst
@@ -0,0 +1,704 @@
+GNU GENERAL PUBLIC LICENSE
+==========================
+
+Version 3, 29 June 2007
+
+Copyright (C) 2007 `Free Software Foundation, Inc. <http://fsf.org/>`_
+
+Everyone is permitted to copy and distribute verbatim copies of this
+license document, but changing it is not allowed.
+
+Preamble
+--------
+
+The GNU General Public License is a free, copyleft license for software
+and other kinds of works.
+
+The licenses for most software and other practical works are designed to
+take away your freedom to share and change the works. By contrast, the
+GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users. We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors. You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price.
+Our General Public Licenses are designed to make sure that you have the
+freedom to distribute copies of free software (and charge for them if
+you wish), that you receive source code or can get it if you want it,
+that you can change the software or use pieces of it in new free
+programs, and that you know you can do these things.
+
+To protect your rights, we need to prevent others from denying you these
+rights or asking you to surrender the rights. Therefore, you have
+certain responsibilities if you distribute copies of the software, or if
+you modify it: responsibilities to respect the freedom of others.
+
+For example, if you distribute copies of such a program, whether gratis
+or for a fee, you must pass on to the recipients the same freedoms that
+you received. You must make sure that they, too, receive or can get the
+source code. And you must show them these terms so they know their
+rights.
+
+Developers that use the GNU GPL protect your rights with two steps:
+
+1. assert copyright on the software, and
+2. offer you this License giving you legal permission to copy,
+ distribute and/or modify it.
+
+For the developers' and authors' protection, the GPL clearly explains
+that there is no warranty for this free software. For both users' and
+authors' sake, the GPL requires that modified versions be marked as
+changed, so that their problems will not be attributed erroneously to
+authors of previous versions.
+
+Some devices are designed to deny users access to install or run
+modified versions of the software inside them, although the manufacturer
+can do so. This is fundamentally incompatible with the aim of protecting
+users' freedom to change the software. The systematic pattern of such
+abuse occurs in the area of products for individuals to use, which is
+precisely where it is most unacceptable. Therefore, we have designed
+this version of the GPL to prohibit the practice for those products. If
+such problems arise substantially in other domains, we stand ready to
+extend this provision to those domains in future versions of the GPL, as
+needed to protect the freedom of users.
+
+Finally, every program is threatened constantly by software patents.
+States should not allow patents to restrict development and use of
+software on general-purpose computers, but in those that do, we wish to
+avoid the special danger that patents applied to a free program could
+make it effectively proprietary. To prevent this, the GPL assures that
+patents cannot be used to render the program non-free.
+
+The precise terms and conditions for copying, distribution and
+modification follow.
+
+TERMS AND CONDITIONS
+--------------------
+
+0. Definitions.
+~~~~~~~~~~~~~~~
+
+*This License* refers to version 3 of the GNU General Public License.
+
+*Copyright* also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
+
+*The Program* refers to any copyrightable work licensed under this
+License. Each licensee is addressed as *you*. *Licensees* and
+*recipients* may be individuals or organizations.
+
+To *modify* a work means to copy from or adapt all or part of the work
+in a fashion requiring copyright permission, other than the making of an
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+earlier work or a work *based on* the earlier work.
+
+A *covered work* means either the unmodified Program or a work based on
+the Program.
+
+To *propagate* a work means to do anything with it that, without
+permission, would make you directly or secondarily liable for
+infringement under applicable copyright law, except executing it on a
+computer or modifying a private copy. Propagation includes copying,
+distribution (with or without modification), making available to the
+public, and in some countries other activities as well.
+
+To *convey* a work means any kind of propagation that enables other
+parties to make or receive copies. Mere interaction with a user through
+a computer network, with no transfer of a copy, is not conveying.
+
+An interactive user interface displays *Appropriate Legal Notices* to
+the extent that it includes a convenient and prominently visible feature
+that
+
+1. displays an appropriate copyright notice, and
+2. tells the user that there is no warranty for the work (except to the
+ extent that warranties are provided), that licensees may convey the
+ work under this License, and how to view a copy of this License.
+
+If the interface presents a list of user commands or options, such as a
+menu, a prominent item in the list meets this criterion.
+
+1. Source Code.
+~~~~~~~~~~~~~~~
+
+The *source code* for a work means the preferred form of the work for
+making modifications to it. *Object code* means any non-source form of a
+work.
+
+A *Standard Interface* means an interface that either is an official
+standard defined by a recognized standards body, or, in the case of
+interfaces specified for a particular programming language, one that is
+widely used among developers working in that language.
+
+The *System Libraries* of an executable work include anything, other
+than the work as a whole, that (a) is included in the normal form of
+packaging a Major Component, but which is not part of that Major
+Component, and (b) serves only to enable use of the work with that Major
+Component, or to implement a Standard Interface for which an
+implementation is available to the public in source code form. A *Major
+Component*, in this context, means a major essential component (kernel,
+window system, and so on) of the specific operating system (if any) on
+which the executable work runs, or a compiler used to produce the work,
+or an object code interpreter used to run it.
+
+The *Corresponding Source* for a work in object code form means all the
+source code needed to generate, install, and (for an executable work)
+run the object code and to modify the work, including scripts to control
+those activities. However, it does not include the work's System
+Libraries, or general-purpose tools or generally available free programs
+which are used unmodified in performing those activities but which are
+not part of the work. For example, Corresponding Source includes
+interface definition files associated with source files for the work,
+and the source code for shared libraries and dynamically linked
+subprograms that the work is specifically designed to require, such as
+by intimate data communication or control flow between those subprograms
+and other parts of the work.
+
+The Corresponding Source need not include anything that users can
+regenerate automatically from other parts of the Corresponding Source.
+
+The Corresponding Source for a work in source code form is that same
+work.
+
+2. Basic Permissions.
+~~~~~~~~~~~~~~~~~~~~~
+
+All rights granted under this License are granted for the term of
+copyright on the Program, and are irrevocable provided the stated
+conditions are met. This License explicitly affirms your unlimited
+permission to run the unmodified Program. The output from running a
+covered work is covered by this License only if the output, given its
+content, constitutes a covered work. This License acknowledges your
+rights of fair use or other equivalent, as provided by copyright law.
+
+You may make, run and propagate covered works that you do not convey,
+without conditions so long as your license otherwise remains in force.
+You may convey covered works to others for the sole purpose of having
+them make modifications exclusively for you, or provide you with
+facilities for running those works, provided that you comply with the
+terms of this License in conveying all material for which you do not
+control copyright. Those thus making or running the covered works for
+you must do so exclusively on your behalf, under your direction and
+control, on terms that prohibit them from making any copies of your
+copyrighted material outside their relationship with you.
+
+Conveying under any other circumstances is permitted solely under the
+conditions stated below. Sublicensing is not allowed; section 10 makes
+it unnecessary.
+
+3. Protecting Users' Legal Rights From Anti-Circumvention Law.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+No covered work shall be deemed part of an effective technological
+measure under any applicable law fulfilling obligations under article 11
+of the WIPO copyright treaty adopted on 20 December 1996, or similar
+laws prohibiting or restricting circumvention of such measures.
+
+When you convey a covered work, you waive any legal power to forbid
+circumvention of technological measures to the extent such circumvention
+is effected by exercising rights under this License with respect to the
+covered work, and you disclaim any intention to limit operation or
+modification of the work as a means of enforcing, against the work's
+users, your or third parties' legal rights to forbid circumvention of
+technological measures.
+
+4. Conveying Verbatim Copies.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+You may convey verbatim copies of the Program's source code as you
+receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice; keep
+intact all notices stating that this License and any non-permissive
+terms added in accord with section 7 apply to the code; keep intact all
+notices of the absence of any warranty; and give all recipients a copy
+of this License along with the Program.
+
+You may charge any price or no price for each copy that you convey, and
+you may offer support or warranty protection for a fee.
+
+5. Conveying Modified Source Versions.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+You may convey a work based on the Program, or the modifications to
+produce it from the Program, in the form of source code under the terms
+of section 4, provided that you also meet all of these conditions:
+
+- a) The work must carry prominent notices stating that you modified it,
+and giving a relevant date. - b) The work must carry prominent notices
+stating that it is released under this License and any conditions added
+under section 7. This requirement modifies the requirement in section 4
+to *keep intact all notices*. - c) You must license the entire work, as
+a whole, under this License to anyone who comes into possession of a
+copy. This License will therefore apply, along with any applicable
+section 7 additional terms, to the whole of the work, and all its parts,
+regardless of how they are packaged. This License gives no permission to
+license the work in any other way, but it does not invalidate such
+permission if you have separately received it. - d) If the work has
+interactive user interfaces, each must display Appropriate Legal
+Notices; however, if the Program has interactive interfaces that do not
+display Appropriate Legal Notices, your work need not make them do so.
+
+A compilation of a covered work with other separate and independent
+works, which are not by their nature extensions of the covered work, and
+which are not combined with it such as to form a larger program, in or
+on a volume of a storage or distribution medium, is called an
+*aggregate* if the compilation and its resulting copyright are not used
+to limit the access or legal rights of the compilation's users beyond
+what the individual works permit. Inclusion of a covered work in an
+aggregate does not cause this License to apply to the other parts of the
+aggregate.
+
+6. Conveying Non-Source Forms.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+You may convey a covered work in object code form under the terms of
+sections 4 and 5, provided that you also convey the machine-readable
+Corresponding Source under the terms of this License, in one of these
+ways:
+
+- a) Convey the object code in, or embodied in, a physical product
+(including a physical distribution medium), accompanied by the
+Corresponding Source fixed on a durable physical medium customarily used
+for software interchange. - b) Convey the object code in, or embodied
+in, a physical product (including a physical distribution medium),
+accompanied by a written offer, valid for at least three years and valid
+for as long as you offer spare parts or customer support for that
+product model, to give anyone who possesses the object code either
+ 1. a copy of the Corresponding Source for all the software in the
+product that is covered by this License, on a durable physical medium
+customarily used for software interchange, for a price no more than your
+reasonable cost of physically performing this conveying of source, or 2.
+access to copy the Corresponding Source from a network server at no
+charge.
+
+- c) Convey individual copies of the object code with a copy of the
+written offer to provide the Corresponding Source. This alternative is
+allowed only occasionally and noncommercially, and only if you received
+the object code with such an offer, in accord with subsection 6b. - d)
+Convey the object code by offering access from a designated place
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+Corresponding Source in the same way through the same place at no
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+Regardless of what server hosts the Corresponding Source, you remain
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+satisfy these requirements. - e) Convey the object code using
+peer-to-peer transmission, provided you inform other peers where the
+object code and Corresponding Source of the work are being offered to
+the general public at no charge under subsection 6d.
+
+A separable portion of the object code, whose source code is excluded
+from the Corresponding Source as a System Library, need not be included
+in conveying the object code work.
+
+A *User Product* is either
+
+1. a *consumer product*, which means any tangible personal property
+ which is normally used for personal, family, or household purposes,
+ or
+2. anything designed or sold for incorporation into a dwelling.
+
+In determining whether a product is a consumer product, doubtful cases
+shall be resolved in favor of coverage. For a particular product
+received by a particular user, *normally used* refers to a typical or
+common use of that class of product, regardless of the status of the
+particular user or of the way in which the particular user actually
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+commercial, industrial or non-consumer uses, unless such uses represent
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+
+*Installation Information* for a User Product means any methods,
+procedures, authorization keys, or other information required to install
+and execute modified versions of a covered work in that User Product
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+must suffice to ensure that the continued functioning of the modified
+object code is in no case prevented or interfered with solely because
+modification has been made.
+
+If you convey an object code work under this section in, or with, or
+specifically for use in, a User Product, and the conveying occurs as
+part of a transaction in which the right of possession and use of the
+User Product is transferred to the recipient in perpetuity or for a
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+Corresponding Source conveyed under this section must be accompanied by
+the Installation Information. But this requirement does not apply if
+neither you nor any third party retains the ability to install modified
+object code on the User Product (for example, the work has been
+installed in ROM).
+
+The requirement to provide Installation Information does not include a
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+for a work that has been modified or installed by the recipient, or for
+the User Product in which it has been modified or installed. Access to a
+network may be denied when the modification itself materially and
+adversely affects the operation of the network or violates the rules and
+protocols for communication across the network.
+
+Corresponding Source conveyed, and Installation Information provided, in
+accord with this section must be in a format that is publicly documented
+(and with an implementation available to the public in source code
+form), and must require no special password or key for unpacking,
+reading or copying.
+
+7. Additional Terms.
+~~~~~~~~~~~~~~~~~~~~
+
+*Additional permissions* are terms that supplement the terms of this
+License by making exceptions from one or more of its conditions.
+Additional permissions that are applicable to the entire Program shall
+be treated as though they were included in this License, to the extent
+that they are valid under applicable law. If additional permissions
+apply only to part of the Program, that part may be used separately
+under those permissions, but the entire Program remains governed by this
+License without regard to the additional permissions.
+
+When you convey a copy of a covered work, you may at your option remove
+any additional permissions from that copy, or from any part of it.
+(Additional permissions may be written to require their own removal in
+certain cases when you modify the work.) You may place additional
+permissions on material, added by you to a covered work, for which you
+have or can give appropriate copyright permission.
+
+Notwithstanding any other provision of this License, for material you
+add to a covered work, you may (if authorized by the copyright holders
+of that material) supplement the terms of this License with terms:
+
+a. Disclaiming warranty or limiting liability differently from the terms
+ of sections 15 and 16 of this License; or
+b. Requiring preservation of specified reasonable legal notices or
+ author attributions in that material or in the Appropriate Legal
+ Notices displayed by works containing it; or
+c. Prohibiting misrepresentation of the origin of that material, or
+ requiring that modified versions of such material be marked in
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+ authors of the material; or
+e. Declining to grant rights under trademark law for use of some trade
+ names, trademarks, or service marks; or
+f. Requiring indemnification of licensors and authors of that material
+ by anyone who conveys the material (or modified versions of it) with
+ contractual assumptions of liability to the recipient, for any
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+ licensors and authors.
+
+All other non-permissive additional terms are considered *further
+restrictions* within the meaning of section 10. If the Program as you
+received it, or any part of it, contains a notice stating that it is
+governed by this License along with a term that is a further
+restriction, you may remove that term. If a license document contains a
+further restriction but permits relicensing or conveying under this
+License, you may add to a covered work material governed by the terms of
+that license document, provided that the further restriction does not
+survive such relicensing or conveying.
+
+If you add terms to a covered work in accord with this section, you must
+place, in the relevant source files, a statement of the additional terms
+that apply to those files, or a notice indicating where to find the
+applicable terms.
+
+Additional terms, permissive or non-permissive, may be stated in the
+form of a separately written license, or stated as exceptions; the above
+requirements apply either way.
+
+8. Termination.
+~~~~~~~~~~~~~~~
+
+You may not propagate or modify a covered work except as expressly
+provided under this License. Any attempt otherwise to propagate or
+modify it is void, and will automatically terminate your rights under
+this License (including any patent licenses granted under the third
+paragraph of section 11).
+
+However, if you cease all violation of this License, then your license
+from a particular copyright holder is reinstated
+
+a. provisionally, unless and until the copyright holder explicitly and
+ finally terminates your license, and
+b. permanently, if the copyright holder fails to notify you of the
+ violation by some reasonable means prior to 60 days after the
+ cessation.
+
+Moreover, your license from a particular copyright holder is reinstated
+permanently if the copyright holder notifies you of the violation by
+some reasonable means, this is the first time you have received notice
+of violation of this License (for any work) from that copyright holder,
+and you cure the violation prior to 30 days after your receipt of the
+notice.
+
+Termination of your rights under this section does not terminate the
+licenses of parties who have received copies or rights from you under
+this License. If your rights have been terminated and not permanently
+reinstated, you do not qualify to receive new licenses for the same
+material under section 10.
+
+9. Acceptance Not Required for Having Copies.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+You are not required to accept this License in order to receive or run a
+copy of the Program. Ancillary propagation of a covered work occurring
+solely as a consequence of using peer-to-peer transmission to receive a
+copy likewise does not require acceptance. However, nothing other than
+this License grants you permission to propagate or modify any covered
+work. These actions infringe copyright if you do not accept this
+License. Therefore, by modifying or propagating a covered work, you
+indicate your acceptance of this License to do so.
+
+10. Automatic Licensing of Downstream Recipients.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Each time you convey a covered work, the recipient automatically
+receives a license from the original licensors, to run, modify and
+propagate that work, subject to this License. You are not responsible
+for enforcing compliance by third parties with this License.
+
+An *entity transaction* is a transaction transferring control of an
+organization, or substantially all assets of one, or subdividing an
+organization, or merging organizations. If propagation of a covered work
+results from an entity transaction, each party to that transaction who
+receives a copy of the work also receives whatever licenses to the work
+the party's predecessor in interest had or could give under the previous
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+work from the predecessor in interest, if the predecessor has it or can
+get it with reasonable efforts.
+
+You may not impose any further restrictions on the exercise of the
+rights granted or affirmed under this License. For example, you may not
+impose a license fee, royalty, or other charge for exercise of rights
+granted under this License, and you may not initiate litigation
+(including a cross-claim or counterclaim in a lawsuit) alleging that any
+patent claim is infringed by making, using, selling, offering for sale,
+or importing the Program or any portion of it.
+
+11. Patents.
+~~~~~~~~~~~~
+
+A *contributor* is a copyright holder who authorizes use under this
+License of the Program or a work on which the Program is based. The work
+thus licensed is called the contributor's *contributor version*.
+
+A contributor's *essential patent claims* are all patent claims owned or
+controlled by the contributor, whether already acquired or hereafter
+acquired, that would be infringed by some manner, permitted by this
+License, of making, using, or selling its contributor version, but do
+not include claims that would be infringed only as a consequence of
+further modification of the contributor version. For purposes of this
+definition, *control* includes the right to grant patent sublicenses in
+a manner consistent with the requirements of this License.
+
+Each contributor grants you a non-exclusive, worldwide, royalty-free
+patent license under the contributor's essential patent claims, to make,
+use, sell, offer for sale, import and otherwise run, modify and
+propagate the contents of its contributor version.
+
+In the following three paragraphs, a *patent license* is any express
+agreement or commitment, however denominated, not to enforce a patent
+(such as an express permission to practice a patent or covenant not to
+sue for patent infringement). To *grant* such a patent license to a
+party means to make such an agreement or commitment not to enforce a
+patent against the party.
+
+If you convey a covered work, knowingly relying on a patent license, and
+the Corresponding Source of the work is not available for anyone to
+copy, free of charge and under the terms of this License, through a
+publicly available network server or other readily accessible means,
+then you must either
+
+1. cause the Corresponding Source to be so available, or
+2. arrange to deprive yourself of the benefit of the patent license for
+ this particular work, or
+3. arrange, in a manner consistent with the requirements of this
+ License, to extend the patent license to downstream recipients.
+
+*Knowingly relying* means you have actual knowledge that, but for the
+patent license, your conveying the covered work in a country, or your
+recipient's use of the covered work in a country, would infringe one or
+more identifiable patents in that country that you have reason to
+believe are valid.
+
+If, pursuant to or in connection with a single transaction or
+arrangement, you convey, or propagate by procuring conveyance of, a
+covered work, and grant a patent license to some of the parties
+receiving the covered work authorizing them to use, propagate, modify or
+convey a specific copy of the covered work, then the patent license you
+grant is automatically extended to all recipients of the covered work
+and works based on it.
+
+A patent license is *discriminatory* if it does not include within the
+scope of its coverage, prohibits the exercise of, or is conditioned on
+the non-exercise of one or more of the rights that are specifically
+granted under this License. You may not convey a covered work if you are
+a party to an arrangement with a third party that is in the business of
+distributing software, under which you make payment to the third party
+based on the extent of your activity of conveying the work, and under
+which the third party grants, to any of the parties who would receive
+the covered work from you, a discriminatory patent license
+
+a. in connection with copies of the covered work conveyed by you (or
+ copies made from those copies), or
+b. primarily for and in connection with specific products or
+ compilations that contain the covered work, unless you entered into
+ that arrangement, or that patent license was granted, prior to 28
+ March 2007.
+
+Nothing in this License shall be construed as excluding or limiting any
+implied license or other defenses to infringement that may otherwise be
+available to you under applicable patent law.
+
+12. No Surrender of Others' Freedom.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you
+may not convey it at all. For example, if you agree to terms that
+obligate you to collect a royalty for further conveying from those to
+whom you convey the Program, the only way you could satisfy both those
+terms and this License would be to refrain entirely from conveying the
+Program.
+
+13. Use with the GNU Affero General Public License.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notwithstanding any other provision of this License, you have permission
+to link or combine any covered work with a work licensed under version 3
+of the GNU Affero General Public License into a single combined work,
+and to convey the resulting work. The terms of this License will
+continue to apply to the part which is the covered work, but the special
+requirements of the GNU Affero General Public License, section 13,
+concerning interaction through a network will apply to the combination
+as such.
+
+14. Revised Versions of this License.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time. Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies that a certain numbered version of the GNU General Public
+License *or any later version* applies to it, you have the option of
+following the terms and conditions either of that numbered version or of
+any later version published by the Free Software Foundation. If the
+Program does not specify a version number of the GNU General Public
+License, you may choose any version ever published by the Free Software
+Foundation.
+
+If the Program specifies that a proxy can decide which future versions
+of the GNU General Public License can be used, that proxy's public
+statement of acceptance of a version permanently authorizes you to
+choose that version for the Program.
+
+Later license versions may give you additional or different permissions.
+However, no additional obligations are imposed on any author or
+copyright holder as a result of your choosing to follow a later version.
+
+15. Disclaimer of Warranty.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM *AS IS* WITHOUT
+WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF
+THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME
+THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+16. Limitation of Liability.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR
+CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES
+ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT
+NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES
+SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE
+WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN
+ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+17. Interpretation of Sections 15 and 16.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If the disclaimer of warranty and limitation of liability provided above
+cannot be given local legal effect according to their terms, reviewing
+courts shall apply local law that most closely approximates an absolute
+waiver of all civil liability in connection with the Program, unless a
+warranty or assumption of liability accompanies a copy of the Program in
+return for a fee.
+
+END OF TERMS AND CONDITIONS
+---------------------------
+
+How to Apply These Terms to Your New Programs
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these
+terms.
+
+To do so, attach the following notices to the program. It is safest to
+attach them to the start of each source file to most effectively state
+the exclusion of warranty; and each file should have at least the
+*copyright* line and a pointer to where the full notice is found.
+
+::
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program does terminal interaction, make it output a short notice
+like this when it starts in an interactive mode:
+
+::
+
+ <program> Copyright (C) <year> <name of author>
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands ``show w`` and ``show c`` should show the
+appropriate parts of the General Public License. Of course, your
+program's commands might be different; for a GUI interface, you would
+use an *about box*.
+
+You should also get your employer (if you work as a programmer) or
+school, if any, to sign a *copyright disclaimer* for the program, if
+necessary. For more information on this, and how to apply and follow the
+GNU GPL, see
+`http://www.gnu.org/licenses/ <http://www.gnu.org/licenses/>`_.
+
+The GNU General Public License does not permit incorporating your
+program into proprietary programs. If your program is a subroutine
+library, you may consider it more useful to permit linking proprietary
+applications with the library. If this is what you want to do, use the
+GNU Lesser General Public License instead of this License. But first,
+please read
+`http://www.gnu.org/philosophy/why-not-lgpl.html <http://www.gnu.org/philosophy/why-not-lgpl.html>`_.
diff --git a/LICENSE.rst b/LICENSE.rst
index 2c47a5b..6c89f88 100644
--- a/LICENSE.rst
+++ b/LICENSE.rst
@@ -6,15 +6,15 @@ lambda copyright
All rights reserved.
Lambda is *free software*: you can redistribute it and/or modify
-it under the terms of the GNU Affero General Public License as
-published by the Free Software Foundation, either version 3 of the
-License, or (at your option) any later version.
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
Lambda is distributed in the hope that it will be useful,
but **without any warranty**; without even the implied warranty of
**merchantability** or **fitness for a particular purpose**.
-See the file `LICENSE-AGPL3.rst <./LICENSE-AGPL3.rst>`__ or
+See the file `LICENSE-GPL3.rst <./LICENSE-GPL3.rst>`__ or
http://www.gnu.org/licenses/ for a full text of the license and the
rights and obligations implied.
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index d90968a..8c18c27 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -12,7 +12,7 @@
# change this after every release
set (SEQAN_APP_VERSION_MAJOR "1")
-set (SEQAN_APP_VERSION_MINOR "9")
+set (SEQAN_APP_VERSION_MINOR "0")
set (SEQAN_APP_VERSION_PATCH "0")
# don't change the following
@@ -86,7 +86,7 @@ message (STATUS "LAMBDA version is: ${SEQAN_APP_VERSION}")
option (LAMBDA_FASTBUILD "Build only blastp and blastx modes (speeds up build)." OFF)
option (LAMBDA_NATIVE_BUILD "Architecture-specific optimizations, i.e. g++ -march=native." ON)
option (LAMBDA_STATIC_BUILD "Include all libraries in the binaries." OFF)
-option (LAMBDA_MMAPPED_DB "Use mmapped access to the database." OFF)
+option (LAMBDA_MMAPPED_DB "Use mmapped access to the database." ON)
option (LAMBDA_LINGAPS_OPT "Add optimized codepaths for linear gap costs (inc. bin size and compile time)." OFF)
if (LAMBDA_FASTBUILD)
@@ -220,7 +220,7 @@ install (TARGETS lambda lambda_indexer
# Install non-binary files for the package to share/lambda
install (FILES ../LICENSE.rst
../LICENSE-BSD.rst
- ../LICENSE-AGPL3.rst
+ ../LICENSE-GPL3.rst
../README.rst
DESTINATION "share/doc/lambda")
diff --git a/src/holders.hpp b/src/holders.hpp
index 4aa9bf9..d397855 100644
--- a/src/holders.hpp
+++ b/src/holders.hpp
@@ -54,7 +54,6 @@ struct StatsHolder
uint64_t hitsMerged;
uint64_t hitsTooShort;
uint64_t hitsMasked;
- std::vector<uint16_t> seedLengths;
// pre-extension
uint64_t hitsFailedPreExtendTest;
@@ -71,12 +70,6 @@ struct StatsHolder
uint64_t hitsFinal;
uint64_t qrysWithHit;
-// times
- double timeGenSeeds;
- double timeSearch;
- double timeSort;
- double timeExtend;
-
StatsHolder()
{
clear();
@@ -88,7 +81,6 @@ struct StatsHolder
hitsMerged = 0;
hitsTooShort = 0;
hitsMasked = 0;
- seedLengths.clear();
hitsFailedPreExtendTest = 0;
hitsPutativeDuplicate = 0;
@@ -101,11 +93,6 @@ struct StatsHolder
hitsFinal = 0;
qrysWithHit = 0;
-
- timeGenSeeds = 0;
- timeSearch = 0;
- timeSort = 0;
- timeExtend = 0;
}
StatsHolder plus(StatsHolder const & rhs)
@@ -114,7 +101,6 @@ struct StatsHolder
hitsMerged += rhs.hitsMerged;
hitsTooShort += rhs.hitsTooShort;
hitsMasked += rhs.hitsMasked;
- append(seedLengths, rhs.seedLengths);
hitsFailedPreExtendTest += rhs.hitsFailedPreExtendTest;
hitsPutativeDuplicate += rhs.hitsPutativeDuplicate;
@@ -127,12 +113,6 @@ struct StatsHolder
hitsFinal += rhs.hitsFinal;
qrysWithHit += rhs.qrysWithHit;
-
- timeGenSeeds += rhs.timeGenSeeds;
- timeSearch += rhs.timeSearch;
- timeSort += rhs.timeSort;
- timeExtend += rhs.timeExtend;
-
return *this;
}
@@ -166,24 +146,19 @@ void printStats(StatsHolder const & stats, LambdaOptions const & options)
std::cout << "Remaining\033[0m"
<< "\n after Seeding "; BLANKS;
std::cout << R << rem;
- if (stats.hitsMasked)
- std::cout << "\n - masked " << R << stats.hitsMasked
- << RR << (rem -= stats.hitsMasked);
- if (options.mergePutativeSiblings)
- std::cout << "\n - merged " << R << stats.hitsMerged
- << RR << (rem -= stats.hitsMerged);
- if (options.filterPutativeDuplicates)
- std::cout << "\n - putative duplicates " << R
- << stats.hitsPutativeDuplicate << RR
- << (rem -= stats.hitsPutativeDuplicate);
- if (options.filterPutativeAbundant)
- std::cout << "\n - putative abundant " << R
- << stats.hitsPutativeAbundant << RR
- << (rem -= stats.hitsPutativeAbundant);
- if (options.preScoring)
- std::cout << "\n - failed pre-extend test " << R
- << stats.hitsFailedPreExtendTest << RR
- << (rem -= stats.hitsFailedPreExtendTest);
+ std::cout << "\n - masked " << R << stats.hitsMasked
+ << RR << (rem -= stats.hitsMasked);
+ std::cout << "\n - merged " << R << stats.hitsMerged
+ << RR << (rem -= stats.hitsMerged);
+ std::cout << "\n - putative duplicates " << R
+ << stats.hitsPutativeDuplicate << RR
+ << (rem -= stats.hitsPutativeDuplicate);
+ std::cout << "\n - putative abundant " << R
+ << stats.hitsPutativeAbundant << RR
+ << (rem -= stats.hitsPutativeAbundant);
+ std::cout << "\n - failed pre-extend test " << R
+ << stats.hitsFailedPreExtendTest << RR
+ << (rem -= stats.hitsFailedPreExtendTest);
std::cout << "\n - failed %-identity test " << R
<< stats.hitsFailedExtendPercentIdentTest << RR
<< (rem -= stats.hitsFailedExtendPercentIdentTest);
@@ -200,31 +175,6 @@ void printStats(StatsHolder const & stats, LambdaOptions const & options)
if (rem != stats.hitsFinal)
std::cout << "WARNING: hits dont add up\n";
-
- std::cout << "Detailed Non-Wall-Clock times:\n"
- << " genSeeds: " << stats.timeGenSeeds << "\n"
- << " search: " << stats.timeSearch << "\n"
- << " sort: " << stats.timeSort << "\n"
- << " extend: " << stats.timeExtend << "\n\n";
-
- if (length(stats.seedLengths))
- {
- double _seedLengthSum = std::accumulate(stats.seedLengths.begin(), stats.seedLengths.end(), 0.0);
- double seedLengthMean = _seedLengthSum / stats.seedLengths.size();
-
- double _seedLengthMeanSqSum = std::inner_product(stats.seedLengths.begin(),
- stats.seedLengths.end(),
- stats.seedLengths.begin(),
- 0.0);
- double seedLengthStdDev = std::sqrt(_seedLengthMeanSqSum / stats.seedLengths.size() -
- seedLengthMean * seedLengthMean);
- uint16_t seedLengthMax = *std::max_element(stats.seedLengths.begin(), stats.seedLengths.end());
-
- std::cout << "SeedStats:\n"
- << " avgLength: " << seedLengthMean << "\n"
- << " stddev: " << seedLengthStdDev << "\n"
- << " max: " << seedLengthMax << "\n\n";
- }
}
if (options.verbosity >= 1)
@@ -399,7 +349,7 @@ public:
// ----------------------------------------------------------------------------
template <typename TGlobalHolder_,
- typename TScoreExtension_>
+ typename TScoreExtension>
class LocalDataHolder
{
public:
@@ -408,7 +358,6 @@ public:
using TSeeds = StringSet<typename Infix<TRedQrySeq const>::Type>;
using TSeedIndex = Index<TSeeds, IndexSa<>>;
using TMatch = typename TGlobalHolder::TMatch;
- using TScoreExtension = TScoreExtension_;
// references to global stuff
diff --git a/src/lambda.cpp b/src/lambda.cpp
index a640b40..88288e4 100644
--- a/src/lambda.cpp
+++ b/src/lambda.cpp
@@ -21,9 +21,6 @@
#include <iostream>
-//TODO TEMPORARY REMOVE
-#define amd64
-
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/arg_parse.h>
@@ -54,12 +51,12 @@ using namespace seqan;
// forwards
inline int
-argConv0(LambdaOptions & options);
+argConv0(LambdaOptions const & options);
//-
template <typename TOutFormat,
BlastTabularSpec h>
inline int
-argConv1(LambdaOptions & options,
+argConv1(LambdaOptions const & options,
TOutFormat const & /**/,
BlastTabularSpecSelector<h> const &);
//-
@@ -67,7 +64,7 @@ template <typename TOutFormat,
BlastTabularSpec h,
BlastProgram p>
inline int
-argConv2(LambdaOptions & options,
+argConv2(LambdaOptions const & options,
TOutFormat const & /**/,
BlastTabularSpecSelector<h> const &,
BlastProgramSelector<p> const &);
@@ -77,7 +74,7 @@ template <typename TOutFormat,
BlastTabularSpec h,
BlastProgram p>
inline int
-argConv3(LambdaOptions & options,
+argConv3(LambdaOptions const & options,
TOutFormat const &,
BlastTabularSpecSelector<h> const &,
BlastProgramSelector<p> const &,
@@ -89,7 +86,7 @@ template <typename TOutFormat,
BlastTabularSpec h,
BlastProgram p>
inline int
-argConv4(LambdaOptions & options,
+argConv4(LambdaOptions const & options,
TOutFormat const & /**/,
BlastTabularSpecSelector<h> const &,
BlastProgramSelector<p> const &,
@@ -103,7 +100,7 @@ template <typename TIndexSpec,
BlastProgram p,
BlastTabularSpec h>
inline int
-realMain(LambdaOptions & options,
+realMain(LambdaOptions const & options,
TOutFormat const & /**/,
BlastTabularSpecSelector<h> const &,
BlastProgramSelector<p> const &,
@@ -136,7 +133,7 @@ int main(int argc, char const ** argv)
// CONVERT Run-time options to compile-time Format-Type
inline int
-argConv0(LambdaOptions & options)
+argConv0(LambdaOptions const & options)
{
CharString output = options.output;
if (endsWith(output, ".gz"))
@@ -160,7 +157,7 @@ argConv0(LambdaOptions & options)
template <typename TOutFormat,
BlastTabularSpec h>
inline int
-argConv1(LambdaOptions & options,
+argConv1(LambdaOptions const & options,
TOutFormat const & /**/,
BlastTabularSpecSelector<h> const &)
{
@@ -209,7 +206,7 @@ template <typename TOutFormat,
BlastTabularSpec h,
BlastProgram p>
inline int
-argConv2(LambdaOptions & options,
+argConv2(LambdaOptions const & options,
TOutFormat const & /**/,
BlastTabularSpecSelector<h> const &,
BlastProgramSelector<p> const &)
@@ -245,7 +242,7 @@ template <typename TOutFormat,
BlastTabularSpec h,
BlastProgram p>
inline int
-argConv3(LambdaOptions & options,
+argConv3(LambdaOptions const & options,
TOutFormat const &,
BlastTabularSpecSelector<h> const &,
BlastProgramSelector<p> const &,
@@ -280,14 +277,42 @@ template <typename TOutFormat,
BlastTabularSpec h,
BlastProgram p>
inline int
-argConv4(LambdaOptions & options,
+argConv4(LambdaOptions const & options,
TOutFormat const & /**/,
BlastTabularSpecSelector<h> const &,
BlastProgramSelector<p> const &,
TRedAlph const & /**/,
TScoreExtension const & /**/)
{
- if (options.dbIndexType == DbIndexType::SUFFIX_ARRAY)
+ int indexType = options.dbIndexType;
+// if (indexType == -1) // autodetect
+// {
+// //TODO FIX THIS WITH NEW EXTENSIONS
+// CharString file = options.dbFile;
+// append(file, ".sa");
+// struct stat buffer;
+// if (stat(toCString(file), &buffer) == 0)
+// {
+// indexType = 0;
+// } else
+// {
+// file = options.dbFile;
+// append(file, ".sa.val"); // FM Index
+// struct stat buffer;
+// if (stat(toCString(file), &buffer) == 0)
+// {
+// indexType = 1;
+// } else
+// {
+// std::cerr << "No Index file could be found, please make sure paths "
+// << "are correct and the files are readable.\n" << std::flush;
+//
+// return -1;
+// }
+// }
+// }
+
+ if (indexType == 0)
return realMain<IndexSa<>>(options,
TOutFormat(),
BlastTabularSpecSelector<h>(),
@@ -316,7 +341,7 @@ template <typename TIndexSpec,
BlastProgram p,
BlastTabularSpec h>
inline int
-realMain(LambdaOptions & options,
+realMain(LambdaOptions const & options,
TOutFormat const & /**/,
BlastTabularSpecSelector<h> const &,
BlastProgramSelector<p> const &,
@@ -330,17 +355,13 @@ realMain(LambdaOptions & options,
"\n======================================================"
"\nVersion ", SEQAN_APP_VERSION, "\n\n");
- int ret = validateIndexOptions<TRedAlph, p>(options);
- if (ret)
- return ret;
-
if (options.verbosity >= 2)
printOptions<TLocalHolder>(options);
TGlobalHolder globalHolder;
// context(globalHolder.outfile).scoringScheme._internalScheme = matr;
- ret = prepareScoring(globalHolder, options);
+ int ret = prepareScoring(globalHolder, options);
if (ret)
return ret;
@@ -352,9 +373,9 @@ realMain(LambdaOptions & options,
if (ret)
return ret;
-// ret = loadSegintervals(globalHolder, options);
-// if (ret)
-// return ret;
+ ret = loadSegintervals(globalHolder, options);
+ if (ret)
+ return ret;
ret = loadQuery(globalHolder, options);
if (ret)
@@ -420,13 +441,9 @@ realMain(LambdaOptions & options,
localHolder.init(t);
// seed
- double buf = sysTime();
- if (!options.adaptiveSeeding)
- {
- res = generateSeeds(localHolder);
- if (res)
- continue;
- }
+ res = generateSeeds(localHolder);
+ if (res)
+ continue;
if (options.doubleIndexing)
{
@@ -434,33 +451,19 @@ realMain(LambdaOptions & options,
if (res)
continue;
}
- localHolder.stats.timeGenSeeds += sysTime() - buf;
// search
- buf = sysTime();
- search(localHolder); //TODO seed refining if iterateMatches gives 0 results
- localHolder.stats.timeSearch += sysTime() - buf;
-
-// // TODO DEBUG
-// for (auto const & m : localHolder.matches)
-// _printMatch(m);
+ search(localHolder);
// sort
- if (options.filterPutativeAbundant || options.filterPutativeDuplicates || options.mergePutativeSiblings)
- {
- buf = sysTime();
- sortMatches(localHolder);
- localHolder.stats.timeSort += sysTime() - buf;
- }
+ sortMatches(localHolder);
// extend
- buf = sysTime();
- if (length(localHolder.matches) > 0)
- res = iterateMatches(localHolder);
- localHolder.stats.timeExtend += sysTime() - buf;
+ res = iterateMatches(localHolder);
if (res)
continue;
+
if ((!options.doubleIndexing) && (TID == 0) &&
(options.verbosity >= 1))
{
@@ -486,7 +489,7 @@ realMain(LambdaOptions & options,
if (!options.doubleIndexing)
{
- myPrint(options, 2, "Runtime total: ", sysTime() - start, "s.\n\n");
+ myPrint(options, 2, "Runtime: ", sysTime() - start, "s.\n\n");
}
printStats(globalHolder.stats, options);
diff --git a/src/lambda.hpp b/src/lambda.hpp
index ccc179c..c83ca44 100644
--- a/src/lambda.hpp
+++ b/src/lambda.hpp
@@ -95,81 +95,6 @@ struct Comp :
// ============================================================================
// --------------------------------------------------------------------------
-// Function readIndexOption()
-// --------------------------------------------------------------------------
-
-inline void
-readIndexOption(std::string & optionString,
- std::string const & optionIdentifier,
- LambdaOptions const & options)
-{
- std::ifstream f{(options.indexDir + "/option:" + optionIdentifier).c_str(),
- std::ios_base::in | std::ios_base::binary};
- if (f.is_open())
- {
- auto fit = directionIterator(f, Input());
- readLine(optionString, fit);
- f.close();
- }
- else
- {
- throw std::runtime_error("ERROR: Expected option specifier:\n" + options.indexDir + "/option:" +
- optionIdentifier + "\nYour index seems incompatible, try to recreate it "
- "and report a bug if the issue persists.");
- }
-}
-
-// --------------------------------------------------------------------------
-// Function validateIndexOptions()
-// --------------------------------------------------------------------------
-
-template <typename TRedAlph,
- BlastProgram p>
-inline int
-validateIndexOptions(LambdaOptions const & options)
-{
- std::string buffer;
- readIndexOption(buffer, "alph_translated", options);
- if (buffer != _alphName(TransAlph<p>()))
- {
- std::cerr << "ERROR: Your index is of translated alphabet type: " << buffer << "\n But lambda expected: "
- << _alphName(TransAlph<p>()) << "\n Did you specify the right -p parameter?\n\n";
- return -1;
-
- }
- buffer.clear();
- readIndexOption(buffer, "alph_reduced", options);
- if (buffer != _alphName(TRedAlph()))
- {
- std::cerr << "ERROR: Your index is of reduced alphabet type: " << buffer << "\n But lambda expected: "
- << _alphName(TRedAlph()) << "\n Did you specify the right -ar parameter?\n\n";
- return -1;
- }
- buffer.clear();
- readIndexOption(buffer, "db_index_type", options);
- unsigned long b = 0;
- if ((!lexicalCast(b, buffer)) || (b != static_cast<unsigned long>(options.dbIndexType)))
- {
- std::cerr << "ERROR: Your index type is: " << _indexName(static_cast<DbIndexType>(std::stoul(buffer)))
- << "\n But lambda expected: " << _indexName(options.dbIndexType)
- << "\n Did you specify the right -di parameter?\n\n";
- return -1;
- }
- if (qIsTranslated(p) && sIsTranslated(p))
- {
- buffer.clear();
- readIndexOption(buffer, "genetic_code", options);
- unsigned long b = 0;
- if ((!lexicalCast(b, buffer)) || (b != static_cast<unsigned long>(options.geneticCode)))
- {
- std::cerr << "WARNING: The codon translation table used during indexing and during search are different. "
- "This is not a problem per se, but is likely not what you want.\n\n";
- }
- }
- return 0;
-}
-
-// --------------------------------------------------------------------------
// Function prepareScoring()
// --------------------------------------------------------------------------
@@ -270,8 +195,9 @@ loadSubjects(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHo
strIdent = "Loading Subj Sequences...";
myPrint(options, 1, strIdent);
- _dbSeqs = options.indexDir;
- append(_dbSeqs, "/translated_seqs");
+ _dbSeqs = options.dbFile;
+ append(_dbSeqs, ".");
+ append(_dbSeqs, _alphName(TransAlph<p>()));
ret = open(globalHolder.subjSeqs, toCString(_dbSeqs), OPEN_RDONLY);
if (ret != true)
@@ -300,8 +226,8 @@ loadSubjects(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHo
strIdent = "Loading Subj Ids...";
myPrint(options, 1, strIdent);
- _dbSeqs = options.indexDir;
- append(_dbSeqs, "/seq_ids");
+ _dbSeqs = options.dbFile;
+ append(_dbSeqs, ".ids");
ret = open(globalHolder.subjIds, toCString(_dbSeqs), OPEN_RDONLY);
if (ret != true)
{
@@ -313,7 +239,7 @@ loadSubjects(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHo
myPrint(options, 1, " done.\n");
myPrint(options, 2, "Runtime: ", finish, "s \n\n");
- context(globalHolder.outfile).dbName = options.indexDir;
+ context(globalHolder.outfile).dbName = options.dbFile;
// if subjects where translated, we don't have the untranslated seqs at all
// but we still need the data for statistics and position un-translation
@@ -323,8 +249,8 @@ loadSubjects(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHo
std::string strIdent = "Loading Lengths of untranslated Subj sequences...";
myPrint(options, 1, strIdent);
- _dbSeqs = options.indexDir;
- append(_dbSeqs, "/untranslated_seq_lengths");
+ _dbSeqs = options.dbFile;
+ append(_dbSeqs, ".untranslengths");
ret = open(globalHolder.untransSubjSeqLengths, toCString(_dbSeqs), OPEN_RDONLY);
if (ret != true)
{
@@ -353,8 +279,24 @@ loadDbIndexFromDisk(TGlobalHolder & globalHolder,
std::string strIdent = "Loading Database Index...";
myPrint(options, 1, strIdent);
double start = sysTime();
- std::string path = toCString(options.indexDir);
- path += "/index";
+ std::string path = toCString(options.dbFile);
+ path += '.' + std::string(_alphName(typename TGlobalHolder::TRedAlph()));
+ if (TGlobalHolder::indexIsFM)
+ path += ".fm";
+ else
+ path += ".sa";
+
+ // Check if the index is of the old format (pre 0.9.0) by looking for different files
+ if ((globalHolder.blastProgram != BlastProgram::BLASTN) && // BLASTN indexes are compatible
+ ((TGlobalHolder::alphReduction && fileExists(toCString(path + ".txt.concat"))) ||
+ (!TGlobalHolder::alphReduction && TGlobalHolder::indexIsFM && !fileExists(toCString(path + ".lf.drv.wtc.24")))))
+ {
+ std::cerr << ((options.verbosity == 0) ? strIdent : std::string())
+ << " failed.\n"
+ << "It appears you tried to open an old index (created before 0.9.0) which "
+ << "is not supported. Please remove the old files and create a new index with lambda_indexer!\n";
+ return 200;
+ }
int ret = open(globalHolder.dbIndex, path.c_str(), OPEN_RDONLY);
if (ret != true)
@@ -376,7 +318,7 @@ loadDbIndexFromDisk(TGlobalHolder & globalHolder,
length(indexSA(globalHolder.dbIndex)), "\n\n");
// this is actually part of prepareScoring(), but the values are just available now
- if (sIsTranslated(TGlobalHolder::blastProgram ))
+ if (sIsTranslated(globalHolder.blastProgram ))
{
// last value has sum of lengths
context(globalHolder.outfile).dbTotalLength = back(globalHolder.untransSubjSeqLengths);
@@ -394,54 +336,54 @@ loadDbIndexFromDisk(TGlobalHolder & globalHolder,
// Function loadSegintervals()
// --------------------------------------------------------------------------
-// template <BlastTabularSpec h,
-// BlastProgram p,
-// typename TRedAlph,
-// typename TIndexSpec,
-// typename TOutFormat>
-// inline int
-// loadSegintervals(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
-// LambdaOptions const & options)
-// {
-//
-// double start = sysTime();
-// std::string strIdent = "Loading Database Masking file...";
-// myPrint(options, 1, strIdent);
-//
-// CharString segFileS = options.dbFile;
-// append(segFileS, ".binseg_s.concat");
-// CharString segFileE = options.dbFile;
-// append(segFileE, ".binseg_e.concat");
-// bool fail = false;
-// struct stat buffer;
-// // file exists
-// if ((stat(toCString(segFileS), &buffer) == 0) &&
-// (stat(toCString(segFileE), &buffer) == 0))
-// {
-// //cut off ".concat" again
-// resize(segFileS, length(segFileS) - 7);
-// resize(segFileE, length(segFileE) - 7);
-//
-// fail = !open(globalHolder.segIntStarts, toCString(segFileS), OPEN_RDONLY);
-// if (!fail)
-// fail = !open(globalHolder.segIntEnds, toCString(segFileE), OPEN_RDONLY);
-// } else
-// {
-// fail = true;
-// }
-//
-// if (fail)
-// {
-// std::cerr << ((options.verbosity == 0) ? strIdent : std::string())
-// << " failed.\n";
-// return 1;
-// }
-//
-// double finish = sysTime() - start;
-// myPrint(options, 1, " done.\n");
-// myPrint(options, 2, "Runtime: ", finish, "s \n\n");
-// return 0;
-// }
+template <BlastTabularSpec h,
+ BlastProgram p,
+ typename TRedAlph,
+ typename TIndexSpec,
+ typename TOutFormat>
+inline int
+loadSegintervals(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
+ LambdaOptions const & options)
+{
+
+ double start = sysTime();
+ std::string strIdent = "Loading Database Masking file...";
+ myPrint(options, 1, strIdent);
+
+ CharString segFileS = options.dbFile;
+ append(segFileS, ".binseg_s.concat");
+ CharString segFileE = options.dbFile;
+ append(segFileE, ".binseg_e.concat");
+ bool fail = false;
+ struct stat buffer;
+ // file exists
+ if ((stat(toCString(segFileS), &buffer) == 0) &&
+ (stat(toCString(segFileE), &buffer) == 0))
+ {
+ //cut off ".concat" again
+ resize(segFileS, length(segFileS) - 7);
+ resize(segFileE, length(segFileE) - 7);
+
+ fail = !open(globalHolder.segIntStarts, toCString(segFileS), OPEN_RDONLY);
+ if (!fail)
+ fail = !open(globalHolder.segIntEnds, toCString(segFileE), OPEN_RDONLY);
+ } else
+ {
+ fail = true;
+ }
+
+ if (fail)
+ {
+ std::cerr << ((options.verbosity == 0) ? strIdent : std::string())
+ << " failed.\n";
+ return 1;
+ }
+
+ double finish = sysTime() - start;
+ myPrint(options, 1, " done.\n");
+ myPrint(options, 2, "Runtime: ", finish, "s \n\n");
+ return 0;
+}
// --------------------------------------------------------------------------
// Function loadQuery()
@@ -546,8 +488,8 @@ template <BlastTabularSpec h,
typename TIndexSpec,
typename TOutFormat>
inline int
-loadQuery(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
- LambdaOptions & options)
+loadQuery(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
+ LambdaOptions const & options)
{
using TGH = GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h>;
double start = sysTime();
@@ -579,7 +521,7 @@ loadQuery(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & global
options);
// sam and bam need original sequences if translation happened
- if (qIsTranslated(TGH::blastProgram) && (options.outFileFormat > 0) &&
+ if (qIsTranslated(globalHolder.blastProgram) && (options.outFileFormat > 0) &&
(options.samBamSeq > 0))
std::swap(origSeqs, globalHolder.untranslatedQrySeqs);
@@ -620,28 +562,6 @@ loadQuery(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & global
<< ".\n";
return -1;
}
-
- if (options.extensionMode == LambdaOptions::ExtensionMode::AUTO)
- {
- if (maxLen <= 100)
- {
- #if 0 // defined(SEQAN_SIMD_ENABLED) && defined(__AVX2__)
- options.extensionMode = LambdaOptions::ExtensionMode::FULL_SIMD;
- options.band = -1;
- #else
- options.extensionMode = LambdaOptions::ExtensionMode::FULL_SERIAL;
- #endif
- options.xDropOff = -1;
- options.filterPutativeAbundant = false;
- options.filterPutativeDuplicates = false;
- options.mergePutativeSiblings = false;
- }
- else
- {
- options.extensionMode = LambdaOptions::ExtensionMode::XDROP;
- }
- }
-
return 0;
}
@@ -764,16 +684,13 @@ seedLooksPromising(LocalDataHolder<TGlobalHolder, TScoreExtension> const & lH,
int64_t effectiveQBegin = m.qryStart;
int64_t effectiveSBegin = m.subjStart;
- uint64_t actualLength = m.qryEnd - m.qryStart;
- uint64_t effectiveLength = std::max(static_cast<uint64_t>(lH.options.seedLength * lH.options.preScoring),
- actualLength);
-
- if (effectiveLength > actualLength)
+ uint64_t effectiveLength = lH.options.seedLength * lH.options.preScoring;
+ if (lH.options.preScoring > 1)
{
effectiveQBegin -= (lH.options.preScoring - 1) *
- actualLength / 2;
+ lH.options.seedLength / 2;
effectiveSBegin -= (lH.options.preScoring - 1) *
- actualLength / 2;
+ lH.options.seedLength / 2;
// std::cout << effectiveQBegin << "\t" << effectiveSBegin << "\n";
int64_t min = std::min(effectiveQBegin, effectiveSBegin);
if (min < 0)
@@ -843,23 +760,21 @@ onFind(LocalDataHolder<TGlobalHolder, TScoreExtension> & lH,
- getSeqOffset(subjOcc)
- lH.options.seedLength);
- TMatch m {static_cast<typename TMatch::TQId>(lH.seedRefs[seedId]),
- static_cast<typename TMatch::TSId>(getSeqNo(subjOcc)),
- static_cast<typename TMatch::TPos>(lH.seedRanks[seedId] * lH.options.seedOffset),
- static_cast<typename TMatch::TPos>(lH.seedRanks[seedId] * lH.options.seedOffset + lH.options.seedLength),
- static_cast<typename TMatch::TPos>(getSeqOffset(subjOcc)),
- static_cast<typename TMatch::TPos>(getSeqOffset(subjOcc) + lH.options.seedLength)};
+ TMatch m{static_cast<typename TMatch::TQId>(lH.seedRefs[seedId]),
+ static_cast<typename TMatch::TSId>(getSeqNo(subjOcc)),
+ static_cast<typename TMatch::TPos>(lH.seedRanks[seedId] * lH.options.seedOffset),
+ static_cast<typename TMatch::TPos>(getSeqOffset(subjOcc))};
bool discarded = false;
auto const halfSubjL = lH.options.seedLength / 2;
- if (!sIsTranslated(TGlobalHolder::blastProgram))
+ if (!sIsTranslated(lH.gH.blastProgram))
{
for (unsigned k = 0; k < length(lH.gH.segIntStarts[m.subjId]); ++k)
{
// more than half of the seed falls into masked interval
if (intervalOverlap(m.subjStart,
- m.subjEnd,
+ m.subjStart + lH.options.seedLength,
lH.gH.segIntStarts[m.subjId][k],
lH.gH.segIntEnds[m.subjId][k])
>= halfSubjL)
@@ -881,190 +796,10 @@ onFind(LocalDataHolder<TGlobalHolder, TScoreExtension> & lH,
lH.matches.emplace_back(m);
}
-template <typename TGlobalHolder,
- typename TScoreExtension,
- typename TSubjOcc>
-inline void
-onFindVariable(LocalDataHolder<TGlobalHolder, TScoreExtension> & lH,
- TSubjOcc subjOcc,
- typename TGlobalHolder::TMatch::TQId const seedId,
- typename TGlobalHolder::TMatch::TPos const seedBegin,
- typename TGlobalHolder::TMatch::TPos const seedLength)
-{
- using TMatch = typename TGlobalHolder::TMatch;
- if (TGlobalHolder::indexIsFM) // positions are reversed
- setSeqOffset(subjOcc,
- length(lH.gH.subjSeqs[getSeqNo(subjOcc)])
- - getSeqOffset(subjOcc)
- - seedLength);
-
- TMatch m {seedId,
- static_cast<typename TGlobalHolder::TMatch::TSId>(getSeqNo(subjOcc)),
- seedBegin,
- static_cast<typename TGlobalHolder::TMatch::TPos>(seedBegin + seedLength),
- static_cast<typename TGlobalHolder::TMatch::TPos>(getSeqOffset(subjOcc)),
- static_cast<typename TGlobalHolder::TMatch::TPos>(getSeqOffset(subjOcc) + seedLength)};
-
- if (!seedLooksPromising(lH, m))
- ++lH.stats.hitsFailedPreExtendTest;
- else
- lH.matches.emplace_back(m);
-}
-
// --------------------------------------------------------------------------
// Function search()
// --------------------------------------------------------------------------
-//TODO experiment with tuned branch prediction
-
-template <typename TIndexIt, typename TNeedleIt, typename TLambda, typename TLambda2>
-inline void
-__goDownNoErrors(TIndexIt const & indexIt,
- TNeedleIt const & needleIt,
- TNeedleIt const & needleItEnd,
- TLambda & continRunnable,
- TLambda2 & reportRunnable)
-{
- TIndexIt nextIndexIt(indexIt);
- if ((needleIt != needleItEnd) &&
- goDown(nextIndexIt, *needleIt) &&
- continRunnable(indexIt, nextIndexIt))
- {
- __goDownNoErrors(nextIndexIt, needleIt + 1, needleItEnd, continRunnable, reportRunnable);
- } else
- {
- reportRunnable(indexIt);
- }
-}
-
-template <typename TIndexIt, typename TNeedleIt, typename TLambda, typename TLambda2>
-inline void
-__goDownErrors(TIndexIt const & indexIt,
- TNeedleIt const & needleIt,
- TNeedleIt const & needleItEnd,
- TLambda & continRunnable,
- TLambda2 & reportRunnable)
-{
- using TAlph = typename Value<TNeedleIt>::Type;
-
- unsigned contin = 0;
-
- if (needleIt != needleItEnd)
- {
- for (unsigned i = 0; i < ValueSize<TAlph>::VALUE; ++i)
- {
- TIndexIt nextIndexIt(indexIt);
- if (goDown(nextIndexIt, static_cast<TAlph>(i)) &&
- continRunnable(indexIt, nextIndexIt))
- {
- ++contin;
- if (ordValue(*needleIt) == i)
- __goDownErrors(nextIndexIt, needleIt + 1, needleItEnd, continRunnable, reportRunnable);
- else
- __goDownNoErrors(nextIndexIt, needleIt + 1, needleItEnd, continRunnable, reportRunnable);
- }
- }
- }
-
- if (contin == 0)
- reportRunnable(indexIt);
-}
-
-template <typename TGlobalHolder,
- typename TScoreExtension>
-inline void
-__serachAdaptive(LocalDataHolder<TGlobalHolder, TScoreExtension> & lH,
- uint64_t const seedLength)
-{
- typedef typename Iterator<typename TGlobalHolder::TDbIndex, TopDown<> >::Type TIndexIt;
-
- // TODO optionize
- size_t constexpr seedHeurFactor = 10;
- size_t constexpr minResults = 1;
-
- size_t needlesSum = lH.gH.redQrySeqs.limits[lH.indexEndQry] - lH.gH.redQrySeqs.limits[lH.indexBeginQry];
- // BROKEN:lengthSum(infix(lH.gH.redQrySeqs, lH.indexBeginQry, lH.indexEndQry));
- // the above is faster anyway (but only works on concatdirect sets)
-
- size_t needlesPos = 0;
-
- TIndexIt root(lH.gH.dbIndex);
- TIndexIt indexIt = root;
-
- for (size_t i = lH.indexBeginQry; i < lH.indexEndQry; ++i)
- {
- for (size_t seedBegin = 0; /* below */; seedBegin += lH.options.seedOffset)
- {
- // skip proteine 'X' or Dna 'N'
- while ((lH.gH.qrySeqs[i][seedBegin] == unknownValue<TransAlph<TGlobalHolder::blastProgram>>()) &&
- (seedBegin <= length(lH.gH.redQrySeqs[i]) - seedLength))
- ++seedBegin;
-
- // termination criterium
- if (seedBegin > length(lH.gH.redQrySeqs[i]) - seedLength)
- break;
-
- indexIt = root;
-
- size_t desiredOccs = length(lH.matches) >= lH.options.maxMatches
- ? minResults
- : (lH.options.maxMatches - length(lH.matches)) * seedHeurFactor /
- ((needlesSum - needlesPos - seedBegin) / lH.options.seedOffset);
-
- if (desiredOccs == 0)
- desiredOccs = minResults;
-
- // go down seedOffset number of characters without errors
- for (size_t k = 0; k < lH.options.seedOffset; ++k)
- if (!goDown(indexIt, lH.gH.redQrySeqs[i][seedBegin + k]))
- break;
- // if unsuccessful, move to next seed
- if (repLength(indexIt) != lH.options.seedOffset)
- continue;
-
- auto continRunnable = [&seedLength, &desiredOccs] (TIndexIt const & prevIndexIt, TIndexIt const & indexIt)
- {
- // NON-ADAPTIVE
-// return (repLength(indexIt) <= seedLength);
- // ADAPTIVE SEEDING:
-
- // always continue if minimum seed length not reached
- if (repLength(indexIt) <= seedLength)
- return true;
-
- // always continue if it means not loosing hits
- if (countOccurrences(indexIt) == countOccurrences(prevIndexIt))
- return true;
-
- // do vodoo heuristics to see if this hit is to frequent
- if (countOccurrences(indexIt) < desiredOccs)
- return false;
-
- return true;
- };
-
- auto reportRunnable = [&seedLength, &lH, &i, &seedBegin] (TIndexIt const & indexIt)
- {
- if (repLength(indexIt) >= seedLength)
- {
- appendValue(lH.stats.seedLengths, repLength(indexIt));
- lH.stats.hitsAfterSeeding += countOccurrences(indexIt);
- for (auto const & occ : getOccurrences(indexIt))
- onFindVariable(lH, occ, i, seedBegin, repLength(indexIt));
- }
- };
-
- __goDownErrors(indexIt,
- begin(lH.gH.redQrySeqs[i], Standard()) + seedBegin + lH.options.seedOffset,
- end(lH.gH.redQrySeqs[i], Standard()),
- continRunnable,
- reportRunnable);
- }
-
- needlesPos += length(lH.gH.redQrySeqs[i]);
- }
-}
-
template <typename BackSpec, typename TLocalHolder>
inline void
__searchDoubleIndex(TLocalHolder & lH)
@@ -1150,19 +885,23 @@ template <typename TLocalHolder>
inline void
search(TLocalHolder & lH)
{
- //TODO implement adaptive seeding with 0-n mismatches
if (lH.options.maxSeedDist == 0)
__search<Backtracking<Exact>>(lH);
- else if (lH.options.adaptiveSeeding)
- __serachAdaptive(lH, lH.options.seedLength);
- else
+ else if (lH.options.hammingOnly)
__search<Backtracking<HammingDistance>>(lH);
+ else
+#if 0 // reactivate if edit-distance seeding is readded
+ __search<Backtracking<EditDistance>>(lH);
+#else
+ return;
+#endif
}
// --------------------------------------------------------------------------
// Function joinAndFilterMatches()
// --------------------------------------------------------------------------
+
template <typename TLocalHolder>
inline void
sortMatches(TLocalHolder & lH)
@@ -1202,85 +941,6 @@ sortMatches(TLocalHolder & lH)
}
}
-// --------------------------------------------------------------------------
-// Function _setFrames()
-// --------------------------------------------------------------------------
-
-template <typename TBlastMatch,
- typename TLocalHolder>
-inline void
-_setFrames(TBlastMatch & bm,
- typename TLocalHolder::TMatch const & m,
- TLocalHolder const & lH)
-{
- if (qIsTranslated(TLocalHolder::TGlobalHolder::blastProgram))
- {
- bm.qFrameShift = (m.qryId % 3) + 1;
- if (m.qryId % 6 > 2)
- bm.qFrameShift = -bm.qFrameShift;
- } else if (qHasRevComp(TLocalHolder::TGlobalHolder::blastProgram))
- {
- bm.qFrameShift = 1;
- if (m.qryId % 2)
- bm.qFrameShift = -bm.qFrameShift;
- } else
- {
- bm.qFrameShift = 0;
- }
-
- if (sIsTranslated(TLocalHolder::TGlobalHolder::blastProgram))
- {
- bm.sFrameShift = (m.subjId % 3) + 1;
- if (m.subjId % 6 > 2)
- bm.sFrameShift = -bm.sFrameShift;
- } else if (sHasRevComp(TLocalHolder::TGlobalHolder::blastProgram))
- {
- bm.sFrameShift = 1;
- if (m.subjId % 2)
- bm.sFrameShift = -bm.sFrameShift;
- } else
- {
- bm.sFrameShift = 0;
- }
-}
-
-// --------------------------------------------------------------------------
-// Function _writeMatches()
-// --------------------------------------------------------------------------
-
-template <typename TBlastRecord,
- typename TLocalHolder>
-inline void
-_writeRecord(TBlastRecord & record,
- TLocalHolder & lH)
-{
- if (length(record.matches) > 0)
- {
- ++lH.stats.qrysWithHit;
- // sort and remove duplicates -> STL, yeah!
- auto const before = record.matches.size();
- record.matches.sort();
- if (!lH.options.filterPutativeDuplicates)
- {
- record.matches.unique();
- lH.stats.hitsDuplicate += before - record.matches.size();
- }
- if (record.matches.size() > lH.options.maxMatches)
- {
- lH.stats.hitsAbundant += record.matches.size() -
- lH.options.maxMatches;
- record.matches.resize(lH.options.maxMatches);
- }
- lH.stats.hitsFinal += record.matches.size();
-
- myWriteRecord(lH, record);
- }
-}
-
-// --------------------------------------------------------------------------
-// Function computeBlastMatch()
-// --------------------------------------------------------------------------
-
template <typename TBlastMatch,
typename TLocalHolder>
inline int
@@ -1304,10 +964,10 @@ computeBlastMatch(TBlastMatch & bm,
// bm.sEnd);
// std::cout << "Query Id: " << m.qryId
-// << "\t TrueQryId: " << getTrueQryId(bm.m, lH.options, TGlobalHolder::blastProgram)
+// << "\t TrueQryId: " << getTrueQryId(bm.m, lH.options, lH.gH.blastProgram)
// << "\t length(qryIds): " << length(qryIds)
// << "Subj Id: " << m.subjId
-// << "\t TrueSubjId: " << getTrueSubjId(bm.m, lH.options, TGlobalHolder::blastProgram)
+// << "\t TrueSubjId: " << getTrueSubjId(bm.m, lH.options, lH.gH.blastProgram)
// << "\t length(subjIds): " << length(subjIds) << "\n\n";
assignSource(bm.alignRow0, infix(lH.gH.qrySeqs[m.qryId], bm.qStart, bm.qEnd));
@@ -1609,17 +1269,53 @@ computeBlastMatch(TBlastMatch & bm,
// std::cout << "ALIGN BEFORE STATS:\n" << bm.align << "\n";
computeAlignmentStats(bm, context(lH.gH.outfile));
+
if (bm.alignStats.alignmentIdentity < lH.options.idCutOff)
return PERCENTIDENT;
// const unsigned long qryLength = length(row0);
computeBitScore(bm, context(lH.gH.outfile));
- computeEValueThreadSafe(bm, context(lH.gH.outfile));
+ // the length adjustment cache must no be written to by multiple threads
+ SEQAN_OMP_PRAGMA(critical(evalue_length_adj_cache))
+ {
+ computeEValue(bm, context(lH.gH.outfile));
+ }
+
if (bm.eValue > lH.options.eCutOff)
+ {
return EVALUE;
+ }
- _setFrames(bm, m, lH);
+ if (qIsTranslated(TLocalHolder::TGlobalHolder::blastProgram))
+ {
+ bm.qFrameShift = (m.qryId % 3) + 1;
+ if (m.qryId % 6 > 2)
+ bm.qFrameShift = -bm.qFrameShift;
+ } else if (qHasRevComp(TLocalHolder::TGlobalHolder::blastProgram))
+ {
+ bm.qFrameShift = 1;
+ if (m.qryId % 2)
+ bm.qFrameShift = -bm.qFrameShift;
+ } else
+ {
+ bm.qFrameShift = 0;
+ }
+
+ if (sIsTranslated(TLocalHolder::TGlobalHolder::blastProgram))
+ {
+ bm.sFrameShift = (m.subjId % 3) + 1;
+ if (m.subjId % 6 > 2)
+ bm.sFrameShift = -bm.sFrameShift;
+ } else if (sHasRevComp(TLocalHolder::TGlobalHolder::blastProgram))
+ {
+ bm.sFrameShift = 1;
+ if (m.subjId % 2)
+ bm.sFrameShift = -bm.sFrameShift;
+ } else
+ {
+ bm.sFrameShift = 0;
+ }
return 0;
}
@@ -1627,7 +1323,7 @@ computeBlastMatch(TBlastMatch & bm,
template <typename TLocalHolder>
inline int
-iterateMatchesExtend(TLocalHolder & lH)
+iterateMatches(TLocalHolder & lH)
{
using TGlobalHolder = typename TLocalHolder::TGlobalHolder;
// using TMatch = typename TGlobalHolder::TMatch;
@@ -1643,8 +1339,8 @@ iterateMatchesExtend(TLocalHolder & lH)
using TBlastRecord = BlastRecord<TBlastMatch>;
// constexpr TPos TPosMax = std::numeric_limits<TPos>::max();
-// constexpr uint8_t qFactor = qHasRevComp(TGlobalHolder::blastProgram) ? 3 : 1;
-// constexpr uint8_t sFactor = sHasRevComp(TGlobalHolder::blastProgram) ? 3 : 1;
+// constexpr uint8_t qFactor = qHasRevComp(lH.gH.blastProgram) ? 3 : 1;
+// constexpr uint8_t sFactor = sHasRevComp(lH.gH.blastProgram) ? 3 : 1;
double start = sysTime();
if (lH.options.doubleIndexing)
@@ -1658,7 +1354,7 @@ iterateMatchesExtend(TLocalHolder & lH)
// std::cout << "Length of matches: " << length(lH.matches);
// for (auto const & m : lH.matches)
// {
-// std::cout << m.qryId << "\t" << getTrueQryId(m,lH.options, TGlobalHolder::blastProgram) << "\n";
+// std::cout << m.qryId << "\t" << getTrueQryId(m,lH.options, lH.gH.blastProgram) << "\n";
// }
// double topMaxMatchesMedianBitScore = 0;
@@ -1671,11 +1367,11 @@ iterateMatchesExtend(TLocalHolder & lH)
++it)
{
itN = std::next(it,1);
- auto const trueQryId = it->qryId / qNumFrames(TGlobalHolder::blastProgram);
+ auto const trueQryId = it->qryId / qNumFrames(lH.gH.blastProgram);
TBlastRecord record(lH.gH.qryIds[trueQryId]);
- record.qLength = (qIsTranslated(TGlobalHolder::blastProgram)
+ record.qLength = (qIsTranslated(lH.gH.blastProgram)
? lH.gH.untransQrySeqLengths[trueQryId]
: length(lH.gH.qrySeqs[it->qryId]));
@@ -1684,7 +1380,7 @@ iterateMatchesExtend(TLocalHolder & lH)
// inner loop over matches per record
for (; it != itEnd; ++it)
{
- auto const trueSubjId = it->subjId / sNumFrames(TGlobalHolder::blastProgram);
+ auto const trueSubjId = it->subjId / sNumFrames(lH.gH.blastProgram);
itN = std::next(it,1);
// std::cout << "FOO\n" << std::flush;
// std::cout << "QryStart: " << it->qryStart << "\n" << std::flush;
@@ -1736,7 +1432,7 @@ iterateMatchesExtend(TLocalHolder & lH)
{
// declare all the rest as putative abundant
while ((it != itEnd) &&
- (trueQryId == it->qryId / qNumFrames(TGlobalHolder::blastProgram)))
+ (trueQryId == it->qryId / qNumFrames(lH.gH.blastProgram)))
{
// not already marked as abundant, duplicate or merged
if (!isSetToSkip(*it))
@@ -1758,56 +1454,57 @@ iterateMatchesExtend(TLocalHolder & lH)
auto & bm = back(record.matches);
bm.qStart = it->qryStart;
- bm.qEnd = it->qryEnd; // it->qryStart + lH.options.seedLength;
+ bm.qEnd = it->qryStart + lH.options.seedLength;
bm.sStart = it->subjStart;
- bm.sEnd = it->subjEnd;//it->subjStart + lH.options.seedLength;
+ bm.sEnd = it->subjStart + lH.options.seedLength;
bm.qLength = record.qLength;
- bm.sLength = sIsTranslated(TGlobalHolder::blastProgram)
+ bm.sLength = sIsTranslated(lH.gH.blastProgram)
? lH.gH.untransSubjSeqLengths[trueSubjId]
: length(lH.gH.subjSeqs[it->subjId]);
// MERGE PUTATIVE SIBLINGS INTO THIS MATCH
- if (lH.options.mergePutativeSiblings)
+ for (auto it2 = itN;
+ (it2 != itEnd) &&
+ (trueQryId == it2->qryId / qNumFrames(lH.gH.blastProgram)) &&
+ (trueSubjId == it2->subjId / sNumFrames(lH.gH.blastProgram));
+ ++it2)
{
- for (auto it2 = itN;
- (it2 != itEnd) &&
- (trueQryId == it2->qryId / qNumFrames(TGlobalHolder::blastProgram)) &&
- (trueSubjId == it2->subjId / sNumFrames(TGlobalHolder::blastProgram));
- ++it2)
+ // same frame
+ if ((it->qryId % qNumFrames(lH.gH.blastProgram) == it2->qryId % qNumFrames(lH.gH.blastProgram)) &&
+ (it->subjId % sNumFrames(lH.gH.blastProgram) == it2->subjId % sNumFrames(lH.gH.blastProgram)))
{
- // same frame
- if ((it->qryId % qNumFrames(TGlobalHolder::blastProgram) == it2->qryId % qNumFrames(TGlobalHolder::blastProgram)) &&
- (it->subjId % sNumFrames(TGlobalHolder::blastProgram) == it2->subjId % sNumFrames(TGlobalHolder::blastProgram)))
- {
-
- // TPos const qDist = (it2->qryStart >= bm.qEnd)
- // ? it2->qryStart - bm.qEnd // upstream
- // : 0; // overlap
- //
- // TPos sDist = TPosMax; // subj match region downstream of *it
- // if (it2->subjStart >= bm.sEnd) // upstream
- // sDist = it2->subjStart - bm.sEnd;
- // else if (it2->subjStart >= it->subjStart) // overlap
- // sDist = 0;
-
- // due to sorting it2->qryStart never <= it->qStart
- // so subject sequences must have same order
- if (it2->subjStart < it->subjStart)
- continue;
-
- long const qDist = it2->qryStart - bm.qEnd;
- long const sDist = it2->subjStart - bm.sEnd;
-
- if ((qDist == sDist) &&
- (qDist <= (long)lH.options.seedGravity))
- {
- bm.qEnd = std::max(bm.qEnd, static_cast<TBlastPos>(it2->qryEnd));
- bm.sEnd = std::max(bm.sEnd, static_cast<TBlastPos>(it2->subjEnd));
- ++lH.stats.hitsMerged;
- setToSkip(*it2);
- }
+// TPos const qDist = (it2->qryStart >= bm.qEnd)
+// ? it2->qryStart - bm.qEnd // upstream
+// : 0; // overlap
+//
+// TPos sDist = TPosMax; // subj match region downstream of *it
+// if (it2->subjStart >= bm.sEnd) // upstream
+// sDist = it2->subjStart - bm.sEnd;
+// else if (it2->subjStart >= it->subjStart) // overlap
+// sDist = 0;
+
+ // due to sorting it2->qryStart never <= it->qStart
+ // so subject sequences must have same order
+ if (it2->subjStart < it->subjStart)
+ continue;
+
+ long const qDist = it2->qryStart - bm.qEnd;
+ long const sDist = it2->subjStart - bm.sEnd;
+
+ if ((qDist == sDist) &&
+ (qDist <= (long)lH.options.seedGravity))
+ {
+ bm.qEnd = std::max(bm.qEnd,
+ static_cast<TBlastPos>(it2->qryStart
+ + lH.options.seedLength));
+ bm.sEnd = std::max(bm.sEnd,
+ static_cast<TBlastPos>(it2->subjStart
+ + lH.options.seedLength));
+ ++lH.stats.hitsMerged;
+
+ setToSkip(*it2);
}
}
}
@@ -1821,8 +1518,8 @@ iterateMatchesExtend(TLocalHolder & lH)
// ++lH.stats.goodMatches;
if (lH.options.outFileFormat > 0)
{
- bm._n_qId = it->qryId / qNumFrames(TGlobalHolder::blastProgram);
- bm._n_sId = it->subjId / sNumFrames(TGlobalHolder::blastProgram);
+ bm._n_qId = it->qryId / qNumFrames(lH.gH.blastProgram);
+ bm._n_sId = it->subjId / sNumFrames(lH.gH.blastProgram);
}
break;
case EVALUE:
@@ -1840,20 +1537,16 @@ iterateMatchesExtend(TLocalHolder & lH)
<< "subjId: " << it->subjId << "\t"
<< "seed qry: " << infix(lH.gH.redQrySeqs,
it->qryStart,
- it->qryEnd)
-// it->qryStart + lH.options.seedLength)
+ it->qryStart + lH.options.seedLength)
<< "\n subj: " << infix(lH.gH.redSubjSeqs,
it->subjStart,
- it->subjEnd)
-// it->subjStart + lH.options.seedLength)
+ it->subjStart + lH.options.seedLength)
<< "\nunred qry: " << infix(lH.gH.qrySeqs,
it->qryStart,
- it->qryEnd)
-// it->qryStart + lH.options.seedLength)
+ it->qryStart + lH.options.seedLength)
<< "\n subj: " << infix(lH.gH.subjSeqs,
it->subjStart,
- it->subjEnd)
-// it->subjStart + lH.options.seedLength)
+ it->subjStart + lH.options.seedLength)
<< "\nmatch qry: " << infix(lH.gH.qrySeqs,
bm.qStart,
bm.qEnd)
@@ -1874,21 +1567,19 @@ iterateMatchesExtend(TLocalHolder & lH)
// PUTATIVE DUBLICATES CHECK
for (auto it2 = itN;
(it2 != itEnd) &&
- (trueQryId == it2->qryId / qNumFrames(TGlobalHolder::blastProgram)) &&
- (trueSubjId == it2->subjId / sNumFrames(TGlobalHolder::blastProgram));
+ (trueQryId == it2->qryId / qNumFrames(lH.gH.blastProgram)) &&
+ (trueSubjId == it2->subjId / sNumFrames(lH.gH.blastProgram));
++it2)
{
// same frame and same range
if ((it->qryId == it2->qryId) &&
(it->subjId == it2->subjId) &&
(intervalOverlap(it2->qryStart,
- it2->qryEnd,
-// it2->qryStart + lH.options.seedLength,
+ it2->qryStart + lH.options.seedLength,
bm.qStart,
bm.qEnd) > 0) &&
(intervalOverlap(it2->subjStart,
- it2->subjEnd,
-// it2->subjStart + lH.options.seedLength,
+ it2->subjStart + lH.options.seedLength,
bm.sStart,
bm.sEnd) > 0))
{
@@ -1913,11 +1604,32 @@ iterateMatchesExtend(TLocalHolder & lH)
// last item or new TrueQryId
if ((itN == itEnd) ||
- (trueQryId != itN->qryId / qNumFrames(TGlobalHolder::blastProgram)))
+ (trueQryId != itN->qryId / qNumFrames(lH.gH.blastProgram)))
break;
}
- _writeRecord(record, lH);
+ if (length(record.matches) > 0)
+ {
+ ++lH.stats.qrysWithHit;
+ // sort and remove duplicates -> STL, yeah!
+ auto const before = record.matches.size();
+ record.matches.sort();
+ if (!lH.options.filterPutativeDuplicates)
+ {
+ record.matches.unique();
+ lH.stats.hitsDuplicate += before - record.matches.size();
+ }
+ if (record.matches.size() > lH.options.maxMatches)
+ {
+ lH.stats.hitsAbundant += record.matches.size() -
+ lH.options.maxMatches;
+ record.matches.resize(lH.options.maxMatches);
+ }
+ lH.stats.hitsFinal += record.matches.size();
+
+ myWriteRecord(lH, record);
+ }
+
}
if (lH.options.doubleIndexing)
@@ -1932,313 +1644,4 @@ iterateMatchesExtend(TLocalHolder & lH)
return 0;
}
-#ifdef SEQAN_SIMD_ENABLED
-template <typename TLocalHolder>
-inline int
-iterateMatchesFullSimd(TLocalHolder & lH)
-{
- using TGlobalHolder = typename TLocalHolder::TGlobalHolder;
- using TMatch = typename TGlobalHolder::TMatch;
- using TPos = typename TMatch::TPos;
- using TBlastPos = uint32_t; //TODO why can't this be == TPos
- using TBlastMatch = BlastMatch<
- typename TLocalHolder::TAlignRow0,
- typename TLocalHolder::TAlignRow1,
- TBlastPos,
- typename Value<typename TGlobalHolder::TQryIds>::Type,// const &,
- typename Value<typename TGlobalHolder::TSubjIds>::Type// const &,
- >;
- using TBlastRecord = BlastRecord<TBlastMatch>;
-
- typedef FreeEndGaps_<True, True, True, True> TFreeEndGaps;
- typedef AlignConfig2<LocalAlignment_<>,
- DPBandConfig<BandOff>,
- TFreeEndGaps,
- TracebackOn<TracebackConfig_<CompleteTrace, GapsLeft> > > TAlignConfig;
-
- typedef int TScoreValue; //TODO don't hardcode
- typedef typename Size<typename TLocalHolder::TAlignRow0>::Type TSize;
- typedef TraceSegment_<TPos, TSize> TTraceSegment;
-
- typedef typename SimdVector<int16_t>::Type TSimdAlign;
-
- unsigned const numAlignments = length(lH.matches);
- unsigned const sizeBatch = LENGTH<TSimdAlign>::VALUE;
- unsigned const fullSize = sizeBatch * ((numAlignments + sizeBatch - 1) / sizeBatch);
-
- String<TScoreValue> results;
- resize(results, numAlignments);
-
- // Create a SIMD scoring scheme.
- Score<TSimdAlign, ScoreSimdWrapper<typename TGlobalHolder::TScoreScheme> > simdScoringScheme(seqanScheme(context(lH.gH.outfile).scoringScheme));
-
- // Prepare string sets with sequences.
- StringSet<typename Source<typename TLocalHolder::TAlignRow0>::Type, Dependent<> > depSetH;
- StringSet<typename Source<typename TLocalHolder::TAlignRow1>::Type, Dependent<> > depSetV;
- reserve(depSetH, fullSize);
- reserve(depSetV, fullSize);
-
-
- auto const trueQryId = lH.matches[0].qryId / qNumFrames(TGlobalHolder::blastProgram);
-
- TBlastRecord record(lH.gH.qryIds[trueQryId]);
- record.qLength = (qIsTranslated(TGlobalHolder::blastProgram)
- ? lH.gH.untransQrySeqLengths[trueQryId]
- : length(lH.gH.qrySeqs[lH.matches[0].qryId]));
-
- size_t maxDist = 0;
- switch (lH.options.band)
- {
- case -3: maxDist = ceil(log2(record.qLength)); break;
- case -2: maxDist = floor(sqrt(record.qLength)); break;
- case -1: break;
- default: maxDist = lH.options.band; break;
- }
-
- TAlignConfig config;//(-maxDist, maxDist);
-
- // create blast matches
- for (auto it = lH.matches.begin(), itEnd = lH.matches.end(); it != itEnd; ++it)
- {
- auto const trueSubjId = it->subjId / sNumFrames(TGlobalHolder::blastProgram);
-
- // create blastmatch in list without copy or move
- record.matches.emplace_back(lH.gH.qryIds [trueQryId],
- lH.gH.subjIds[trueSubjId]);
-
- auto & bm = back(record.matches);
- auto & m = *it;
-
- bm.qLength = record.qLength;
- bm.sLength = sIsTranslated(TGlobalHolder::blastProgram)
- ? lH.gH.untransSubjSeqLengths[trueSubjId]
- : length(lH.gH.subjSeqs[it->subjId]);
-
- long lenDiff = (long)it->subjStart - (long)it->qryStart;
-
- TPos sStart;
- TPos qStart;
- if (lenDiff >= 0)
- {
- sStart = lenDiff;
- qStart = 0;
- }
- else
- {
- sStart = 0;
- qStart = -lenDiff;
- }
- TPos sEnd = std::min(sStart + length(lH.gH.qrySeqs[it->qryId]), length(lH.gH.subjSeqs[it->subjId]));
-
- assignSource(bm.alignRow0, infix(lH.gH.qrySeqs[it->qryId], qStart, length(lH.gH.qrySeqs[it->qryId])));
- assignSource(bm.alignRow1, infix(lH.gH.subjSeqs[it->subjId], sStart, sEnd));
-
-
- appendValue(depSetH, source(bm.alignRow0));
- appendValue(depSetV, source(bm.alignRow1));
-
- _setFrames(bm, *it, lH);
- }
-
- // fill up last batch
- for (size_t i = numAlignments; i < fullSize; ++i)
- {
- appendValue(depSetH, source(back(record.matches).alignRow0));
- appendValue(depSetV, source(back(record.matches).alignRow1));
- }
-
- // Run alignments in batches.
- auto matchIt = record.matches.begin();
- for (auto pos = 0u; pos < fullSize; pos += sizeBatch)
- {
- auto infSetH = infixWithLength(depSetH, pos, sizeBatch);
- auto infSetV = infixWithLength(depSetV, pos, sizeBatch);
-
- TSimdAlign resultsBatch;
-
- StringSet<String<TTraceSegment> > trace;
- resize(trace, sizeBatch, Exact());
-
- _prepareAndRunSimdAlignment(resultsBatch, trace, infSetH, infSetV, simdScoringScheme, config, typename TLocalHolder::TScoreExtension());
-
- // copy results and finish traceback
- // TODO(rrahn): Could be parallelized!
- // to for_each call
- for(auto x = pos; x < pos + sizeBatch && x < numAlignments; ++x)
- {
- results[x] = resultsBatch[x - pos];
- _adaptTraceSegmentsTo(matchIt->alignRow0, matchIt->alignRow1, trace[x - pos]);
- ++matchIt;
- }
- }
-
- // TODO share this code with above function
- for (auto it = record.matches.begin(), itEnd = record.matches.end(); it != itEnd; /*below*/)
- {
- TBlastMatch & bm = *it;
-
- bm.sStart = beginPosition(bm.alignRow1);
- bm.qStart = beginPosition(bm.alignRow0);
- bm.sEnd = endPosition(bm.alignRow1);
- bm.qEnd = endPosition(bm.alignRow0);
-
- computeAlignmentStats(bm, context(lH.gH.outfile));
-
- if (bm.alignStats.alignmentIdentity < lH.options.idCutOff)
- {
- ++lH.stats.hitsFailedExtendPercentIdentTest;
- it = record.matches.erase(it);
- continue;
- }
-
- computeBitScore(bm, context(lH.gH.outfile));
-
- computeEValueThreadSafe(bm, context(lH.gH.outfile));
-
- if (bm.eValue > lH.options.eCutOff)
- {
- ++lH.stats.hitsFailedExtendEValueTest;
- it = record.matches.erase(it);
- continue;
- }
-
- ++it;
- }
-
- _writeRecord(record, lH);
-
- return 0;
-}
-
-#endif // SEQAN_SIMD_ENABLED
-
-template <typename TLocalHolder>
-inline int
-iterateMatchesFullSerial(TLocalHolder & lH)
-{
- using TGlobalHolder = typename TLocalHolder::TGlobalHolder;
- using TMatch = typename TGlobalHolder::TMatch;
- using TPos = typename TMatch::TPos;
- using TBlastPos = uint32_t; //TODO why can't this be == TPos
- using TBlastMatch = BlastMatch<
- typename TLocalHolder::TAlignRow0,
- typename TLocalHolder::TAlignRow1,
- TBlastPos,
- typename Value<typename TGlobalHolder::TQryIds>::Type,// const &,
- typename Value<typename TGlobalHolder::TSubjIds>::Type// const &,
- >;
- using TBlastRecord = BlastRecord<TBlastMatch>;
-
- auto const trueQryId = lH.matches[0].qryId / qNumFrames(TGlobalHolder::blastProgram);
-
- TBlastRecord record(lH.gH.qryIds[trueQryId]);
- record.qLength = (qIsTranslated(TGlobalHolder::blastProgram)
- ? lH.gH.untransQrySeqLengths[trueQryId]
- : length(lH.gH.qrySeqs[lH.matches[0].qryId]));
-
- unsigned maxDist = 0;
- switch (lH.options.band)
- {
- case -3: maxDist = ceil(log2(record.qLength)); break;
- case -2: maxDist = floor(sqrt(record.qLength)); break;
- case -1: break;
- default: maxDist = lH.options.band; break;
- }
-
- // create blast matches
- for (auto it = lH.matches.begin(), itEnd = lH.matches.end(); it != itEnd; ++it)
- {
- auto const trueSubjId = it->subjId / sNumFrames(TGlobalHolder::blastProgram);
-
- // create blastmatch in list without copy or move
- record.matches.emplace_back(lH.gH.qryIds [trueQryId],
- lH.gH.subjIds[trueSubjId]);
-
- auto & bm = back(record.matches);
- auto & m = *it;
-
- bm.qLength = record.qLength;
- bm.sLength = sIsTranslated(TGlobalHolder::blastProgram)
- ? lH.gH.untransSubjSeqLengths[trueSubjId]
- : length(lH.gH.subjSeqs[it->subjId]);
-
- long lenDiff = (long)it->subjStart - (long)it->qryStart;
-
- TPos sStart;
- TPos qStart;
- if (lenDiff >= 0)
- {
- sStart = lenDiff;
- qStart = 0;
- }
- else
- {
- sStart = 0;
- qStart = -lenDiff;
- }
- TPos sEnd = std::min(sStart + length(lH.gH.qrySeqs[it->qryId]), length(lH.gH.subjSeqs[it->subjId]));
-
- assignSource(bm.alignRow0, infix(lH.gH.qrySeqs[it->qryId], qStart, length(lH.gH.qrySeqs[it->qryId])));
- assignSource(bm.alignRow1, infix(lH.gH.subjSeqs[it->subjId], sStart, sEnd));
-
-// localAlignment2(bm.alignRow0,
-// bm.alignRow1,
-// seqanScheme(context(lH.gH.outfile).scoringScheme),
-// -maxDist,
-// maxDist,
-// lH.alignContext);
- localAlignment(bm.alignRow0,
- bm.alignRow1,
- seqanScheme(context(lH.gH.outfile).scoringScheme),
- -maxDist,
- maxDist);
-
- bm.sStart = beginPosition(bm.alignRow1);
- bm.qStart = beginPosition(bm.alignRow0);
- bm.sEnd = endPosition(bm.alignRow1);
- bm.qEnd = endPosition(bm.alignRow0);
-
- computeAlignmentStats(bm, context(lH.gH.outfile));
-
- if (bm.alignStats.alignmentIdentity < lH.options.idCutOff)
- {
- ++lH.stats.hitsFailedExtendPercentIdentTest;
- record.matches.pop_back();
- continue;
- }
-
- computeBitScore(bm, context(lH.gH.outfile));
-
- computeEValueThreadSafe(bm, context(lH.gH.outfile));
-
- if (bm.eValue > lH.options.eCutOff)
- {
- ++lH.stats.hitsFailedExtendEValueTest;
- record.matches.pop_back();
- continue;
- }
-
- _setFrames(bm, m, lH);
- }
-
- _writeRecord(record, lH);
-
- return 0;
-}
-
-template <typename TLocalHolder>
-inline int
-iterateMatches(TLocalHolder & lH)
-{
-#ifdef SEQAN_SIMD_ENABLED
- if (lH.options.extensionMode == LambdaOptions::ExtensionMode::FULL_SIMD)
- return iterateMatchesFullSimd(lH);
- else
-#endif
- if (lH.options.extensionMode == LambdaOptions::ExtensionMode::FULL_SERIAL)
- return iterateMatchesFullSerial(lH);
- else
- return iterateMatchesExtend(lH);
-}
-
#endif // HEADER GUARD
diff --git a/src/lambda_indexer.cpp b/src/lambda_indexer.cpp
index 90eafd9..d53f0df 100644
--- a/src/lambda_indexer.cpp
+++ b/src/lambda_indexer.cpp
@@ -19,9 +19,8 @@
// lambda.cpp: Main File for the main application
// ==========================================================================
-#include <initializer_list>
-
#include <seqan/basic.h>
+
#include <seqan/arg_parse.h>
#include <seqan/seq_io.h>
@@ -179,24 +178,24 @@ realMain(LambdaIndexerOptions const & options,
if (sIsTranslated(p))
_saveOriginalSeqLengths(originalSeqs.limits, options);
-// // convert the seg file to seqan binary format
-// ret = convertMaskingFile(length(originalSeqs), options);
-// if (ret)
-// return ret;
+ // convert the seg file to seqan binary format
+ ret = convertMaskingFile(length(originalSeqs), options);
+ if (ret)
+ return ret;
// translate or swap depending on program
translateOrSwap(translatedSeqs, originalSeqs, options);
}
// dump translated and unreduced sequences (except where they are included in index)
- if ((options.alphReduction != 0) || (options.dbIndexType == DbIndexType::FM_INDEX))
+ if ((options.alphReduction != 0) || (options.dbIndexType != 0))
dumpTranslatedSeqs(translatedSeqs, options);
// see if final sequence set actually fits into index
if (!checkIndexSize(translatedSeqs))
return -1;
- if (options.dbIndexType == DbIndexType::FM_INDEX)
+ if (options.dbIndexType == 1)
{
using TIndexSpec = TFMIndex<TIndexSpecSpec>;
generateIndexAndDump<TIndexSpec,TIndexSpecSpec>(translatedSeqs,
@@ -212,21 +211,6 @@ realMain(LambdaIndexerOptions const & options,
TRedAlph());
}
- // dump options
- for (auto && s : std::initializer_list<std::pair<std::string, std::string>>
- {
- { options.indexDir + "/option:db_index_type", std::to_string(static_cast<uint32_t>(options.dbIndexType))},
- { options.indexDir + "/option:alph_original", std::string(_alphName(OrigSubjAlph<p>())) },
- { options.indexDir + "/option:alph_translated", std::string(_alphName(TransAlph<p>())) },
- { options.indexDir + "/option:alph_reduced", std::string(_alphName(TRedAlph())) },
- { options.indexDir + "/option:genetic_code", std::to_string(options.geneticCode) }
- })
- {
- std::ofstream f{std::get<0>(s).c_str(), std::ios_base::out | std::ios_base::binary};
- f << std::get<1>(s);
- f.close();
- }
-
return 0;
}
diff --git a/src/lambda_indexer.hpp b/src/lambda_indexer.hpp
index ce40b9f..54fc759 100644
--- a/src/lambda_indexer.hpp
+++ b/src/lambda_indexer.hpp
@@ -113,8 +113,8 @@ loadSubjSeqsAndIds(TCDStringSet<String<TOrigAlph>> & originalSeqs,
myPrint(options, 1, "Dumping Subj Ids...");
//TODO save to TMPDIR instead
- CharString _path = options.indexDir;
- append(_path, "/seq_ids");
+ CharString _path = options.dbFile;
+ append(_path, ".ids");
save(ids, toCString(_path));
myPrint(options, 1, " done.\n");
@@ -139,8 +139,8 @@ _saveOriginalSeqLengths(TLimits limits, // we want copy!
myPrint(options, 1, " dumping untranslated subject lengths...");
//TODO save to TMPDIR instead
- CharString _path = options.indexDir;
- append(_path, "/untranslated_seq_lengths");
+ CharString _path = options.dbFile;
+ append(_path, ".untranslengths");
save(limits, toCString(_path));
}
@@ -184,7 +184,7 @@ dumpTranslatedSeqs(TCDStringSet<String<TTransAlph>> const & translatedSeqs,
myPrint(options, 1, "Dumping unreduced Subj Sequences...");
//TODO save to TMPDIR instead
- std::string _path = options.indexDir + "/translated_seqs";
+ std::string _path = options.dbFile + '.' + std::string(_alphName(TTransAlph()));
save(translatedSeqs, _path.c_str());
myPrint(options, 1, " done.\n");
@@ -252,132 +252,132 @@ checkIndexSize(TCDStringSet<String<TRedAlph>> const & seqs)
return true;
}
-// // --------------------------------------------------------------------------
-// // Function loadSubj()
-// // --------------------------------------------------------------------------
-//
-// inline int
-// convertMaskingFile(uint64_t numberOfSeqs,
-// LambdaIndexerOptions const & options)
-//
-// {
-// StringSet<String<unsigned>, Owner<ConcatDirect<>>> segIntStarts;
-// StringSet<String<unsigned>, Owner<ConcatDirect<>>> segIntEnds;
-// // resize(segIntervals, numberOfSeqs, Exact());
-//
-// if (options.segFile != "")
-// {
-// myPrint(options, 1, "Constructing binary seqan masking from seg-file...");
-//
-// std::ifstream stream;
-// stream.open(toCString(options.segFile));
-// if (!stream.is_open())
-// {
-// std::cerr << "ERROR: could not open seg file.\n";
-// return -1;
-// }
-//
-// auto reader = directionIterator(stream, Input());
-//
-// // StringSet<String<Tuple<unsigned, 2>>> _segIntervals;
-// // auto & _segIntervals = segIntervals;
-// // resize(_segIntervals, numberOfSeqs, Exact());
-// StringSet<String<unsigned>> _segIntStarts;
-// StringSet<String<unsigned>> _segIntEnds;
-// resize(_segIntStarts, numberOfSeqs, Exact());
-// resize(_segIntEnds, numberOfSeqs, Exact());
-// CharString buf;
-// // std::tuple<unsigned, unsigned> tup;
-//
-// // auto curSeq = begin(_segIntervals);
-// unsigned curSeq = 0;
-// while (value(reader) == '>')
-// {
-// // if (curSeq == end(_segIntervals))
-// // return -7;
-// if (curSeq == numberOfSeqs)
-// {
-// std::cerr << "ERROR: seg file has more entries then database.\n";
+// --------------------------------------------------------------------------
+// Function loadSubj()
+// --------------------------------------------------------------------------
+
+inline int
+convertMaskingFile(uint64_t numberOfSeqs,
+ LambdaIndexerOptions const & options)
+
+{
+ StringSet<String<unsigned>, Owner<ConcatDirect<>>> segIntStarts;
+ StringSet<String<unsigned>, Owner<ConcatDirect<>>> segIntEnds;
+// resize(segIntervals, numberOfSeqs, Exact());
+
+ if (options.segFile != "")
+ {
+ myPrint(options, 1, "Constructing binary seqan masking from seg-file...");
+
+ std::ifstream stream;
+ stream.open(toCString(options.segFile));
+ if (!stream.is_open())
+ {
+ std::cerr << "ERROR: could not open seg file.\n";
+ return -1;
+ }
+
+ auto reader = directionIterator(stream, Input());
+
+// StringSet<String<Tuple<unsigned, 2>>> _segIntervals;
+// auto & _segIntervals = segIntervals;
+// resize(_segIntervals, numberOfSeqs, Exact());
+ StringSet<String<unsigned>> _segIntStarts;
+ StringSet<String<unsigned>> _segIntEnds;
+ resize(_segIntStarts, numberOfSeqs, Exact());
+ resize(_segIntEnds, numberOfSeqs, Exact());
+ CharString buf;
+// std::tuple<unsigned, unsigned> tup;
+
+// auto curSeq = begin(_segIntervals);
+ unsigned curSeq = 0;
+ while (value(reader) == '>')
+ {
+// if (curSeq == end(_segIntervals))
// return -7;
-// }
-// skipLine(reader);
-// if (atEnd(reader))
-// break;
-//
-// unsigned curInt = 0;
-// while ((!atEnd(reader)) && (value(reader) != '>'))
-// {
-// resize(_segIntStarts[curSeq], length(_segIntStarts[curSeq])+1);
-// resize(_segIntEnds[curSeq], length(_segIntEnds[curSeq])+1);
-// clear(buf);
-// readUntil(buf, reader, IsWhitespace());
-//
-// // std::get<0>(tup) = strtoumax(toCString(buf), 0, 10);
-// _segIntStarts[curSeq][curInt] = strtoumax(toCString(buf), 0, 10);
-// skipUntil(reader, IsDigit());
-//
-// clear(buf);
-// readUntil(buf, reader, IsWhitespace());
-//
-// // std::get<1>(tup) = strtoumax(toCString(buf), 0, 10);
-// _segIntEnds[curSeq][curInt] = strtoumax(toCString(buf), 0, 10);
-//
-// // appendValue(*curSeq, tup);
-//
-// skipLine(reader);
-// curInt++;
-// }
-// if (atEnd(reader))
-// break;
-// else
-// curSeq++;
-// }
-// // if (curSeq != end(_segIntervals))
-// // return -9;
-// if (curSeq != (numberOfSeqs - 1))
-// {
-// std::cerr << "ERROR: seg file has less entries (" << curSeq + 1
-// << ") than database (" << numberOfSeqs << ").\n";
+ if (curSeq == numberOfSeqs)
+ {
+ std::cerr << "ERROR: seg file has more entries then database.\n";
+ return -7;
+ }
+ skipLine(reader);
+ if (atEnd(reader))
+ break;
+
+ unsigned curInt = 0;
+ while ((!atEnd(reader)) && (value(reader) != '>'))
+ {
+ resize(_segIntStarts[curSeq], length(_segIntStarts[curSeq])+1);
+ resize(_segIntEnds[curSeq], length(_segIntEnds[curSeq])+1);
+ clear(buf);
+ readUntil(buf, reader, IsWhitespace());
+
+// std::get<0>(tup) = strtoumax(toCString(buf), 0, 10);
+ _segIntStarts[curSeq][curInt] = strtoumax(toCString(buf), 0, 10);
+ skipUntil(reader, IsDigit());
+
+ clear(buf);
+ readUntil(buf, reader, IsWhitespace());
+
+// std::get<1>(tup) = strtoumax(toCString(buf), 0, 10);
+ _segIntEnds[curSeq][curInt] = strtoumax(toCString(buf), 0, 10);
+
+// appendValue(*curSeq, tup);
+
+ skipLine(reader);
+ curInt++;
+ }
+ if (atEnd(reader))
+ break;
+ else
+ curSeq++;
+ }
+// if (curSeq != end(_segIntervals))
// return -9;
-// }
-//
-// segIntStarts.concat = concat(_segIntStarts);
-// segIntStarts.limits = stringSetLimits(_segIntStarts);
-// segIntEnds.concat = concat(_segIntEnds);
-// segIntEnds.limits = stringSetLimits(_segIntEnds);
-// // segIntEnds = _segIntEnds;
-// // segIntervals = _segIntervals; // non-concatdirect to concatdirect
-//
-// stream.close();
-//
-// } else
+ if (curSeq != (numberOfSeqs - 1))
+ {
+ std::cerr << "ERROR: seg file has less entries (" << curSeq + 1
+ << ") than database (" << numberOfSeqs << ").\n";
+ return -9;
+ }
+
+ segIntStarts.concat = concat(_segIntStarts);
+ segIntStarts.limits = stringSetLimits(_segIntStarts);
+ segIntEnds.concat = concat(_segIntEnds);
+ segIntEnds.limits = stringSetLimits(_segIntEnds);
+// segIntEnds = _segIntEnds;
+// segIntervals = _segIntervals; // non-concatdirect to concatdirect
+
+ stream.close();
+
+ } else
+ {
+ myPrint(options, 1, "No Seg-File specified, no masking will take place.\n");
+// resize(segIntervals, numberOfSeqs, Exact());
+ resize(segIntStarts, numberOfSeqs, Exact());
+ resize(segIntEnds, numberOfSeqs, Exact());
+ }
+
+// for (unsigned u = 0; u < length(segIntStarts); ++u)
// {
-// myPrint(options, 1, "No Seg-File specified, no masking will take place.\n");
-// // resize(segIntervals, numberOfSeqs, Exact());
-// resize(segIntStarts, numberOfSeqs, Exact());
-// resize(segIntEnds, numberOfSeqs, Exact());
+// myPrint(options, 1,u, ": ";
+// for (unsigned v = 0; v < length(segIntStarts[u]); ++v)
+// {
+// myPrint(options, 1,'(', segIntStarts[u][v], ", ", segIntEnds[u][v], ") ";
+// }
+// myPrint(options, 1,'\n';
// }
-//
-// // for (unsigned u = 0; u < length(segIntStarts); ++u)
-// // {
-// // myPrint(options, 1,u, ": ";
-// // for (unsigned v = 0; v < length(segIntStarts[u]); ++v)
-// // {
-// // myPrint(options, 1,'(', segIntStarts[u][v], ", ", segIntEnds[u][v], ") ";
-// // }
-// // myPrint(options, 1,'\n';
-// // }
-// myPrint(options, 1, "Dumping binary seqan mask file...");
-// CharString _path = options.dbFile;
-// append(_path, ".binseg_s");
-// save(segIntStarts, toCString(_path));
-// _path = options.dbFile;
-// append(_path, ".binseg_e");
-// save(segIntEnds, toCString(_path));
-// myPrint(options, 1, " done.\n");
-// myPrint(options, 2, "\n");
-// return 0;
-// }
+ myPrint(options, 1, "Dumping binary seqan mask file...");
+ CharString _path = options.dbFile;
+ append(_path, ".binseg_s");
+ save(segIntStarts, toCString(_path));
+ _path = options.dbFile;
+ append(_path, ".binseg_e");
+ save(segIntEnds, toCString(_path));
+ myPrint(options, 1, " done.\n");
+ myPrint(options, 2, "\n");
+ return 0;
+}
// --------------------------------------------------------------------------
// Function createSuffixArray()
@@ -566,10 +566,13 @@ generateIndexAndDump(StringSet<TString, TSpec> & seqs,
// Dump Index
myPrint(options, 1, "Writing Index to disk...");
s = sysTime();
- std::string path = options.indexDir + "/index";
-
+ std::string path = toCString(options.dbFile);
+ path += '.' + std::string(_alphName(TRedAlph()));
+ if (indexIsFM)
+ path += ".fm";
+ else
+ path += ".sa";
save(dbIndex, path.c_str());
-
e = sysTime() - s;
myPrint(options, 1, " done.\n");
myPrint(options, 2, "Runtime: ", e, "s \n");
diff --git a/src/match.hpp b/src/match.hpp
index d44d99a..bc664b5 100644
--- a/src/match.hpp
+++ b/src/match.hpp
@@ -44,10 +44,10 @@ struct Match
TQId qryId;
TSId subjId;
TPos qryStart;
- TPos qryEnd;
+// TPos qryEnd;
TPos subjStart;
- TPos subjEnd;
+// TPos subjEnd;
// Match()
// :
@@ -67,13 +67,13 @@ struct Match
inline bool operator== (Match const & m2) const
{
- return std::tie(qryId, subjId, qryStart, subjStart, qryEnd, subjEnd)
- == std::tie(m2.qryId, m2.subjId, m2.qryStart, m2.subjStart, m2.qryEnd, m2.subjEnd);
+ return std::tie(qryId, subjId, qryStart, subjStart/*, qryEnd, subjEnd*/)
+ == std::tie(m2.qryId, m2.subjId, m2.qryStart, m2.subjStart/*, m2.qryEnd, m2.subjEnd*/);
}
inline bool operator< (Match const & m2) const
{
- return std::tie(qryId, subjId, qryStart, subjStart, qryEnd, subjEnd)
- < std::tie(m2.qryId, m2.subjId, m2.qryStart, m2.subjStart, m2.qryEnd, m2.subjEnd);
+ return std::tie(qryId, subjId, qryStart, subjStart/*, qryEnd, subjEnd*/)
+ < std::tie(m2.qryId, m2.subjId, m2.qryStart, m2.subjStart/*, m2.qryEnd, m2.subjEnd*/);
}
};
@@ -272,16 +272,16 @@ myHyperSortSingleIndex(std::vector<Match<TAlph>> & matches,
// m1.subjEnd = std::max(m1.subjEnd, m2.subjEnd);
// }
-template <typename TAlph>
-inline void
-_printMatch(Match<TAlph> const & m)
-{
- std::cout << "MATCH Query " << m.qryId
- << "(" << m.qryStart << ", " << m.qryEnd
- << ") on Subject "<< m.subjId
- << "(" << m.subjStart << ", " << m.subjEnd
- << ")" << std::endl << std::flush;
-}
+
+// inline void
+// _printMatch(Match const & m)
+// {
+// std::cout << "MATCH Query " << m.qryId
+// << "(" << m.qryStart << ", " << m.qryEnd
+// << ") on Subject "<< m.subjId
+// << "(" << m.subjStart << ", " << m.subjEnd
+// << ")" << std::endl << std::flush;
+// }
diff --git a/src/misc.hpp b/src/misc.hpp
index ddd0967..bd6de73 100644
--- a/src/misc.hpp
+++ b/src/misc.hpp
@@ -412,41 +412,6 @@ appendToStatus(std::stringstream & status,
}
// ----------------------------------------------------------------------------
-// Function computeEValueThreadSafe
-// ----------------------------------------------------------------------------
-
-template <typename TBlastMatch,
- typename TScore,
- BlastProgram p,
- BlastTabularSpec h>
-inline double
-computeEValueThreadSafe(TBlastMatch & match,
- BlastIOContext<TScore, p, h> & context)
-{
-#if defined(__FreeBSD__) && defined(STDLIB_LLVM)
- // https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=192320
- static std::vector<std::unordered_map<uint64_t, uint64_t>> _cachedLengthAdjustmentsArray(omp_get_num_threads());
- static std::unordered_map<uint64_t, uint64_t> & _cachedLengthAdjustments = _cachedLengthAdjustmentsArray[omp_get_thread_num()];
-#else
- static thread_local std::unordered_map<uint64_t, uint64_t> _cachedLengthAdjustments;
-#endif
-
- // convert to 64bit and divide for translated sequences
- uint64_t ql = match.qLength / (qIsTranslated(context.blastProgram) ? 3 : 1);
- // length adjustment not yet computed
- if (_cachedLengthAdjustments.find(ql) == _cachedLengthAdjustments.end())
- _cachedLengthAdjustments[ql] = _lengthAdjustment(context.dbTotalLength, ql, context.scoringScheme);
-
- uint64_t adj = _cachedLengthAdjustments[ql];
-
- match.eValue = _computeEValue(match.alignStats.alignmentScore,
- ql - adj,
- context.dbTotalLength - adj,
- context.scoringScheme);
- return match.eValue;
-}
-
-// ----------------------------------------------------------------------------
// remove tag type
// ----------------------------------------------------------------------------
diff --git a/src/options.hpp b/src/options.hpp
index b73dc5b..7441cf9 100644
--- a/src/options.hpp
+++ b/src/options.hpp
@@ -104,10 +104,9 @@ struct DefaultIndexStringSpec<StringSet<TString, TSpec>>
template <typename TDirection, typename TStorageSpec>
struct FormattedFileContext<FormattedFile<Bam, TDirection, BlastTabular>, TStorageSpec>
{
- typedef typename DefaultIndexStringSpec<StringSet<void, void>>::Type TStringSpec; // see above
- typedef StringSet<Segment<String<char, TStringSpec>, InfixSegment> > TNameStore;
- typedef NameStoreCache<TNameStore> TNameStoreCache;
- typedef BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> Type;
+ typedef StringSet<Segment<String<char, MMap<> >, InfixSegment> > TNameStore;
+ typedef NameStoreCache<TNameStore> TNameStoreCache;
+ typedef BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> Type;
};
}
@@ -123,8 +122,7 @@ struct LambdaFMIndexConfig
#else
using TAlloc = Alloc<>;
#endif
-// using Bwt = WaveletTree<void, WTRDConfig<LengthSum, TAlloc> >;
- using Bwt = Levels<void, LevelsRDConfig<LengthSum, TAlloc, 1, 3> >;
+ using Bwt = WaveletTree<void, WTRDConfig<LengthSum, TAlloc> >;
using Sentinels = Levels<void, LevelsRDConfig<LengthSum, TAlloc> >;
static const unsigned SAMPLING = 10;
@@ -189,22 +187,11 @@ bool setEnv(TString const & key, TValue & value)
}
// ==========================================================================
-// Option Enums
-// ==========================================================================
-
-enum class DbIndexType : uint8_t
-{
- SUFFIX_ARRAY,
- FM_INDEX,
- BI_FM_INDEX
-};
-
-// ==========================================================================
// Classes
// ==========================================================================
// --------------------------------------------------------------------------
-// Class SharedOptions
+// Class LambdaOptions
// --------------------------------------------------------------------------
// This struct stores the options from the command line.
@@ -216,9 +203,13 @@ struct SharedOptions
std::string commandLine;
- std::string indexDir;
+ std::string dbFile;
- DbIndexType dbIndexType;
+ int dbIndexType = 0;
+ // for indexer, the file format of database sequences
+ // for main app, the file format of query sequences
+ // 0 -- fasta, 1 -- fastq
+// int fileFormat = 0;
int alphReduction = 0;
@@ -242,9 +233,6 @@ struct SharedOptions
}
};
-// --------------------------------------------------------------------------
-// Class LambdaOptions
-// --------------------------------------------------------------------------
struct LambdaOptions : public SharedOptions
{
@@ -267,7 +255,6 @@ struct LambdaOptions : public SharedOptions
// bool semiGlobal;
bool doubleIndexing = true;
- bool adaptiveSeeding;
unsigned seedLength = 0;
unsigned maxSeedDist = 1;
@@ -294,18 +281,8 @@ struct LambdaOptions : public SharedOptions
int idCutOff = 0;
unsigned long maxMatches = 500;
- enum class ExtensionMode : uint8_t
- {
- AUTO,
- XDROP,
- FULL_SERIAL,
- FULL_SIMD
- };
- ExtensionMode extensionMode;
-
bool filterPutativeDuplicates = true;
bool filterPutativeAbundant = true;
- bool mergePutativeSiblings = true;
int preScoring = 0; // 0 = off, 1 = seed, 2 = region (
double preScoringThresh = 0.0;
@@ -316,14 +293,9 @@ struct LambdaOptions : public SharedOptions
}
};
-// --------------------------------------------------------------------------
-// Class LambdaIndexerOptions
-// --------------------------------------------------------------------------
-
struct LambdaIndexerOptions : public SharedOptions
{
- std::string dbFile;
-// std::string segFile = "";
+ std::string segFile = "";
std::string algo = "";
bool truncateIDs;
@@ -338,7 +310,7 @@ struct LambdaIndexerOptions : public SharedOptions
// ==========================================================================
// --------------------------------------------------------------------------
-// Function sharedSetup()
+// Function displayCopyright()
// --------------------------------------------------------------------------
void
@@ -349,7 +321,7 @@ sharedSetup(ArgumentParser & parser)
std::string(SEQAN_REVISION) + ")";
setVersion(parser, versionString);
setDate(parser, __DATE__);
- setShortCopyright(parser, "2013-2016 Hannes Hauswedell, released under the GNU AGPL v3 (or later); "
+ setShortCopyright(parser, "2013-2016 Hannes Hauswedell, released under the GNU GPL v3 (or later); "
"2016 Knut Reinert and Freie Universität Berlin, released under the 3-clause-BSDL");
setCitation(parser, "Hauswedell et al (2014); doi: 10.1093/bioinformatics/btu439");
@@ -358,18 +330,18 @@ sharedSetup(ArgumentParser & parser)
" Copyright (c) 2013-2016, Hannes Hauswedell\n"
" All rights reserved.\n"
"\n"
- " This program is free software: you can redistribute it and/or modify\n"
- " it under the terms of the GNU Affero General Public License as\n"
- " published by the Free Software Foundation, either version 3 of the\n"
- " License, or (at your option) any later version.\n"
+ " Lambda is free software: you can redistribute it and/or modify\n"
+ " it under the terms of the GNU General Public License as published by\n"
+ " the Free Software Foundation, either version 3 of the License, or\n"
+ " (at your option) any later version.\n"
"\n"
" Lambda is distributed in the hope that it will be useful,\n"
" but WITHOUT ANY WARRANTY; without even the implied warranty of\n"
" MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n"
" GNU General Public License for more details.\n"
"\n"
- " You should have received a copy of the GNU Affero General Public License\n"
- " along with this program. If not, see <http://www.gnu.org/licenses/>.\n"
+ " You should have received a copy of the GNU General Public License\n"
+ " along with Lambda. If not, see <http://www.gnu.org/licenses/>.\n"
"\n"
" Copyright (c) 2016 Knut Reinert and Freie Universität Berlin\n"
" All rights reserved.\n"
@@ -438,7 +410,7 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)
// Define usage line and long description.
addUsageLine(parser, "[\\fIOPTIONS\\fP] \\fI-q QUERY.fasta\\fP "
- "\\fI-i INDEX.lambda\\fP "
+ "\\fI-d DATABASE.fasta\\fP "
"[\\fI-o output.m8\\fP]");
sharedSetup(parser);
@@ -451,12 +423,12 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)
setValidValues(parser, "query", toCString(concat(getFileExtensions(SeqFileIn()), ' ')));
setRequired(parser, "q");
- addOption(parser, ArgParseOption("i", "index",
- "The database index (created by the lambda_indexer executable).",
+ addOption(parser, ArgParseOption("d", "database",
+ "Path to original database sequences (a precomputed index with .sa or .fm needs to exist!).",
ArgParseArgument::INPUT_FILE,
"IN"));
- setRequired(parser, "index");
- setValidValues(parser, "index", ".lambda");
+ setValidValues(parser, "database", toCString(concat(getFileExtensions(SeqFileIn()), ' ')));
+ setRequired(parser, "d");
addOption(parser, ArgParseOption("di", "db-index-type",
"database index is in this format.",
@@ -655,14 +627,6 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)
// ArgParseArgument::INTEGER));
// setDefaultValue(parser, "ungapped-seeds", "1");
- addOption(parser, ArgParseOption("as", "adaptive-seeding",
- "SECRET",
- ArgParseArgument::STRING,
- "STR"));
- setValidValues(parser, "adaptive-seeding", "on off");
- setDefaultValue(parser, "adaptive-seeding", "on");
- setAdvanced(parser, "adaptive-seeding");
-
addOption(parser, ArgParseOption("sl", "seed-length",
"Length of the seeds (default = 14 for BLASTN).",
ArgParseArgument::INTEGER));
@@ -673,7 +637,7 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)
"Offset for seeding (if unset = seed-length, non-overlapping; "
"default = 5 for BLASTN).",
ArgParseArgument::INTEGER));
- setDefaultValue(parser, "seed-offset", "5");
+ setDefaultValue(parser, "seed-offset", "10");
setAdvanced(parser, "seed-offset");
addOption(parser, ArgParseOption("sd", "seed-delta",
@@ -727,14 +691,6 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)
setDefaultValue(parser, "filter-putative-abundant", "on");
setAdvanced(parser, "filter-putative-abundant");
- addOption(parser, ArgParseOption("pm", "merge-putative-siblings",
- "Merge seed from one region, "
- "stop searching if the remaining realm looks unfeasable.",
- ArgParseArgument::STRING));
- setValidValues(parser, "merge-putative-siblings", "on off");
- setDefaultValue(parser, "merge-putative-siblings", "on");
- setAdvanced(parser, "merge-putative-siblings");
-
// addOption(parser, ArgParseOption("se",
// "seedminevalue",
// "after postproc worse seeds are "
@@ -803,17 +759,6 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)
setMinValue(parser, "band", "-3");
setAdvanced(parser, "band");
- addOption(parser, ArgParseOption("em", "extension-mode",
- "Choice of extension algorithms.",
- ArgParseArgument::STRING));
-#ifdef SEQAN_SIMD_ENABLED
- setValidValues(parser, "extension-mode", "auto xdrop fullSerial fullSIMD");
-#else
- setValidValues(parser, "extension-mode", "auto xdrop fullSerial");
-#endif
- setDefaultValue(parser, "extension-mode", "auto");
- setAdvanced(parser, "extension-mode");
-
addTextSection(parser, "Tuning");
addText(parser, "Tuning the seeding parameters and (de)activating alphabet "
"reduction has a strong "
@@ -859,9 +804,6 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)
// Extract option values.
getOptionValue(options.queryFile, parser, "query");
-
- getOptionValue(options.indexDir, parser, "index");
-
// if (endsWith(options.queryFile, ".fastq") ||
// endsWith(options.queryFile, ".fq"))
// options.fileFormat = 1;
@@ -987,10 +929,6 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)
options.versionInformationToOutputFile = (buffer == "on");
clear(buffer);
- getOptionValue(buffer, parser, "adaptive-seeding");
- options.adaptiveSeeding = (buffer == "on");
-
- clear(buffer);
getOptionValue(options.seedLength, parser, "seed-length");
if ((!isSet(parser, "seed-length")) &&
(options.blastProgram == BlastProgram::BLASTN))
@@ -999,7 +937,7 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)
if (isSet(parser, "seed-offset"))
getOptionValue(options.seedOffset, parser, "seed-offset");
else
- options.seedOffset = options.seedLength / 2;
+ options.seedOffset = options.seedLength;
if (isSet(parser, "seed-gravity"))
getOptionValue(options.seedGravity, parser, "seed-gravity");
@@ -1071,17 +1009,11 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)
getOptionValue(buffer, parser, "filter-putative-abundant");
options.filterPutativeAbundant = (buffer == "on");
- getOptionValue(buffer, parser, "merge-putative-siblings");
- options.mergePutativeSiblings = (buffer == "on");
-
// TODO always prescore 1
getOptionValue(options.preScoring, parser, "pre-scoring");
if ((!isSet(parser, "pre-scoring")) &&
(options.alphReduction == 0))
options.preScoring = 1;
- // for adaptive seeding we take the full resized seed (and no surroundings)
-// if (options.adaptiveSeeding)
-// options.preScoring = 1;
getOptionValue(options.preScoringThresh, parser, "pre-scoring-threshold");
// if (options.preScoring == 0)
@@ -1091,33 +1023,6 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)
getOptionValue(numbuf, parser, "num-matches");
options.maxMatches = static_cast<unsigned long>(numbuf);
- getOptionValue(buffer, parser, "extension-mode");
- if (buffer == "fullSIMD")
- {
- options.extensionMode = LambdaOptions::ExtensionMode::FULL_SIMD;
- options.filterPutativeAbundant = false;
- options.filterPutativeDuplicates = false;
- options.mergePutativeSiblings = false;
- options.xDropOff = -1;
- options.band = -1;
- }
- else if (buffer == "fullSerial")
- {
- options.extensionMode = LambdaOptions::ExtensionMode::FULL_SERIAL;
- options.filterPutativeAbundant = false;
- options.filterPutativeDuplicates = false;
- options.mergePutativeSiblings = false;
- options.xDropOff = -1;
- }
- else if (buffer == "xdrop")
- {
- options.extensionMode = LambdaOptions::ExtensionMode::XDROP;
- }
- else
- {
- options.extensionMode = LambdaOptions::ExtensionMode::AUTO;
- }
-
return ArgumentParser::PARSE_OK;
}
@@ -1129,7 +1034,7 @@ parseCommandLine(LambdaIndexerOptions & options, int argc, char const ** argv)
ArgumentParser parser("lambda_indexer");
// Define usage line and long description.
- addUsageLine(parser, "[\\fIOPTIONS\\fP] \\-d DATABASE.fasta [-i INDEX.lambda]\\fP");
+ addUsageLine(parser, "[\\fIOPTIONS\\fP] \\-d DATABASE.fasta\\fP");
sharedSetup(parser);
@@ -1143,20 +1048,21 @@ parseCommandLine(LambdaIndexerOptions & options, int argc, char const ** argv)
setRequired(parser, "database");
setValidValues(parser, "database", toCString(concat(getFileExtensions(SeqFileIn()), ' ')));
-// addOption(parser, ArgParseOption("s",
-// "segfile",
-// "SEG intervals for database"
-// "(optional).",
-// ArgParseArgument::INPUT_FILE));
-// setValidValues(parser, "segfile", "seg");
-// hideOption(parser, "segfile"); // TODO remove completely
+ addOption(parser, ArgParseOption("s",
+ "segfile",
+ "SEG intervals for database"
+ "(optional).",
+ ArgParseArgument::INPUT_FILE));
+
+ setValidValues(parser, "segfile", "seg");
addSection(parser, "Output Options");
- addOption(parser, ArgParseOption("i", "index",
- "The output directory for the index files (defaults to \"DATABASE.lambda\").",
- ArgParseArgument::INPUT_FILE,
- "OUT"));
- setValidValues(parser, "index", ".lambda");
+// addOption(parser, ArgParseOption("o",
+// "output",
+// "Index of database sequences",
+// ArgParseArgument::OUTPUT_FILE,
+// "OUT"));
+// setValidValues(parser, "output", "sa fm");
addOption(parser, ArgParseOption("di", "db-index-type",
"Suffix array or full-text minute space.",
@@ -1280,7 +1186,7 @@ parseCommandLine(LambdaIndexerOptions & options, int argc, char const ** argv)
return res;
// Extract option values
-// getOptionValue(options.segFile, parser, "segfile");
+ getOptionValue(options.segFile, parser, "segfile");
getOptionValue(options.algo, parser, "algorithm");
if ((options.algo == "mergesort") || (options.algo == "quicksort") || (options.algo == "quicksortbuckets"))
{
@@ -1296,29 +1202,6 @@ parseCommandLine(LambdaIndexerOptions & options, int argc, char const ** argv)
getOptionValue(buffer, parser, "truncate-ids");
options.truncateIDs = (buffer == "on");
-
- getOptionValue(options.dbFile, parser, "database");
- if (isSet(parser, "index"))
- getOptionValue(options.indexDir, parser, "index");
- else
- options.indexDir = options.dbFile + ".lambda";
-
-
- if (fileExists(options.indexDir.c_str()))
- {
- std::cerr << "ERROR: An output directory already exists at " << options.indexDir << '\n'
- << "Remove it, or choose a different location.\n";
- return ArgumentParser::PARSE_ERROR;
- }
- else
- {
- if (mkdir(options.indexDir.c_str(), S_IRWXU | S_IRGRP | S_IXGRP | S_IROTH | S_IXOTH))
- {
- std::cerr << "ERROR: Cannot create output directory at " << options.indexDir << '\n';;
- return ArgumentParser::PARSE_ERROR;
- }
- }
-
return ArgumentParser::PARSE_OK;
}
@@ -1329,13 +1212,13 @@ parseCommandLineShared(SharedOptions & options, ArgumentParser & parser)
int buf = 0;
std::string buffer;
+ getOptionValue(options.dbFile, parser, "database");
+
getOptionValue(buffer, parser, "db-index-type");
if (buffer == "sa")
- options.dbIndexType = DbIndexType::SUFFIX_ARRAY;
- else if (buffer == "bifm")
- options.dbIndexType = DbIndexType::BI_FM_INDEX;
- else
- options.dbIndexType = DbIndexType::FM_INDEX;
+ options.dbIndexType = 0;
+ else // if fm
+ options.dbIndexType = 1;
getOptionValue(buffer, parser, "program");
if (buffer == "blastn")
@@ -1391,10 +1274,6 @@ parseCommandLineShared(SharedOptions & options, ArgumentParser & parser)
return ArgumentParser::PARSE_OK;
}
-// --------------------------------------------------------------------------
-// Function _alphName()
-// --------------------------------------------------------------------------
-
constexpr const char *
_alphName(AminoAcid const & /**/)
{
@@ -1437,26 +1316,6 @@ _alphName(Dna5 const & /**/)
return "dna5";
}
-// --------------------------------------------------------------------------
-// Function _indexName()
-// --------------------------------------------------------------------------
-
-inline std::string
-_indexName(DbIndexType const t)
-{
- switch (t)
- {
- case DbIndexType::SUFFIX_ARRAY: return "suffix_array";
- case DbIndexType::FM_INDEX: return "fm_index";
- case DbIndexType::BI_FM_INDEX: return "bi_fm_index";
- }
- return "ERROR_UNKNOWN_INDEX_TYPE";
-}
-
-// --------------------------------------------------------------------------
-// Function printOptions()
-// --------------------------------------------------------------------------
-
template <typename TLH>
inline void
printOptions(LambdaOptions const & options)
@@ -1475,7 +1334,7 @@ printOptions(LambdaOptions const & options)
std::cout << "OPTIONS\n"
<< " INPUT\n"
<< " query file: " << options.queryFile << "\n"
- << " index directory: " << options.indexDir << "\n"
+ << " db file: " << options.dbFile << "\n"
<< " db index type: " << (TGH::indexIsFM
? "FM-Index\n"
: "SA-Index\n")
@@ -1538,7 +1397,6 @@ printOptions(LambdaOptions const & options)
<< " putative-duplicates: " << (options.filterPutativeDuplicates
? std::string("on")
: std::string("off")) << "\n"
-
<< " SCORING\n"
<< " scoring scheme: " << options.scoringMethod << "\n"
<< " score-match: " << (options.scoringMethod
@@ -1549,36 +1407,10 @@ printOptions(LambdaOptions const & options)
: std::to_string(options.misMatch)) << "\n"
<< " score-gap: " << options.gapExtend << "\n"
<< " score-gap-open: " << options.gapOpen << "\n"
- << " EXTENSION\n";
- switch (options.extensionMode)
- {
- case LambdaOptions::ExtensionMode::AUTO:
- std::cout
- << " extensionMode: auto (depends on query length)\n"
+ << " EXTENSION\n"
<< " x-drop: " << options.xDropOff << "\n"
<< " band: " << bandStr << "\n"
- << " [depending on the automatically chosen mode x-drop or band might get disabled.\n";
- break;
- case LambdaOptions::ExtensionMode::XDROP:
- std::cout
- << " extensionMode: individual\n"
- << " x-drop: " << options.xDropOff << "\n"
- << " band: " << bandStr << "\n";
- break;
- case LambdaOptions::ExtensionMode::FULL_SERIAL:
- std::cout
- << " extensionMode: batch, but serialized\n"
- << " x-drop: not used\n"
- << " band: " << bandStr << "\n";
- break;
- case LambdaOptions::ExtensionMode::FULL_SIMD:
- std::cout
- << " extensionMode: batch with SIMD\n"
- << " x-drop: not used\n"
- << " band: not used\n";
- break;
- }
- std::cout << " BUILD OPTIONS:\n"
+ << " BUILD OPTIONS:\n"
<< " cmake_build_type: " << std::string(CMAKE_BUILD_TYPE) << "\n"
<< " fastbuild: "
#if defined(FASTBUILD)
@@ -1610,14 +1442,6 @@ printOptions(LambdaOptions const & options)
#else
<< "off\n"
#endif
- << " seqan_simd: "
- #if defined(SEQAN_SIMD_ENABLED) && defined(__AVX2__)
- << "avx2\n"
- #elif defined(SEQAN_SIMD_ENABLED) && defined(__SSE4_2__)
- << "sse4\n"
- #else
- << "off\n"
- #endif
<< "\n";
}
diff --git a/src/output.hpp b/src/output.hpp
index 3dd199e..f0d9a2f 100644
--- a/src/output.hpp
+++ b/src/output.hpp
@@ -110,15 +110,14 @@ blastMatchOneCigar(TCigar & cigar,
TLocalHolder const & lH)
{
using TCElem = typename Value<TCigar>::Type;
- using TGlobalHolder = typename TLocalHolder::TGlobalHolder;
SEQAN_ASSERT_EQ(length(m.alignRow0), length(m.alignRow1));
// translate positions into dna space
- unsigned const transFac = qIsTranslated(TGlobalHolder::blastProgram) ? 3 : 1;
+ unsigned const transFac = qIsTranslated(lH.gH.blastProgram) ? 3 : 1;
// clips resulting from translation / frameshift are always hard clips
unsigned const leftFrameClip = std::abs(m.qFrameShift) - 1;
- unsigned const rightFrameClip = qIsTranslated(TGlobalHolder::blastProgram) ? (m.qLength - leftFrameClip) % 3 : 0;
+ unsigned const rightFrameClip = qIsTranslated(lH.gH.blastProgram) ? (m.qLength - leftFrameClip) % 3 : 0;
// regular clipping from local alignment (regions outside match) can be hard or soft
unsigned const leftClip = m.qStart * transFac;
unsigned const rightClip = (length(source(m.alignRow0)) - m.qEnd) * transFac;
@@ -193,7 +192,6 @@ blastMatchTwoCigar(TCigar & dnaCigar,
TLocalHolder const & lH)
{
using TCElem = typename Value<TCigar>::Type;
- using TGlobalHolder = typename TLocalHolder::TGlobalHolder;
SEQAN_ASSERT_EQ(length(m.alignRow0), length(m.alignRow1));
@@ -303,7 +301,7 @@ myWriteHeader(TGH & globalHolder, TLambdaOptions const & options)
context(globalHolder.outfile).fields = options.columns;
auto & versionString = context(globalHolder.outfile).versionString;
clear(versionString);
- append(versionString, _programTagToString(TGH::blastProgram));
+ append(versionString, _programTagToString(globalHolder.blastProgram));
append(versionString, " 2.2.26+ [created by LAMBDA");
if (options.versionInformationToOutputFile)
{
@@ -320,7 +318,7 @@ myWriteHeader(TGH & globalHolder, TLambdaOptions const & options)
auto & subjIds = contigNames(context);
// set sequence lengths
- if (sIsTranslated(TGH::blastProgram))
+ if (sIsTranslated(globalHolder.blastProgram))
{
//TODO can we get around a copy?
subjSeqLengths = globalHolder.untransSubjSeqLengths;
@@ -427,7 +425,6 @@ template <typename TLH, typename TRecord>
inline void
myWriteRecord(TLH & lH, TRecord const & record)
{
- using TGH = typename TLH::TGlobalHolder;
if (lH.options.outFileFormat == 0) // BLAST
{
SEQAN_OMP_PRAGMA(critical(filewrite))
@@ -448,7 +445,7 @@ myWriteRecord(TLH & lH, TRecord const & record)
for (auto & bamR : bamRecords)
{
// untranslate for sIsTranslated
- if (sIsTranslated(TGH::blastProgram))
+ if (sIsTranslated(lH.gH.blastProgram))
{
bamR.beginPos = mIt->sStart * 3 + std::abs(mIt->sFrameShift) - 1;
if (mIt->sFrameShift < 0)
@@ -475,16 +472,16 @@ myWriteRecord(TLH & lH, TRecord const & record)
{
clear(protCigar);
// native protein
- if ((TGH::blastProgram == BlastProgram::BLASTP) || (TGH::blastProgram == BlastProgram::TBLASTN))
+ if ((lH.gH.blastProgram == BlastProgram::BLASTP) || (lH.gH.blastProgram == BlastProgram::TBLASTN))
blastMatchOneCigar(protCigar, *mIt, lH);
- else if (qIsTranslated(TGH::blastProgram)) // translated
+ else if (qIsTranslated(lH.gH.blastProgram)) // translated
blastMatchTwoCigar(bamR.cigar, protCigar, *mIt, lH);
else // BLASTN can't have protein sequence
blastMatchOneCigar(bamR.cigar, *mIt, lH);
}
else
{
- if ((TGH::blastProgram != BlastProgram::BLASTP) && (TGH::blastProgram != BlastProgram::TBLASTN))
+ if ((lH.gH.blastProgram != BlastProgram::BLASTP) && (lH.gH.blastProgram != BlastProgram::TBLASTN))
blastMatchOneCigar(bamR.cigar, *mIt, lH);
}
// we want to include the seq
@@ -501,7 +498,7 @@ myWriteRecord(TLH & lH, TRecord const & record)
(endPosition(mIt->alignRow0) != endPosition(mPrevIt->alignRow0)));
}
- if (TGH::blastProgram == BlastProgram::BLASTN)
+ if (lH.gH.blastProgram == BlastProgram::BLASTN)
{
if (lH.options.samBamHardClip)
{
@@ -515,7 +512,7 @@ myWriteRecord(TLH & lH, TRecord const & record)
bamR.seq = source(mIt->alignRow0);
}
}
- else if (qIsTranslated(TGH::blastProgram))
+ else if (qIsTranslated(lH.gH.blastProgram))
{
if (lH.options.samBamHardClip)
{
@@ -574,7 +571,7 @@ myWriteRecord(TLH & lH, TRecord const & record)
int8_t(mIt->sFrameShift), 'c');
if (lH.options.samBamTags[SamBamExtraTags<>::Q_AA_SEQ])
{
- if ((TGH::blastProgram == BlastProgram::BLASTN) || (!writeSeq))
+ if ((lH.gH.blastProgram == BlastProgram::BLASTN) || (!writeSeq))
appendTagValue(bamR.tags,
std::get<0>(SamBamExtraTags<>::keyDescPairs[SamBamExtraTags<>::Q_AA_SEQ]),
"*", 'Z');
--
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