[med-svn] [Git][med-team/lambda-align][master] 5 commits: New upstream version 1.0.3
Michael R. Crusoe
gitlab at salsa.debian.org
Sat Feb 17 20:21:20 UTC 2018
Michael R. Crusoe pushed to branch master at Debian Med / lambda-align
Commits:
142f48e4 by Michael R. Crusoe at 2018-02-17T09:30:44-08:00
New upstream version 1.0.3
- - - - -
5ba1150e by Michael R. Crusoe at 2018-02-17T09:30:48-08:00
Update upstream source from tag 'upstream/1.0.3'
Update to upstream version '1.0.3'
with Debian dir f30a179d18680e921a29bd81266cc1b7d842aee3
- - - - -
8975dc19 by Michael R. Crusoe at 2018-02-17T09:35:51-08:00
1.0.3
- - - - -
5ab03172 by Michael R. Crusoe at 2018-02-17T11:27:11-08:00
Add CWL descriptions
- - - - -
9c3a2f5c by Michael R. Crusoe at 2018-02-17T12:19:24-08:00
Run the unit tests, also as AutoPkgTests
- - - - -
12 changed files:
- + debian/README.source
- debian/changelog
- debian/control
- + debian/cwl/lambda.cwl
- + debian/cwl/lambda_indexer.cwl
- − debian/lintian-overrides
- debian/patches/force-link-rt-pthread.patch
- debian/rules
- + debian/tests/control
- + debian/tests/run-tests
- src/holders.hpp
- src/options.hpp
Changes:
=====================================
debian/README.source
=====================================
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,4 @@
+The cwl/ directory was generated thusly:
+
+All binaries were called with --write-ctd and those CTDs were converted to CWL
+using https://github.com/WorkflowConversion/CTDConverter
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,14 @@
-lambda-align (1.0.2-2) UNRELEASED; urgency=medium
+lambda-align (1.0.3-1) unstable; urgency=medium
+ [ Steffen Moeller ]
* Added ref to OMICtools registry.
- -- Steffen Moeller <moeller at debian.org> Fri, 30 Jun 2017 19:04:18 +0200
+ [ Michael R. Crusoe ]
+ * New upstream release fixes Seqan 2.4.0 compat
+ * Include CWL descriptions
+ * Run the unit tests and make them available as AutoPkgTests
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Sat, 17 Feb 2018 12:19:04 -0800
lambda-align (1.0.2-1) unstable; urgency=medium
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -1,21 +1,25 @@
Source: lambda-align
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Sascha Steinbiss <satta at debian.org>,
+ Michael R. Crusoe <michael.crusoe at gmail.com>
Section: science
Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Sascha Steinbiss <satta at debian.org>
Build-Depends: debhelper (>= 10),
- libseqan2-dev (>= 2.2.0+dfsg-2~),
+ libseqan2-dev,
cmake,
zlib1g-dev,
- libbz2-dev
-Standards-Version: 4.0.0
+ libbz2-dev,
+ openssl
+Standards-Version: 4.1.3
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/lambda-align.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/lambda-align.git
Homepage: https://seqan.github.io/lambda
Package: lambda-align
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Suggests: cwl-runner
Description: Local Aligner for Massive Biological DatA
Lambda is a local biosequence aligner optimized for many query sequences
and searches in protein space. It is compatible to the de facto standard tool
=====================================
debian/cwl/lambda.cwl
=====================================
--- /dev/null
+++ b/debian/cwl/lambda.cwl
@@ -0,0 +1,376 @@
+#!/usr/bin/env cwl-runner
+
+# This CWL file was automatically generated using CTDConverter.
+# Visit https://github.com/WorkflowConversion/CTDConverter for more information.
+
+baseCommand: lambda
+class: CommandLineTool
+cwlVersion: v1.0
+doc: "Lambda is a local aligner optimized for many query sequences and searches in\
+ \ protein space. It is compatible to BLAST, but much faster than BLAST and many\
+ \ other comparable tools.\nDetailed information is available in the wiki: <https://github.com/seqan/lambda/wiki>\n\
+ \n\n\nFor more information, visit http://www.seqan.de"
+inputs:
+- default: 'false'
+ doc: Display the help message with advanced options.
+ id: param_full-help
+ inputBinding:
+ prefix: -full-help
+ label: Display the help message with advanced options.
+ type:
+ - 'null'
+ - string
+- default: '1'
+ doc: 'Turn this option off to disable version update notifications of the application. '
+ id: param_version-check
+ inputBinding:
+ prefix: -version-check
+ label: 'Turn this option off to disable version update notifications of the application. '
+ type:
+ - 'null'
+ - string
+- default: 'false'
+ doc: Display long copyright information.
+ id: param_copyright
+ inputBinding:
+ prefix: -copyright
+ label: Display long copyright information.
+ type:
+ - 'null'
+ - string
+- default: '1'
+ doc: 'Display more/less diagnostic output during operation: 0 [only errors]; 1 [default];
+ 2 [+run-time, options and statistics].'
+ id: param_verbosity
+ inputBinding:
+ prefix: -verbosity
+ label: 'Display more/less diagnostic output during operation: 0 [only errors]; 1
+ [default]; 2 [+run-time, options and statistics].'
+ type:
+ - 'null'
+ - int
+- doc: Query sequences.
+ id: param_query
+ inputBinding:
+ prefix: -query
+ label: Query sequences.
+ type: File
+- doc: Path to original database sequences (a precomputed index with .sa or .fm needs
+ to exist!).
+ id: param_database
+ inputBinding:
+ prefix: -database
+ label: Path to original database sequences (a precomputed index with .sa or .fm
+ needs to exist!).
+ type: File
+- default: fm
+ doc: database index is in this format.
+ id: param_db-index-type
+ inputBinding:
+ prefix: -db-index-type
+ label: database index is in this format.
+ type:
+ - 'null'
+ - string
+- default: output.m8
+ doc: Filename for output output file
+ id: param_output_filename
+ inputBinding:
+ prefix: -output
+ label: Filename for output output file
+ type:
+ - 'null'
+ - string
+- default: std
+ doc: Print specified column combination and/or order (.m8 and .m9 outputs only);
+ call -oc help for more details.
+ id: param_output-columns
+ inputBinding:
+ prefix: -output-columns
+ label: Print specified column combination and/or order (.m8 and .m9 outputs only);
+ call -oc help for more details.
+ type:
+ - 'null'
+ - string
+- default: '0'
+ doc: Output only matches above this threshold (checked before e-value check).
+ id: param_percent-identity
+ inputBinding:
+ prefix: -percent-identity
+ label: Output only matches above this threshold (checked before e-value check).
+ type:
+ - 'null'
+ - int
+- default: '0.1'
+ doc: Output only matches that score below this threshold.
+ id: param_e-value
+ inputBinding:
+ prefix: -e-value
+ label: Output only matches that score below this threshold.
+ type:
+ - 'null'
+ - double
+- default: '500'
+ doc: Print at most this number of matches per query.
+ id: param_num-matches
+ inputBinding:
+ prefix: -num-matches
+ label: Print at most this number of matches per query.
+ type:
+ - 'null'
+ - int
+- default: 'off'
+ doc: BAM files require all subject names to be written to the header. For SAM this
+ is not required, so Lambda does not automatically do it to save space (especially
+ for protein database this is a lot!). If you still want them with SAM, e.g. for
+ better BAM compatibility, use this option.
+ id: param_sam-with-refheader
+ inputBinding:
+ prefix: -sam-with-refheader
+ label: BAM files require all subject names to be written to the header. For SAM
+ this is not required, so Lambda does not automatically do it to save space (especially
+ for protein database this is a lot!). If you still want them with SAM, e.g. for
+ better BAM compatibility, use this option.
+ type:
+ - 'null'
+ - string
+- default: uniq
+ doc: Write matching DNA subsequence into SAM/BAM file (BLASTN). For BLASTX and TBLASTX
+ the matching protein sequence is "untranslated" and positions retransformed to
+ the original sequence. For BLASTP and TBLASTN there is no DNA sequence so a "*"
+ is written to the SEQ column. The matching protein sequence can be written as
+ an optional tag, see --sam-bam-tags. If set to uniq than the sequence is omitted
+ iff it is identical to the previous match's subsequence.
+ id: param_sam-bam-seq
+ inputBinding:
+ prefix: -sam-bam-seq
+ label: Write matching DNA subsequence into SAM/BAM file (BLASTN). For BLASTX and
+ TBLASTX the matching protein sequence is "untranslated" and positions retransformed
+ to the original sequence. For BLASTP and TBLASTN there is no DNA sequence so a
+ "*" is written to the SEQ column. The matching protein sequence can be written
+ as an optional tag, see --sam-bam-tags. If set to uniq than the sequence is omitted
+ iff it is identical to the previous match's subsequence.
+ type:
+ - 'null'
+ - string
+- default: AS NM ZE ZI ZF
+ doc: Write the specified optional columns to the SAM/BAM file. Call --sam-bam-tags
+ help for more details.
+ id: param_sam-bam-tags
+ inputBinding:
+ prefix: -sam-bam-tags
+ label: Write the specified optional columns to the SAM/BAM file. Call --sam-bam-tags
+ help for more details.
+ type:
+ - 'null'
+ - string
+- default: hard
+ doc: Whether to hard-clip or soft-clip the regions beyond the local match. Soft-clipping
+ retains the full sequence in the output file, but obviously uses more space.
+ id: param_sam-bam-clip
+ inputBinding:
+ prefix: -sam-bam-clip
+ label: Whether to hard-clip or soft-clip the regions beyond the local match. Soft-clipping
+ retains the full sequence in the output file, but obviously uses more space.
+ type:
+ - 'null'
+ - string
+- default: '8'
+ doc: number of threads to run concurrently.
+ id: param_threads
+ inputBinding:
+ prefix: -threads
+ label: number of threads to run concurrently.
+ type:
+ - 'null'
+ - int
+- default: none
+ doc: controls double-indexing.
+ id: param_query-index-type
+ inputBinding:
+ prefix: -query-index-type
+ label: controls double-indexing.
+ type:
+ - 'null'
+ - string
+- default: blastx
+ doc: Blast Operation Mode.
+ id: param_program
+ inputBinding:
+ prefix: -program
+ label: Blast Operation Mode.
+ type:
+ - 'null'
+ - string
+- default: '1'
+ doc: The translation table to use for nucl -> amino acid translation(not for BlastN,
+ BlastP). See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c for
+ ids (default is generic). Six frames are generated.
+ id: param_genetic-code
+ inputBinding:
+ prefix: -genetic-code
+ label: The translation table to use for nucl -> amino acid translation(not for BlastN,
+ BlastP). See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c for
+ ids (default is generic). Six frames are generated.
+ type:
+ - 'null'
+ - int
+- default: murphy10
+ doc: Alphabet Reduction for seeding phase (ignored for BLASTN).
+ id: param_alphabet-reduction
+ inputBinding:
+ prefix: -alphabet-reduction
+ label: Alphabet Reduction for seeding phase (ignored for BLASTN).
+ type:
+ - 'null'
+ - string
+- default: '10'
+ doc: Length of the seeds (default = 14 for BLASTN).
+ id: param_seed-length
+ inputBinding:
+ prefix: -seed-length
+ label: Length of the seeds (default = 14 for BLASTN).
+ type:
+ - 'null'
+ - int
+- default: '10'
+ doc: Offset for seeding (if unset = seed-length, non-overlapping; default = 5 for
+ BLASTN).
+ id: param_seed-offset
+ inputBinding:
+ prefix: -seed-offset
+ label: Offset for seeding (if unset = seed-length, non-overlapping; default = 5
+ for BLASTN).
+ type:
+ - 'null'
+ - int
+- default: '1'
+ doc: maximum seed distance.
+ id: param_seed-delta
+ inputBinding:
+ prefix: -seed-delta
+ label: maximum seed distance.
+ type:
+ - 'null'
+ - int
+- default: '2'
+ doc: evaluate score of a region NUM times the size of the seed before extension
+ (0 -> no pre-scoring, 1 -> evaluate seed, n-> area around seed, as well; default
+ = 1 if no reduction is used).
+ id: param_pre-scoring
+ inputBinding:
+ prefix: -pre-scoring
+ label: evaluate score of a region NUM times the size of the seed before extension
+ (0 -> no pre-scoring, 1 -> evaluate seed, n-> area around seed, as well; default
+ = 1 if no reduction is used).
+ type:
+ - 'null'
+ - int
+- default: '2.0'
+ doc: minimum average score per position in pre-scoring region.
+ id: param_pre-scoring-threshold
+ inputBinding:
+ prefix: -pre-scoring-threshold
+ label: minimum average score per position in pre-scoring region.
+ type:
+ - 'null'
+ - double
+- default: 'on'
+ doc: filter hits that will likely duplicate a match already found.
+ id: param_filter-putative-duplicates
+ inputBinding:
+ prefix: -filter-putative-duplicates
+ label: filter hits that will likely duplicate a match already found.
+ type:
+ - 'null'
+ - string
+- default: 'on'
+ doc: If the maximum number of matches per query are found already, stop searching
+ if the remaining realm looks unfeasable.
+ id: param_filter-putative-abundant
+ inputBinding:
+ prefix: -filter-putative-abundant
+ label: If the maximum number of matches per query are found already, stop searching
+ if the remaining realm looks unfeasable.
+ type:
+ - 'null'
+ - string
+- default: '62'
+ doc: use '45' for Blosum45; '62' for Blosum62 (default); '80' for Blosum80; [ignored
+ for BlastN]
+ id: param_scoring-scheme
+ inputBinding:
+ prefix: -scoring-scheme
+ label: use '45' for Blosum45; '62' for Blosum62 (default); '80' for Blosum80; [ignored
+ for BlastN]
+ type:
+ - 'null'
+ - int
+- default: '-1'
+ doc: Score per gap character (default = -2 for BLASTN).
+ id: param_score-gap
+ inputBinding:
+ prefix: -score-gap
+ label: Score per gap character (default = -2 for BLASTN).
+ type:
+ - 'null'
+ - int
+- default: '-11'
+ doc: Additional cost for opening gap (default = -5 for BLASTN).
+ id: param_score-gap-open
+ inputBinding:
+ prefix: -score-gap-open
+ label: Additional cost for opening gap (default = -5 for BLASTN).
+ type:
+ - 'null'
+ - int
+- default: '2'
+ doc: Match score [only BLASTN])
+ id: param_score-match
+ inputBinding:
+ prefix: -score-match
+ label: Match score [only BLASTN])
+ type:
+ - 'null'
+ - int
+- default: '-3'
+ doc: Mismatch score [only BLASTN]
+ id: param_score-mismatch
+ inputBinding:
+ prefix: -score-mismatch
+ label: Mismatch score [only BLASTN]
+ type:
+ - 'null'
+ - int
+- default: '30'
+ doc: Stop Banded extension if score x below the maximum seen (-1 means no xdrop).
+ id: param_x-drop
+ inputBinding:
+ prefix: -x-drop
+ label: Stop Banded extension if score x below the maximum seen (-1 means no xdrop).
+ type:
+ - 'null'
+ - int
+- default: '-3'
+ doc: Size of the DP-band used in extension (-3 means log2 of query length; -2 means
+ sqrt of query length; -1 means full dp; n means band of size 2n+1)
+ id: param_band
+ inputBinding:
+ prefix: -band
+ label: Size of the DP-band used in extension (-3 means log2 of query length; -2
+ means sqrt of query length; -1 means full dp; n means band of size 2n+1)
+ type:
+ - 'null'
+ - int
+label: the Local Aligner for Massive Biological DatA
+outputs:
+- doc: File to hold reports on hits (.m* are blastall -m* formats; .m8 is tab-seperated,
+ .m9 is tab-seperated with with comments, .m0 is pairwise format).
+ id: param_output
+ label: File to hold reports on hits (.m* are blastall -m* formats; .m8 is tab-seperated,
+ .m9 is tab-seperated with with comments, .m0 is pairwise format).
+ outputBinding:
+ glob: $(inputs.param_output_filename)
+ type:
+ - 'null'
+ - File
=====================================
debian/cwl/lambda_indexer.cwl
=====================================
--- /dev/null
+++ b/debian/cwl/lambda_indexer.cwl
@@ -0,0 +1,144 @@
+#!/usr/bin/env cwl-runner
+
+# This CWL file was automatically generated using CTDConverter.
+# Visit https://github.com/WorkflowConversion/CTDConverter for more information.
+
+baseCommand: lambda_indexer
+class: CommandLineTool
+cwlVersion: v1.0
+doc: "Lambda is a local aligner optimized for many query sequences and searches in\
+ \ protein space. It is compatible to BLAST, but much faster than BLAST and many\
+ \ other comparable tools.\nDetailed information is available in the wiki: <https://github.com/seqan/lambda/wiki>\n\
+ This is the indexer_binary for creating lambda-compatible databases.\n\n\n\nFor\
+ \ more information, visit http://www.seqan.de"
+inputs:
+- default: 'false'
+ doc: Display the help message with advanced options.
+ id: param_full-help
+ inputBinding:
+ prefix: -full-help
+ label: Display the help message with advanced options.
+ type:
+ - 'null'
+ - string
+- default: '1'
+ doc: 'Turn this option off to disable version update notifications of the application. '
+ id: param_version-check
+ inputBinding:
+ prefix: -version-check
+ label: 'Turn this option off to disable version update notifications of the application. '
+ type:
+ - 'null'
+ - string
+- default: 'false'
+ doc: Display long copyright information.
+ id: param_copyright
+ inputBinding:
+ prefix: -copyright
+ label: Display long copyright information.
+ type:
+ - 'null'
+ - string
+- default: '1'
+ doc: 'Display more/less diagnostic output during operation: 0 [only errors]; 1 [default];
+ 2 [+run-time, options and statistics].'
+ id: param_verbosity
+ inputBinding:
+ prefix: -verbosity
+ label: 'Display more/less diagnostic output during operation: 0 [only errors]; 1
+ [default]; 2 [+run-time, options and statistics].'
+ type:
+ - 'null'
+ - int
+- doc: Database sequences.
+ id: param_database
+ inputBinding:
+ prefix: -database
+ label: Database sequences.
+ type: File
+- doc: SEG intervals for database(optional).
+ id: param_segfile
+ inputBinding:
+ prefix: -segfile
+ label: SEG intervals for database(optional).
+ type:
+ - 'null'
+ - File
+- default: fm
+ doc: Suffix array or full-text minute space.
+ id: param_db-index-type
+ inputBinding:
+ prefix: -db-index-type
+ label: Suffix array or full-text minute space.
+ type:
+ - 'null'
+ - string
+- default: 'on'
+ doc: Truncate IDs at first whitespace. This saves a lot of space and is irrelevant
+ for all LAMBDA output formats other than BLAST Pairwise (.m0).
+ id: param_truncate-ids
+ inputBinding:
+ prefix: -truncate-ids
+ label: Truncate IDs at first whitespace. This saves a lot of space and is irrelevant
+ for all LAMBDA output formats other than BLAST Pairwise (.m0).
+ type:
+ - 'null'
+ - string
+- default: blastx
+ doc: Blast Operation Mode.
+ id: param_program
+ inputBinding:
+ prefix: -program
+ label: Blast Operation Mode.
+ type:
+ - 'null'
+ - string
+- default: '1'
+ doc: The translation table to use (not for BlastN, BlastP). See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
+ for ids (default is generic).
+ id: param_genetic-code
+ inputBinding:
+ prefix: -genetic-code
+ label: The translation table to use (not for BlastN, BlastP). See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
+ for ids (default is generic).
+ type:
+ - 'null'
+ - int
+- default: murphy10
+ doc: Alphabet Reduction for seeding phase (ignored for BLASTN).
+ id: param_alphabet-reduction
+ inputBinding:
+ prefix: -alphabet-reduction
+ label: Alphabet Reduction for seeding phase (ignored for BLASTN).
+ type:
+ - 'null'
+ - string
+- default: radixsort
+ doc: Algorithm for SA construction (also used for FM; see Memory Requirements below!).
+ id: param_algorithm
+ inputBinding:
+ prefix: -algorithm
+ label: Algorithm for SA construction (also used for FM; see Memory Requirements
+ below!).
+ type:
+ - 'null'
+ - string
+- default: '8'
+ doc: number of threads to run concurrently (ignored if a == skew7ext).
+ id: param_threads
+ inputBinding:
+ prefix: -threads
+ label: number of threads to run concurrently (ignored if a == skew7ext).
+ type:
+ - 'null'
+ - int
+- default: /home/mcrusoe/debian/lambda-align
+ doc: temporary directory used by skew, defaults to working directory.
+ id: param_tmp-dir
+ inputBinding:
+ prefix: -tmp-dir
+ label: temporary directory used by skew, defaults to working directory.
+ type:
+ - 'null'
+ - string
+label: indexer for creating lambda-compatible databases
=====================================
debian/lintian-overrides deleted
=====================================
--- a/debian/lintian-overrides
+++ /dev/null
@@ -1,4 +0,0 @@
-# The term 'iff' actually exists and means 'if anf only if'.
-lambda-align: spelling-error-in-binary usr/bin/lambda iff if
-lambda-align: spelling-error-in-binary usr/bin/lambda_indexer iff if
-lambda-align: spelling-error-in-manpage usr/share/man/man1/lambda.1.gz iff if
=====================================
debian/patches/force-link-rt-pthread.patch
=====================================
--- a/debian/patches/force-link-rt-pthread.patch
+++ b/debian/patches/force-link-rt-pthread.patch
@@ -2,9 +2,9 @@ Description: enforce linking of -lrt -lpthread
This patch makes sure that these get linked even though they might
be missing in $SEQAN_LIBRARIES (until this is fixed in libseqan2-dev).
Author: Sascha Steinbiss <satta at debian.org>
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -207,8 +207,8 @@
+--- lambda-align.orig/src/CMakeLists.txt
++++ lambda-align/src/CMakeLists.txt
+@@ -208,8 +208,8 @@
radix_inplace.h)
# Add dependencies found by find_package (SeqAn).
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -25,3 +25,6 @@ override_dh_installman:
override_dh_auto_configure:
dh_auto_configure -- -DLAMBDA_NATIVE_BUILD=OFF -DLAMBDA_MMAPPED_DB=ON -DCMAKE_BUILD_TYPE=Release
+
+override_dh_auto_test:
+ cd build/tests && ctest --parallel $(shell nproc)
=====================================
debian/tests/control
=====================================
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-tests
+Depends: lambda-align, openssl, gzip, coreutils, diffutils
+Restrictions: allow-stderr
=====================================
debian/tests/run-tests
=====================================
--- /dev/null
+++ b/debian/tests/run-tests
@@ -0,0 +1,8 @@
+#!/bin/sh -e
+
+mkdir build
+cd build
+cmake ../
+for binary in $(dpkg -L lambda-align); do ln -s ${binary} bin/; done
+ctest --parallel $(nproc)
+
=====================================
src/holders.hpp
=====================================
--- a/src/holders.hpp
+++ b/src/holders.hpp
@@ -385,7 +385,16 @@ public:
ArrayGaps>;
using TAlignRow1 = Gaps<typename Infix<typename Value<typename TGlobalHolder::TTransSubjSeqs>::Type>::Type,
ArrayGaps>;
- using TDPContext = DPContext<typename Value<typename TGlobalHolder::TScoreScheme>::Type, TScoreExtension>;
+#if (SEQAN_VERSION_MINOR < 4)
+ using TDPContext = DPContext<typename Value<typename TGlobalHolder::TScoreScheme>::Type, TScoreExtension>;
+#else
+ using TCellValue = int16_t;
+ using TDPCell = DPCell_<TCellValue, TScoreExtension>;
+ using TTraceValue = typename TraceBitMap_<TCellValue>::Type;
+ using TScoreHost = String<TDPCell, Alloc<OverAligned> >;
+ using TTraceHost = String<TTraceValue, Alloc<OverAligned> >;
+ using TDPContext = DPContext<TDPCell, TTraceValue, TScoreHost, TTraceHost>;
+#endif
using TAliExtContext = AliExtContext_<TAlignRow0, TAlignRow1, TDPContext>;
TAliExtContext alignContext;
=====================================
src/options.hpp
=====================================
--- a/src/options.hpp
+++ b/src/options.hpp
@@ -420,14 +420,14 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)
"Query sequences.",
ArgParseArgument::INPUT_FILE,
"IN"));
- setValidValues(parser, "query", toCString(concat(getFileExtensions(SeqFileIn()), ' ')));
+ setValidValues(parser, "query", getFileExtensions(SeqFileIn()));
setRequired(parser, "q");
addOption(parser, ArgParseOption("d", "database",
"Path to original database sequences (a precomputed index with .sa or .fm needs to exist!).",
ArgParseArgument::INPUT_FILE,
"IN"));
- setValidValues(parser, "database", toCString(concat(getFileExtensions(SeqFileIn()), ' ')));
+ setValidValues(parser, "database", getFileExtensions(SeqFileIn()));
setRequired(parser, "d");
addOption(parser, ArgParseOption("di", "db-index-type",
@@ -1048,7 +1048,7 @@ parseCommandLine(LambdaIndexerOptions & options, int argc, char const ** argv)
ArgParseArgument::INPUT_FILE,
"IN"));
setRequired(parser, "database");
- setValidValues(parser, "database", toCString(concat(getFileExtensions(SeqFileIn()), ' ')));
+ setValidValues(parser, "database", getFileExtensions(SeqFileIn()));
addOption(parser, ArgParseOption("s",
"segfile",
View it on GitLab: https://salsa.debian.org/med-team/lambda-align/compare/4f23d31f46f45d1210693cbc9479bed7245b0215...9c3a2f5c9a29e4b56f468f1393e6e8ec5ca32c83
---
View it on GitLab: https://salsa.debian.org/med-team/lambda-align/compare/4f23d31f46f45d1210693cbc9479bed7245b0215...9c3a2f5c9a29e4b56f468f1393e6e8ec5ca32c83
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