[med-svn] [gmap] 05/11: d/rules: use mkdir -p to create man page dirs d/control: add help2man Build-dep d/gmap.1: removed d/manpages: removed gmap.1
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Sat Aug 22 06:25:59 UTC 2015
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository gmap.
commit 1bd109cbfd97f8a15080054edcbf26ac6c8e6a5a
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Mon Jun 15 11:50:31 2015 +0200
d/rules: use mkdir -p to create man page dirs
d/control: add help2man Build-dep
d/gmap.1: removed
d/manpages: removed gmap.1
---
debian/control | 3 +-
debian/gmap.1 | 405 --------------------------------------------------------
debian/manpages | 1 -
debian/rules | 6 +-
4 files changed, 6 insertions(+), 409 deletions(-)
diff --git a/debian/control b/debian/control
index db3819b..ec2c66a 100644
--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,8 @@ Section: non-free/science
XS-Autobuild: no
Priority: optional
Build-Depends: debhelper (>= 9),
- autotools-dev
+ autotools-dev,
+ help2man
Standards-Version: 3.9.6
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/gmap.git
Vcs-Git: git://anonscm.debian.org/debian-med/gmap.git
diff --git a/debian/gmap.1 b/debian/gmap.1
deleted file mode 100644
index cfb1f91..0000000
--- a/debian/gmap.1
+++ /dev/null
@@ -1,405 +0,0 @@
-.TH GMAP "1" "GMAP 2014-12-23" "User Commands"
-.SH NAME
-gmap \- Genomic Mapping and Alignment Program
-.SH SYNOPSIS
-.B gmap
-[\fI\,OPTIONS\/\fR...] \fI\,<FASTA files\/\fR...\fI\,>, or\/\fR cat <FASTA files...> | gmap [OPTIONS...]
-.SH DESCRIPTION
-Align the sequences QUERY to the reference, specified with
-\fB-d\fR or \fB-g\fR.
-.SH OPTIONS
-.SS Input options (must include \fB\-d\fR or \fB\-g\fR)
-.TP
-\fB\-D\fR, \fB\-\-dir\fR=\fI\,directory\/\fR
-Genome directory. Default (as specified by \fB\-\-with\-gmapdb\fR to the configure program) is
-\fI\,/var/cache/gmap\/\fP
-.TP
-\fB\-d\fR, \fB\-\-db\fR=\fI\,STRING\/\fR
-Genome database. If argument is '?' (with
-the quotes), this command lists available databases.
-.TP
-\fB\-k\fR, \fB\-\-kmer\fR=\fI\,INT\/\fR
-kmer size to use in genome database (allowed values: 16 or less).
-If not specified, the program will find the highest available
-kmer size in the genome database
-.TP
-\fB\-\-sampling\fR=\fI\,INT\/\fR
-Sampling to use in genome database. If not specified, the program
-will find the smallest available sampling value in the genome database
-within selected k\-mer size
-.TP
-\fB\-G\fR, \fB\-\-genomefull\fR
-Use full genome (all ASCII chars allowed;
-built explicitly during setup), not
-compressed version
-.TP
-\fB\-g\fR, \fB\-\-gseg\fR=\fI\,filename\/\fR
-User\-supplied genomic segment
-.TP
-\fB\-1\fR, \fB\-\-selfalign\fR
-Align one sequence against itself in FASTA format via stdin
-(Useful for getting protein translation of a nucleotide sequence)
-.TP
-\fB\-2\fR, \fB\-\-pairalign\fR
-Align two sequences in FASTA format via stdin, first one being
-genomic and second one being cDNA
-.TP
-\fB\-\-cmdline\fR=\fI\,STRING\/\fR,STRING
-Align these two sequences provided on the command line,
-first one being genomic and second one being cDNA
-.TP
-\fB\-q\fR, \fB\-\-part\fR=\fI\,INT\/\fR/INT
-Process only the i\-th out of every n sequences
-e.g., 0/100 or 99/100 (useful for distributing jobs
-to a computer farm).
-.TP
-\fB\-\-input\-buffer\-size\fR=\fI\,INT\/\fR
-Size of input buffer (program reads this many sequences
-at a time for efficiency) (default 1000)
-.SS
-.SS
-Computation options
-.TP
-\fB\-B\fR, \fB\-\-batch\fR=\fI\,INT\/\fR
-Batch mode (default = 2)
- Mode Offsets Positions Genome
- 0 see note mmap mmap
- 1 see note mmap & preload mmap
- (default) 2 see note mmap & preload mmap & preload
- 3 see note allocate mmap & preload
- 4 see note allocate allocate
- 5 expand allocate allocate
-
-Note: For a single sequence, all data structures use mmap.
-If mmap not available and allocate not chosen, then will use fileio (very slow)
-.TP
-Note about \fB\-\-batch\fR and offsets: Expansion of offsets can be controlled
-independently by the \fB\-\-expand\-offsets\fR flag. The \fB\-\-batch\fR=\fI\,5\/\fR option is equivalent
-to \fB\-\-batch\fR=\fI\,4\/\fR plus \fB\-\-expand\-offsets\fR=\fI\,1\/\fR
-.TP
-\fB\-\-expand\-offsets\fR=\fI\,INT\/\fR
-Whether to expand the genomic offsets index
-Values: 0 (no, default), or 1 (yes).
-Expansion gives faster alignment, but requires more memory
-.TP
-\fB\-\-nosplicing\fR
-Turns off splicing (useful for aligning genomic sequences
-onto a genome)
-.TP
-\fB\-\-min\-intronlength\fR=\fI\,INT\/\fR
-Min length for one internal intron (default 9). Below this size,
-a genomic gap will be considered a deletion rather than an intron.
-.TP
-\fB\-K\fR, \fB\-\-intronlength\fR=\fI\,INT\/\fR
-Max length for one internal intron (default 200000)
-.TP
-\fB\-w\fR, \fB\-\-localsplicedist\fR=\fI\,INT\/\fR
-Max length for known splice sites at ends of sequence
-(default 2000000)
-.TP
-\fB\-L\fR, \fB\-\-totallength\fR=\fI\,INT\/\fR
-Max total intron length (default 2400000)
-.TP
-\fB\-x\fR, \fB\-\-chimera\-margin\fR=\fI\,INT\/\fR
-Amount of unaligned sequence that triggers
-search for the remaining sequence (default 30).
-Enables alignment of chimeric reads, and may help
-with some non\-chimeric reads. To turn off, set to
-zero.
-.TP
-\fB\-\-no\-chimeras\fR
-Turns off finding of chimeras. Same effect as \fB\-\-chimera\-margin\fR=\fI\,0\/\fR
-.TP
-\fB\-t\fR, \fB\-\-nthreads\fR=\fI\,INT\/\fR
-Number of worker threads
-.TP
-\fB\-c\fR, \fB\-\-chrsubset\fR=\fI\,string\/\fR
-Limit search to given chromosome
-.TP
-\fB\-z\fR, \fB\-\-direction\fR=\fI\,STRING\/\fR
-cDNA direction (sense_force, antisense_force,
-sense_filter, antisense_filter,or auto (default))
-.TP
-\fB\-H\fR, \fB\-\-trimendexons\fR=\fI\,INT\/\fR
-Trim end exons with fewer than given number of matches
-(in nt, default 9)
-.TP
-\fB\-\-canonical\-mode\fR=\fI\,INT\/\fR
-Reward for canonical and semi\-canonical introns
-0=low reward, 1=high reward (default), 2=low reward for
-high\-identity sequences and high reward otherwise
-.TP
-\fB\-\-cross\-species\fR
-Use a more sensitive search for canonical splicing, which helps especially
-for cross\-species alignments and other difficult cases
-.TP
-\fB\-\-allow\-close\-indels\fR=\fI\,INT\/\fR
-Allow an insertion and deletion close to each other
-(0=no, 1=yes (default), 2=only for high\-quality alignments)
-.TP
-\fB\-\-microexon\-spliceprob\fR=\fI\,FLOAT\/\fR
-Allow microexons only if one of the splice site probabilities is
-greater than this value (default 0.95)
-.TP
-\fB\-\-cmetdir\fR=\fI\,STRING\/\fR
-Directory for methylcytosine index files (created using cmetindex)
-(default is location of genome index files specified using \fB\-D\fR, \fB\-V\fR, and \fB\-d\fR)
-.TP
-\fB\-\-atoidir\fR=\fI\,STRING\/\fR
-Directory for A\-to\-I RNA editing index files (created using atoiindex)
-(default is location of genome index files specified using \fB\-D\fR, \fB\-V\fR, and \fB\-d\fR)
-.TP
-\fB\-\-mode\fR=\fI\,STRING\/\fR
-Alignment mode: standard (default), cmet\-stranded, cmet\-nonstranded,
-atoi\-stranded, or atoi\-nonstranded. Non\-standard modes requires you
-to have previously run the cmetindex or atoiindex programs on the genome
-.TP
-\fB\-p\fR, \fB\-\-prunelevel\fR
-Pruning level: 0=no pruning (default), 1=poor seqs,
-2=repetitive seqs, 3=poor and repetitive
-.PP
-Output types
-.TP
-\fB\-S\fR, \fB\-\-summary\fR
-Show summary of alignments only
-.TP
-\fB\-A\fR, \fB\-\-align\fR
-Show alignments
-.TP
-\fB\-3\fR, \fB\-\-continuous\fR
-Show alignment in three continuous lines
-.TP
-\fB\-4\fR, \fB\-\-continuous\-by\-exon\fR
-Show alignment in three lines per exon
-.TP
-\fB\-Z\fR, \fB\-\-compress\fR
-Print output in compressed format
-.TP
-\fB\-E\fR, \fB\-\-exons\fR=\fI\,STRING\/\fR
-Print exons ("cdna" or "genomic")
-.TP
-\fB\-P\fR, \fB\-\-protein_dna\fR
-Print protein sequence (cDNA)
-.TP
-\fB\-Q\fR, \fB\-\-protein_gen\fR
-Print protein sequence (genomic)
-.TP
-\fB\-f\fR, \fB\-\-format\fR=\fI\,INT\/\fR
-Other format for output (also note the \fB\-A\fR and \fB\-S\fR options
- and other options listed under Output types):
- psl (or 1) = PSL (BLAT) format,
- gff3_gene (or 2) = GFF3 gene format,
- gff3_match_cdna (or 3) = GFF3 cDNA_match format,
- gff3_match_est (or 4) = GFF3 EST_match format,
- splicesites (or 6) = splicesites output (for GSNAP splicing file),
- introns = introns output (for GSNAP splicing file),
- map_exons (or 7) = IIT FASTA exon map format,
- map_ranges (or 8) = IIT FASTA range map format,
- coords (or 9) = coords in table format,
- sampe = SAM format (setting paired_read bit in flag),
- samse = SAM format (without setting paired_read bit)
-.PP
-Output options
-.TP
-\fB\-n\fR, \fB\-\-npaths\fR=\fI\,INT\/\fR
-Maximum number of paths to show (default 5). If set to 1, GMAP
-will not report chimeric alignments, since those imply
-two paths. If you want a single alignment plus chimeric
-alignments, then set this to be 0.
-.TP
-\fB\-\-suboptimal\-score\fR=\fI\,INT\/\fR
-Report only paths whose score is within this value of the
-best path. By default, if this option is not provided,
-the program prints all paths found.
-.TP
-\fB\-O\fR, \fB\-\-ordered\fR
-Print output in same order as input (relevant
-only if there is more than one worker thread)
-.TP
-\fB\-5\fR, \fB\-\-md5\fR
-Print MD5 checksum for each query sequence
-.TP
-\fB\-o\fR, \fB\-\-chimera\-overlap\fR
-Overlap to show, if any, at chimera breakpoint
-.TP
-\fB\-\-failsonly\fR
-Print only failed alignments, those with no results
-.TP
-\fB\-\-nofails\fR
-Exclude printing of failed alignments
-.TP
-\fB\-V\fR, \fB\-\-snpsdir\fR=\fI\,STRING\/\fR
-Directory for SNPs index files (created using snpindex) (default is
-location of genome index files specified using \fB\-D\fR and \fB\-d\fR)
-.TP
-\fB\-v\fR, \fB\-\-use\-snps\fR=\fI\,STRING\/\fR
-Use database containing known SNPs (in <STRING>.iit, built
-previously using snpindex) for tolerance to SNPs
-.TP
-\fB\-\-split\-output\fR=\fI\,STRING\/\fR
-Basename for multiple\-file output, separately for nomapping,
-uniq, mult, (and chimera, if \fB\-\-chimera\-margin\fR is selected)
-.TP
-\fB\-\-failed\-input\fR=\fI\,STRING\/\fR
-Print completely failed alignments as input FASTA or FASTQ format
-to the given file. If the \fB\-\-split\-output\fR flag is also given, this file
-is generated in addition to the output in the .nomapping file.
-.TP
-\fB\-\-append\-output\fR
-When \fB\-\-split\-output\fR or \fB\-\-failedinput\fR is given, this flag will append output
-to the existing files. Otherwise, the default is to create new files.
-.TP
-\fB\-\-output\-buffer\-size\fR=\fI\,INT\/\fR
-Buffer size, in queries, for output thread (default 1000). When the number
-of results to be printed exceeds this size, the worker threads are halted
-until the backlog is cleared
-.TP
-\fB\-F\fR, \fB\-\-fulllength\fR
-Assume full\-length protein, starting with Met
-.TP
-\fB\-a\fR, \fB\-\-cdsstart\fR=\fI\,INT\/\fR
-Translate codons from given nucleotide (1\-based)
-.TP
-\fB\-T\fR, \fB\-\-truncate\fR
-Truncate alignment around full\-length protein, Met to Stop
-Implies \fB\-F\fR flag.
-.TP
-\fB\-Y\fR, \fB\-\-tolerant\fR
-Translates cDNA with corrections for frameshifts
-.PP
-Options for GFF3 output
-.TP
-\fB\-\-gff3\-add\-separators\fR=\fI\,INT\/\fR
-Whether to add a ### separator after each query sequence
-Values: 0 (no), 1 (yes, default)
-.PP
-Options for SAM output
-.TP
-\fB\-\-no\-sam\-headers\fR
-Do not print headers beginning with '@'
-.TP
-\fB\-\-sam\-use\-0M\fR
-Insert 0M in CIGAR between adjacent insertions and deletions
-Required by Picard, but can cause errors in other tools
-.TP
-\fB\-\-force\-xs\-dir\fR
-For RNA\-Seq alignments, disallows XS:A:? when the sense direction
-is unclear, and replaces this value arbitrarily with XS:A:+.
-May be useful for some programs, such as Cufflinks, that cannot
-handle XS:A:?. However, if you use this flag, the reported value
-of XS:A:+ in these cases will not be meaningful.
-.TP
-\fB\-\-md\-lowercase\-snp\fR
-In MD string, when known SNPs are given by the \fB\-v\fR flag,
-prints difference nucleotides as lower\-case when they,
-differ from reference but match a known alternate allele
-.TP
-\fB\-\-action\-if\-cigar\-error\fR
-Action to take if there is a disagreement between CIGAR length and sequence length
-Allowed values: ignore, warning (default), abort
-.TP
-\fB\-\-read\-group\-id\fR=\fI\,STRING\/\fR
-Value to put into read\-group id (RG\-ID) field
-.TP
-\fB\-\-read\-group\-name\fR=\fI\,STRING\/\fR
-Value to put into read\-group name (RG\-SM) field
-.TP
-\fB\-\-read\-group\-library\fR=\fI\,STRING\/\fR
-Value to put into read\-group library (RG\-LB) field
-.TP
-\fB\-\-read\-group\-platform\fR=\fI\,STRING\/\fR
-Value to put into read\-group library (RG\-PL) field
-.PP
-Options for quality scores
-.TP
-\fB\-\-quality\-protocol\fR=\fI\,STRING\/\fR
-Protocol for input quality scores. Allowed values:
-illumina (ASCII 64\-126) (equivalent to \fB\-J\fR 64 \fB\-j\fR \fB\-31\fR)
-sanger (ASCII 33\-126) (equivalent to \fB\-J\fR 33 \fB\-j\fR 0)
-.TP
-Default is sanger (no quality print shift)
-SAM output files should have quality scores in sanger protocol
-.IP
-Or you can specify the print shift with this flag:
-.TP
-\fB\-j\fR, \fB\-\-quality\-print\-shift\fR=\fI\,INT\/\fR
-Shift FASTQ quality scores by this amount in output
-(default is 0 for sanger protocol; to change Illumina input
-to Sanger output, select \fB\-31\fR)
-.PP
-External map file options
-.TP
-\fB\-M\fR, \fB\-\-mapdir\fR=\fI\,directory\/\fR
-Map directory
-.TP
-\fB\-m\fR, \fB\-\-map\fR=\fI\,iitfile\/\fR
-Map file. If argument is '?' (with the quotes),
-this lists available map files.
-.TP
-\fB\-e\fR, \fB\-\-mapexons\fR
-Map each exon separately
-.TP
-\fB\-b\fR, \fB\-\-mapboth\fR
-Report hits from both strands of genome
-.TP
-\fB\-u\fR, \fB\-\-flanking\fR=\fI\,INT\/\fR
-Show flanking hits (default 0)
-.TP
-\fB\-\-print\-comment\fR
-Show comment line for each hit
-.PP
-Alignment output options
-.TP
-\fB\-N\fR, \fB\-\-nolengths\fR
-No intron lengths in alignment
-.TP
-\fB\-I\fR, \fB\-\-invertmode\fR=\fI\,INT\/\fR
-Mode for alignments to genomic (\-) strand:
-0=Don't invert the cDNA (default)
-1=Invert cDNA and print genomic (\-) strand
-2=Invert cDNA and print genomic (+) strand
-.TP
-\fB\-i\fR, \fB\-\-introngap\fR=\fI\,INT\/\fR
-Nucleotides to show on each end of intron (default 3)
-.TP
-\fB\-l\fR, \fB\-\-wraplength\fR=\fI\,INT\/\fR
-Wrap length for alignment (default 50)
-.PP
-Filtering output options
-.TP
-\fB\-\-min\-trimmed\-coverage\fR=\fI\,FLOAT\/\fR
-Do not print alignments with trimmed coverage less
-this value (default=0.0, which means no filtering)
-Note that chimeric alignments will be output regardless
-of this filter
-.TP
-\fB\-\-min\-identity\fR=\fI\,FLOAT\/\fR
-Do not print alignments with identity less
-this value (default=0.0, which means no filtering)
-Note that chimeric alignments will be output regardless
-of this filter
-.PP
-Help options
-.TP
-\fB\-\-version\fR
-Show version
-.TP
-\fB\-\-help\fR
-Show this help message
-.SH ENVIRONMENT
-.TP
-\fBGMAPDB\fR
-genome directory (eqivalent to \fB-D\fR)
-.SH FILES
-.TP
-~/.gmaprc
-configuration file
-.SH AUTHOR
-Thomas D. Wu and Colin K. Watanabe
-.SH "REPORTING BUGS"
-Report bugs to Thomas Wu <twu at gene.com>.
-.SH COPYRIGHT
-Copyright 2005 Genentech, Inc. All rights reserved.
-.SH "SEE ALSO"
-\fBgmap_build\fR(1), \fBgsnap\fR(1)
-.br
diff --git a/debian/manpages b/debian/manpages
index 75e8123..d3aa4ba 100644
--- a/debian/manpages
+++ b/debian/manpages
@@ -1,3 +1,2 @@
-debian/gmap.1
debian/gmap_build.1
debian/gsnap.1
diff --git a/debian/rules b/debian/rules
index e787923..54d8c86 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,5 +1,7 @@
#!/usr/bin/make -f
+export DH_VERBOSE=1
+
export DH_OPTIONS
pkg := $(shell dpkg-parsechangelog --show-field=Source)
version := $(shell dpkg-parsechangelog --show-field=Version)
@@ -12,7 +14,7 @@ ifeq ($(DEB_HOST_ARCH), i386)
EXTRA_CONFIGURE_ARGS += --enable-sse4.1=no --disable-simd
endif
-HELP2MAN = help2man --no-info --help-option="--help" --version-string="$(version)" --no-discard-stderr
+HELP2MAN = help2man --no-info --help-option="''" --version-string="$(version)"
%:
dh $@ --with autotools_dev
@@ -21,7 +23,7 @@ override_dh_auto_configure:
dh_auto_configure -- --enable-shared --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap $(EXTRA_CONFIGURE_ARGS)
override_dh_auto_install:
- mkdir $(mandir)
+ mkdir -p $(mandir)
$(HELP2MAN) --name='Genomic Mapping and Alignment Program'\
$(bindir)/gmap |debian/filter.pl >$(mandir)/gmap.1;
--
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