[med-svn] [daligner] 01/07: Refer to upstream README for command reference
Afif Elghraoui
afif at moszumanska.debian.org
Wed Oct 12 07:08:09 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
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commit 7991619e43fde63616c9b3d274d70e2a96736434
Author: Afif Elghraoui <afif at debian.org>
Date: Tue Oct 11 20:59:10 2016 -0700
Refer to upstream README for command reference
I cannot continue maintaining the manpages without upstream
support. Monitoring changes to the README and revising them
for the manpages takes up too much time.
---
debian/control | 1 -
debian/man/HPCdaligner.1.md | 77 ------------------------------
debian/man/HPCmapper.1.md | 46 ------------------
debian/man/LAcat.1.md | 29 -----------
debian/man/LAcheck.1.md | 41 ----------------
debian/man/LAdump.1.md | 52 --------------------
debian/man/LAindex.1.md | 27 -----------
debian/man/LAmerge.1.md | 37 --------------
debian/man/LAshow.1.md | 72 ----------------------------
debian/man/LAsort.1.md | 31 ------------
debian/man/LAsplit.1.md | 33 -------------
debian/man/Makefile | 12 -----
debian/man/daligner.1 | 12 +++++
debian/man/daligner.1.md | 114 --------------------------------------------
debian/rules | 20 ++++----
15 files changed, 24 insertions(+), 580 deletions(-)
diff --git a/debian/control b/debian/control
index 80804ba..fd26071 100644
--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,6 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Afif Elghraoui <afif at ghraoui.name>
Build-Depends:
debhelper (>= 9),
- pandoc,
Standards-Version: 3.9.6
Homepage: https://dazzlerblog.wordpress.com
Vcs-Git: git://anonscm.debian.org/debian-med/daligner.git
diff --git a/debian/man/HPCdaligner.1.md b/debian/man/HPCdaligner.1.md
deleted file mode 100644
index 48d2a66..0000000
--- a/debian/man/HPCdaligner.1.md
+++ /dev/null
@@ -1,77 +0,0 @@
-% HPCdaligner(1) 1.0
-%
-% August 2015
-
-# NAME
-
-HPCdaligner - generate a script to run **daligner**(1)
-
-# SYNOPSIS
-
-**HPCdaligner** [**-vbAI**] [**-k***int(14)*] [**-w***int(6)*]
- [**-h***int(35)*] [**-t***int*] [**-M***int*]
- [**-e***double(.70)*] [**-l***int(1000)*] [**-s***int(100)*] [**-H***int*]
- [**-m***track*]+ [**-dal***int(4)*] [**-deg***int(25)*]
- *path:db|dam* [*first:int*[-*last:int*]]
-
-# DESCRIPTION
-
-**HPCdaligner** writes a UNIX shell script to the standard output that consists
-of a sequence of commands that effectively run **daligner**(1) on all pairs of
-blocks of a split database and then externally sorts and merges them using
-**LAsort**(1) and **LAmerge**(1) into a collection of alignment files with
-names *path.#.las* where # ranges from 1 to the number of blocks the database
-is split into. These sorted files if concatenated by say **LAcat**(1)
-would contain all the alignments in sorted order (of a-read, then b-read, and so on).
-Moreover, all overlaps for a given a-read are guaranteed to not be split across
-files, so one can run artifact analyzers or error correction on each sorted
-file in parallel.
-
-The database must have been previously split by **DBsplit**(1) and all the
-parameters, except **-v**, **-dal**, and **-deg**, are passed through to the
-calls to **daligner**(1). The defaults for these parameters are as for
-**daligner**(1). The **-v** flag, for verbose-mode, is also passed to all
-calls to **LAsort**(1) and **LAmerge**(1). **-dal** and **-deg** options are
-described later.
-
-For a database divided into N sub-blocks, the calls to **daligner**(1) will
-produce in total 2TN^2 .las files assuming daligner runs with T threads.
-These will then be sorted and merged into N^2 sorted .las files, one for each
-block pair. These are then merged in ceil(log_deg N) phases where the number of
-files decreases geometrically in **-deg** until there is 1 file per row of the
-N x N block matrix. So at the end one has N sorted .las files that when
-concatenated would give a single large sorted overlap file.
-
-The **-dal** option (default 4) gives the desired number of block comparisons
-per call to **daligner**(1). Some must contain *dal*-1 comparisons, and the
-first *dal*-2 block comparisons even less, but the **HPCdaligner** "planner"
-does the best it can to give an average load of dal block comparisons per
-command. The **-deg** option (default 25) gives the maximum number of files
-that will be merged in a single **LAmerge**(1) command. The planner makes the
-most even k-ary tree of merges, where the number of levels is ceil(log_deg N).
-
-If the integers *first* and *last* are missing, then the script produced
-is for every block in the database. If *first* is present, then
-**HPCdaligner** produces an incremental script that compares blocks *first*
-through *last* (*last* = *first* if not present) against each other and all
-previous blocks 1 through *first*-1, and then incrementally updates the .las
-files for blocks 1 through *first*-1, and creates the .las files for
-blocks *first* through *last*.
-
-Each UNIX command line output by the **HPCdaligner** can be a batch job
-(we use the && operator to combine several commands into one line to make this
-so). Dependencies between jobs can be maintained simply by first running all
-the **daligner**(1) jobs, then all the initial sort jobs, and then all the
-jobs in each phase of the external merge sort. Each of these phases is
-separated by an informative comment line for your scripting convenience.
-
-# SEE ALSO
-
-**daligner**(1)
-**LAsort**(1)
-**LAmerge**(1)
-**LAshow**(1)
-**LAcat**(1)
-**LAsplit**(1)
-**LAcheck**(1)
-**HPCmapper**(1)
diff --git a/debian/man/HPCmapper.1.md b/debian/man/HPCmapper.1.md
deleted file mode 100644
index 7c8de5d..0000000
--- a/debian/man/HPCmapper.1.md
+++ /dev/null
@@ -1,46 +0,0 @@
-% HPCmapper(1) 1.0
-%
-% August 2015
-
-# NAME
-
-HPCmapper - generate a script to map reads
-
-# SYNOPSIS
-
-**HPCmapper** [**-vb**] [**-k***int(20)*] [**-w***int(6)*] [**-h***int(50)*]
- [**-t***int*] [**-M***int*] [**-e***double(.85)*]
- [**-l***int(1000)*] [**-s***int(100)*] [**-H***int*]
- [**-m***track*]+ [**-dal***int(4)*] [**-deg***int(25)*]
- *ref:db|dam* *reads:db|dam* [*first:int*[-*last:int*]]
-
-# DESCRIPTION
-
-**HPCmapper** writes a UNIX shell script to the standard output that
-consists of a sequence of commands that effectively "maps" every read in
-the DB *reads* against a reference set of sequences in the DB *ref*,
-recording all the found local alignments in the sequence of files
-*ref.reads.1.las*, *ref.reads.2.las*, and so on, where *ref.reads.k.las*
-contains the alignments between all of *ref* and the k'th block of
-*reads*. The parameters are exactly the same as for **HPCdaligner**(1)
-save that the **-k**, **-h**, and **-e** defaults are set
-appropriately for mapping, and the **-A** and **-I** options
-make no sense as *ref* and *reads* are expected to be distinct
-data sets.
-
-If the integers *first* and *last* are missing, then the
-script produced is for every block in the database *reads*.
-If *first* is present then **HPCmapper** produces an script
-that compares blocks *first* through *last* (*last* = *first*
-if not present) against DAM *ref*.
-
-# SEE ALSO
-
-**daligner**(1)
-**LAsort**(1)
-**LAmerge**(1)
-**LAshow**(1)
-**LAcat**(1)
-**LAsplit**(1)
-**LAcheck**(1)
-**HPCdaligner**(1)
diff --git a/debian/man/LAcat.1.md b/debian/man/LAcat.1.md
deleted file mode 100644
index 8e1f472..0000000
--- a/debian/man/LAcat.1.md
+++ /dev/null
@@ -1,29 +0,0 @@
-% LAcat(1) 1.0
-%
-% August 2015
-
-# NAME
-
-LAcat - concatenate .las files
-
-# SYNOPSIS
-
-**LAcat** *source:las* > *target.las*
-
-# DESCRIPTION
-
-Given argument *source*, find all files *source*.1.las, *source*.2.las, ...
-*source*.n.las where *source*.i.las exists for every i in [1,n]. Then
-concatenate these files in order into a single .las file and pipe the result
-to the standard output.
-
-# SEE ALSO
-
-**daligner**(1)
-**LAsort**(1)
-**LAmerge**(1)
-**LAshow**(1)
-**LAsplit**(1)
-**LAcheck**(1)
-**HPCdaligner**(1)
-**HPCmapper**(1)
diff --git a/debian/man/LAcheck.1.md b/debian/man/LAcheck.1.md
deleted file mode 100644
index 6525fa7..0000000
--- a/debian/man/LAcheck.1.md
+++ /dev/null
@@ -1,41 +0,0 @@
-% LAcheck(1) 1.0
-%
-% August 2015
-
-# NAME
-
-LAcheck - verify structural integrity of .las files
-
-# SYNOPSIS
-
-**LAcheck** [**-vS**] *src1:db|dam* [*src2:db|dam*] *align:las* ...
-
-# DESCRIPTION
-
-LAcheck checks each .las file for structural integrity, where the a- and
-b-sequences come from *src1* or from *src1* and *src2*, respectively.
-That is, it makes sure each file makes sense as a plausible .las file,
-e.g. values are not out of bound, the number of records is correct, the number
-of trace points for a record is correct, and so on. The exit status is 0 if
-every file is deemed good, and 1 if at least one of the files looks corrupted.
-
-# OPTIONS
-
-**-S**
-: Also check that the alignments are in sorted order
-
-**-v**
-: Print a line for each .las file saying either the file is OK or reporting
- the first error. If the **-v** option is not set, then the program
- runs silently.
-
-# SEE ALSO
-
-**daligner**(1)
-**LAsort**(1)
-**LAmerge**(1)
-**LAshow**(1)
-**LAcat**(1)
-**LAsplit**(1)
-**HPCdaligner**(1)
-**HPCmapper**(1)
diff --git a/debian/man/LAdump.1.md b/debian/man/LAdump.1.md
deleted file mode 100644
index 709f8d9..0000000
--- a/debian/man/LAdump.1.md
+++ /dev/null
@@ -1,52 +0,0 @@
-% LAdump(1) 1.0+20151214
-%
-% January 2016
-
-# NAME
-
-LAdump - display daligner local alignments in a simple format
-
-# SYNOPSIS
-
-**LAdump** [**-cdt**] [**-o**] *src1:db|dam* [ *src2:db|dam* ]
- *align:las* [ *reads:FILE* | *reads:range* ... ]
-
-# DESCRIPTION
-
-Like **LAshow**(1), **LAdump** allows one to display the local alignments (LAs) of a subset of the
-piles in an .las file and select which information to show about them. The difference
-is that the information is written in a very simple "1-code" ASCII format that makes it
-easy for one to read and parse the information for further use. For each LA the pair of
-reads is output on a line. **-c** requests that one further output the coordinates of the
-LA segments be output. The **-d** option requests that the number of difference in the LA
-be output, and **-t** requests that the tracepoint information be output. Finally, **-o**
-requests that only LAs that are proper overlaps be output.
-
-The format is very simple. Each requested piece of information occurs on a line. The
-first character of every line is a "1-code" character that tells you what information
-to expect on the line. The rest of the line contains information where each item is
-separated by a single blank space. The trace point line gives the number of trace
-point intervals in the LA and is immediately followed by that many lines containing
-a pair of integers giving the # of differences and b-displacement in each successive
-trace point interval.
-
- P #a #b - (#a,#b) have an LA between them
- C #ab #ae #bb #be - [#ab,#ae] aligns with [#bb,#be]
- D # - there are # differences in the LA
- T #n - there are #n trace point intervals for the LA
- (#d #y )^#n - there are #d difference aligning the #y bp's of B with the
- next fixed-size interval of A
- + X # - Total amount of X (X = P or T)
- % X # - Maximum amount of X in any pile (X = P or T)
- @ T # - Maximum number of trace points in any trace
-
-1-code lines that begin with +, %, or @ are always the first lines in the output.
-They give size information about what is contained in the output. Specifically,
-'+ X #' gives the total number of LAs (X=P), or the total number of trace point
-intervals (X=T) in the file . '% X #' gives the maximum number of LAs (X=P) or
-the maximum number of trace point intervals (X=T) in a given *pile* (collection of
-LAs all with the same a-read (applies only to sorted .las files). Finally @ T #
-gives the maximum # of trace point intervals in any trace within the file.
-
-# SEE ALSO
-**daligner**(1)
diff --git a/debian/man/LAindex.1.md b/debian/man/LAindex.1.md
deleted file mode 100644
index b583a0d..0000000
--- a/debian/man/LAindex.1.md
+++ /dev/null
@@ -1,27 +0,0 @@
-% LAindex(1) 1.0+20151214
-%
-% January 2016
-
-# NAME
-
-LAindex - index Daligner alignment files
-
-# SYNOPSIS
-
-**LAindex** **-v** *source:las* ...
-
-# DESCRIPTION
-
-**LAindex** takes a series of one or more sorted .las files and produces a "pile
-index" for each one. If the input file has name *X.las*, then the name of its
-index file is *.X.las.idx*. For each A-read pile encoded in the .las file,
-the index contains the offset to the first local alignment with A in the file.
-The index starts with four 64-bit integers that encode the numbers % P, + T, % T,
-and @ T described for **LAdump**(1), and then an offset for each pile beginning
-with the first A-read in the file (which may not be read 0). The index is meant
-to allow programs that process piles to more efficiently read just the piles
-they need at any momment int time, as opposed to having to sequentially scan
-through the .las file.
-
-# SEE ALSO
-**daligner**(1)
diff --git a/debian/man/LAmerge.1.md b/debian/man/LAmerge.1.md
deleted file mode 100644
index 7a38d4b..0000000
--- a/debian/man/LAmerge.1.md
+++ /dev/null
@@ -1,37 +0,0 @@
-% LAmerge(1) 1.0
-%
-% August 2015
-
-# NAME
-
-LAmerge - merge .las files into a single sorted file
-
-# SYNOPSIS
-
-**LAmerge** [**-v**] *merge:las* *parts:las* `...`
-
-# DESCRIPTION
-
-Merge the .las files *parts* into a singled sorted file *merge*, where it is
-assumed that the input *parts* files are sorted. Due to operating system
-limits, the number of *parts* files must be <= 252. With the **-v** option
-set, the program reports the number of records read and written.
-
-Used correctly, **LAmerge** and **LAsort**(1) together allow one to perform
-an "external" sort that produces a collection of sorted files containing in
-aggregate all the local alignments found by the **daligner**(1), such that
-their concatenation is sorted in order of (a,b,o,ab). In particular, this
-means that all the alignments for a given a-read will be found consecutively
-in one of the files. So computations that need to look at all the alignments
-for a given read can operate in simple sequential scans of these sorted files.
-
-# SEE ALSO
-
-**daligner**(1)
-**LAsort**(1)
-**LAshow**(1)
-**LAcat**(1)
-**LAsplit**(1)
-**LAcheck**(1)
-**HPCdaligner**(1)
-**HPCmapper**(1)
diff --git a/debian/man/LAshow.1.md b/debian/man/LAshow.1.md
deleted file mode 100644
index f9c0c21..0000000
--- a/debian/man/LAshow.1.md
+++ /dev/null
@@ -1,72 +0,0 @@
-% LAshow(1) 1.0
-%
-% August 2015
-
-# NAME
-
-LAshow - display local alignments from .las files
-
-# SYNOPSIS
-
-**LAshow** [**-caroUF**] [**-i***int(4)*] [**-w***int(100)*]
-[**-b***int(10)*] *src1:db|dam* [*src2:db|dam*] *align:las*
-[*reads:FILE* | *reads:range* ... ]
-
-# DESCRIPTION
-
-**LAshow** produces a printed listing of the local alignments contained in the
-specified .las file, where the a- and b-reads come from *src1* or from *src1*
-and *src2*, respectively. If a file or list of read ranges is given, then only
-the overlaps for which the a-read is in the set specified by the file or list
-are displayed. See **DBshow**(1) for an explanation of how the file and list
-of read ranges are interpreted.
-
-# OPTIONS
-
-**-F**
-: Reverse the roles of the a- and b- reads in the display
-
-**-U**
-: Use uppercase for DNA sequence instead of the default lowercase
-
-**-i***indentation*
-: Set the indent for the cartoon and/or alignment displays if they are
- requested. (default: 4)
-
-**-b***num_symbols*
-: Set the number of symbols on either side of the aligned segments in an
- alignment display. (default: 10)
-
-**-w***w*
-: This parameter is used for the display modes specified
- by **-a** and **-r**. (default: 100)
-
-**-o**
-: Only display alignments that are proper overlaps-- that is, where a
- sequence end occurs at each end of the alignment
-
-## DISPLAY MODES
-
-**-c**
-: Cartoon rendering of the alignment
-
-**-a**, **-r**
-: Display an alignment of the local alignment
-
-The **-a** option puts exactly *w* columns per segment of
-the display, whereas the **-r** option puts exactly *w* a-read symbols in each
-segment of the display. The **-r** display mode is useful when one wants to
-visually compare two alignments involving the same a-read. If a combination of
-the **-c**, **-a**, and **-r** flags is set, then the cartoon comes first,
-then the **-a** alignment, and lastly the **-r** alignment.
-
-# SEE ALSO
-
-**daligner**(1)
-**LAsort**(1)
-**LAmerge**(1)
-**LAcat**(1)
-**LAsplit**(1)
-**LAcheck**(1)
-**HPCdaligner**(1)
-**HPCmapper**(1)
diff --git a/debian/man/LAsort.1.md b/debian/man/LAsort.1.md
deleted file mode 100644
index 2d8ee58..0000000
--- a/debian/man/LAsort.1.md
+++ /dev/null
@@ -1,31 +0,0 @@
-% LAsort(1) 1.0
-%
-% August 2015
-
-# NAME
-
-LAsort - sort .las alignment files
-
-# SYNOPSIS
-
-**LAsort** [**-v**] *align:las* ...
-
-# DESCRIPTION
-
-Sort each .las alignment file specified on the command line. For each file
-it reads in all the overlaps in the file and sorts them in lexicographical
-order of (a,b,o,ab) assuming each alignment is recorded as
-a[ab,ae] x b^o[bb,be]. It then writes them all to a file named *align.S.las*
-(assuming that the input file was *align.las*). With the **-v** option set,
-the program reports the number of records read and written.
-
-## SEE ALSO
-
-**daligner**(1)
-**LAmerge**(1)
-**LAshow**(1)
-**LAcat**(1)
-**LAsplit**(1)
-**LAcheck**(1)
-**HPCdaligner**(1)
-**HPCmapper**(1)
diff --git a/debian/man/LAsplit.1.md b/debian/man/LAsplit.1.md
deleted file mode 100644
index 3452d50..0000000
--- a/debian/man/LAsplit.1.md
+++ /dev/null
@@ -1,33 +0,0 @@
-% LAsplit(1) 1.0
-%
-% August 2015
-
-# NAME
-
-LAsplit - divide an .las alignment file
-
-# SYNOPSIS
-
-**LAsplit** *target:las* {*parts:int* | *path:db|dam*} < *source.las*
-
-# DESCRIPTION
-
-If the second argument is an integer n, then divide the alignment file
-*source*, piped in through the standard input, as evenly as possible into n
-alignment files with the name *target.i.las* for i in [1,n], subject to the
-restriction that all alignment records for a given a-read are in the same file.
-
-If the second argument refers to a database *path.db* that has been
-partitioned, then divide the input alignment file into block .las files where
-all records whose a-read is in *path.i.db* are in *align.i.las*.
-
-# SEE ALSO
-
-**daligner**(1)
-**LAsort**(1)
-**LAmerge**(1)
-**LAshow**(1)
-**LAcat**(1)
-**LAcheck**(1)
-**HPCdaligner**(1)
-**HPCmapper**(1)
diff --git a/debian/man/Makefile b/debian/man/Makefile
deleted file mode 100644
index 7733e1b..0000000
--- a/debian/man/Makefile
+++ /dev/null
@@ -1,12 +0,0 @@
-
-MANPAGES = $(basename $(wildcard *.1.md))
-
-all: $(MANPAGES)
-
-%.1: %.1.md
- pandoc -s -f markdown -t man $< > $@
-
-clean:
- $(RM) $(MANPAGES)
-
-.PHONY: clean
diff --git a/debian/man/daligner.1 b/debian/man/daligner.1
new file mode 100644
index 0000000..2ab3eb8
--- /dev/null
+++ b/debian/man/daligner.1
@@ -0,0 +1,12 @@
+.TH DALIGNER 1 "October 2016"
+.SH NAME
+daligner \- local alignment discovery between long nucleotide sequencing reads
+.SH SYNOPSIS
+.B daligner
+.RI [ options ] " files" ...
+.SH DESCRIPTION
+These tools permit one to find all significant local alignments between reads encoded in a Dazzler database.
+The assumption is that the reads are from a Pacific Biosciences RS II long read sequencer.
+That is, the reads are long and noisy, up to 15% on average.
+.SH OPTIONS
+For a complete description of available commands and their options, see /usr/share/doc/daligner/README.md
diff --git a/debian/man/daligner.1.md b/debian/man/daligner.1.md
deleted file mode 100644
index acb4b22..0000000
--- a/debian/man/daligner.1.md
+++ /dev/null
@@ -1,114 +0,0 @@
-% DALIGNER(1) 1.0
-%
-% August 2015
-
-# NAME
-
-daligner - long read aligner
-
-# SYNOPSIS
-
-**daligner**
-[**-vbAI**]
-[**-k***int(14)*] [**-w***int(6)*] [**-h***int(35)*]
-[**-t***int*] [**-M***int*]
-[**-e***double(.70)*] [**-l***int(1000)*] [**-s***int(100)*] [**-H***int*]
-[**-m***track*]+ *subject:db|dam* *target:db|dam* ...
-
-# DESCRIPTION
-Compare sequences in the trimmed *subject* block against those in the list of
-*target* blocks searching for local alignments involving at least **-l** base
-pairs (default 1000) or more, that have an average correlation rate of **-e**
-(default 70%). The local alignments found will be output in a sparse encoding
-where a trace point on the alignment is recorded every **-s** base pairs of
-the a-read (default 100bp). Reads are compared in both orientations and local
-alignments meeting the criteria are output to one of several created files
-described below. The **-v** option turns on a verbose reporting mode that gives
-statistics on each major step of the computation.
-
-The options **-k**, **-h**, and **-w** control the initial filtration search
-for possible matches between reads. Specifically, our search code looks for a
-pair of diagonal bands of width 2^w (default 2^6 = 64) that contain a
-collection of exact matching k-mers (default 14) between the two reads,
-such that the total number of bases covered by the k-mer hits is h
-(default 35). k cannot be larger than 32 in the current implementation.
-If the **-b** option is set, then the **daligner** assumes the data has a
-strong compositional bias (e.g. >65% AT rich), and at the cost of a bit more
-time, dynamically adjusts k-mer sizes depending on compositional bias, so that
-the mers used have an effective specificity of 4^k.
-
-If there are one or more interval tracks specified with the **-m** option, then
-the reads of the DB or DB's to which the mask applies are soft masked with
-the union of the intervals of all the interval tracks that apply, that is any
-k-mers that contain any bases in any of the masked intervals are ignored for
-the purposes of seeding a match. An interval track is a track, such as the
-"dust" track created by DBdust, that encodes a set of intervals over either
-the untrimmed or trimmed DB.
-
-Invariably, some k-mers are significantly over-represented (e.g. homopolymer
-runs). These k-mers create an excessive number of matching k-mer pairs and
-left unaddressed would cause daligner to overflow the available physical
-memory. One way to deal with this is to explicitly set the **-t** parameter
-which suppresses the use of any k-mer that occurs more than *t* times in either
-the subject or target block. However, a better way to handle the situation is
-to let the program automatically select a value of *t* that meets a given
-memory usage limit specified (in Gb) by the **-M** parameter. By default
-**daligner** will use the amount of physical memory as the choice for **-M**.
-If you want to use less, say only 8Gb on a 24Gb HPC cluster node because you
-want to run 3 **daligner** jobs on the node, then specify **-M***8*.
-Specifying **-M***0* basically indicates that you do not want **daligner** to
-self adjust k-mer suppression to fit within a given amount of memory.
-
-For each subject, target pair of blocks, say X and Y, the program reports
-alignments where the a-read is in X and the b-read is in Y, and vice versa.
-However, if the **-A** option is set ("A" for "asymmetric") then just overlaps
-where the a-read is in X and the b-read is in Y are reported, and if X = Y,
-then it further reports only those overlaps where the a-read index is less than the b-read index. In either case, if the **-I** option is set
-("I" for "identity") then when X = Y, overlaps between different
-portions of the same read will also be found and reported.
-
-Each found alignment is recorded as -- a[ab,ae] x bo[bb,be] -- where a and b
-are the indices (in the trimmed DB) of the reads that overlap, o indicates
-whether the b-read is from the same or opposite strand, and [ab,ae] and
-[bb,be] are the intervals of a and bo, respectively, that align. The program
-places these alignment records in files whose name is of the form
-X.Y.[C|N]#.las where C indicates that the b-reads are complemented and N
-indicates they are not (both comparisons are performed) and # is
-the thread that detected and wrote out the collection of alignments contained
-in the file. That is the file X.Y.O#.las contains the alignments produced by
-thread # for which the a-read is from X and the b-read is from Y and in
-orientation O. The command
-**daligner -A** *X* *Y* produces 2\*NTHREAD thread files X.Y.?.las and
-**daligner** *X* *Y* produces 4\*NTHREAD files X.Y.?.las and Y.X.?.las
-(unless *X*=*Y* in which case only NTHREAD files, X.X.?.las, are produced).
-
-By default, **daligner** compares all overlaps between reads in the database
-that are greater than the minimum cutoff set when the DB or DBs were split,
-typically 1 or 2 Kbp. However, the HGAP assembly pipeline only wants to
-correct large reads, say 8Kbp or over, and so needs only the overlaps where
-the a-read is one of the large reads. By setting the **-H** parameter to say N,
-one alters **daligner** so that it only reports overlaps where the a-read is
-over N base-pairs long.
-
-While the default parameter settings are good for raw Pacbio data, **daligner**
-can be used for efficiently finding alignments in corrected reads or other
-less noisy reads. For example, for mapping applications against .dams, we run
-
-**daligner** **-k**20 **-h**60 **-e**.85
-
-and on corrected reads, we typically run
-
-**daligner** **-k**25 **-w**5 **-h**60 **-e**.95 **-s**500
-
-and at these settings it is very fast.
-
-# SEE ALSO
-
-**LAsort**(1)
-**LAmerge**(1)
-**LAshow**(1)
-**LAcat**(1)
-**LAsplit**(1)
-**LAcheck**(1)
-**HPCdaligner**(1)
-**HPCmapper**(1)
diff --git a/debian/rules b/debian/rules
index dbae735..f66f8e7 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,7 +1,7 @@
#!/usr/bin/make -f
#DH_VERBOSE = 1
-#include /usr/share/dpkg/default.mk
+include /usr/share/dpkg/default.mk
# The upstream build system doesn't honor CPPFLAGS
CFLAGS := $(CPPFLAGS) $(CFLAGS)
@@ -9,10 +9,14 @@ CFLAGS := $(CPPFLAGS) $(CFLAGS)
%:
dh $@ --parallel
-override_dh_auto_build:
- dh_auto_build
- $(MAKE) -C debian/man
-
-override_dh_auto_clean:
- dh_auto_clean
- $(MAKE) -C debian/man clean
+override_dh_auto_install:
+ dh_auto_install
+ mkdir -p $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1
+ for command in $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/*; \
+ do \
+ if [ $$(basename $$command) != daligner ] ; \
+ then \
+ ln -s daligner.1 \
+ $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1/$$(basename $$command).1 ; \
+ fi; \
+ done
--
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