[med-svn] [gmap] 06/11: d/rules: update, use help2man to generate the man page d/gsnap.1: deleted d/mapnages: delete gsnap.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 1f7e8d49acbcd1f4e2e848529619f6d2cf33b468
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Fri Aug 21 16:06:58 2015 +0200
d/rules: update, use help2man to generate the man page
d/gsnap.1: deleted
d/mapnages: delete gsnap.1
---
debian/gsnap.1 | 514 --------------------------------------------------------
debian/manpages | 1 -
debian/rules | 13 +-
3 files changed, 8 insertions(+), 520 deletions(-)
diff --git a/debian/gsnap.1 b/debian/gsnap.1
deleted file mode 100644
index 3924169..0000000
--- a/debian/gsnap.1
+++ /dev/null
@@ -1,514 +0,0 @@
-.TH GSNAP "1" "GMAP 2014-12-23" "User Commands"
-.SH NAME
-gsnap \- Genomic Short-read Nucleotide Alignment Program
-.SH SYNOPSIS
-.B gsnap
-[\fI\,OPTIONS\/\fR...] \fI\,<FASTA file>, or\/\fR cat <FASTA file> | gmap [OPTIONS...]
-.SH DESCRIPTION
-.SS
-Input options (must include \fB\-d\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
-.TP
-\fB\-\-use\-sarray\fR=\fI\,INT\/\fR
-Whether to use a suffix array, which will give increased speed.
-Allowed values: 0 (no), 1 (yes, plus GSNAP/GMAP algorithm, default),
-or 2 (yes, and use only suffix array algorithm).
-Note that suffix arrays will bias against SNP alleles in
-SNP\-tolerant alignment.
-.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\-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)
-.TP
-\fB\-\-barcode\-length\fR=\fI\,INT\/\fR
-Amount of barcode to remove from start of read
-(default 0)
-.TP
-\fB\-o\fR, \fB\-\-orientation\fR=\fI\,STRING\/\fR
-Orientation of paired\-end reads
-Allowed values: FR (fwd\-rev, or typical Illumina; default),
-RF (rev\-fwd, for circularized inserts), or FF (fwd\-fwd, same strand)
-.TP
-\fB\-\-fastq\-id\-start\fR=\fI\,INT\/\fR
-Starting position of identifier in FASTQ header, space\-delimited (>= 1)
-.TP
-\fB\-\-fastq\-id\-end\fR=\fI\,INT\/\fR
-Ending position of identifier in FASTQ header, space\-delimited (>= 1)
- Examples:
- @HWUSI\-EAS100R:6:73:941:1973#0/1
- start=1, end=1 (default) => identifier is HWUSI\-EAS100R:6:73:941:1973#0
- @SRR001666.1 071112_SLXA\-EAS1_s_7:5:1:817:345 length=36
- start=1, end=1 => identifier is SRR001666.1
- start=2, end=2 => identifier is 071112_SLXA\-EAS1_s_7:5:1:817:345
- start=1, end=2 => identifier is SRR001666.1 071112_SLXA\-EAS1_s_7:5:1:817:345
-.TP
-\fB\-\-force\-single\-end\fR
-When multiple FASTQ files are provided on the command line, GSNAP assumes
-they are matching paired\-end files. This flag treats each file as single\-end.
-.TP
-\fB\-\-filter\-chastity\fR=\fI\,STRING\/\fR
-Skips reads marked by the Illumina chastity program. Expecting a string
-after the accession having a 'Y' after the first colon, like this:
-.TP
- at accession 1:Y:0:CTTGTA
-where the 'Y' signifies filtering by chastity.
-Values: off (default), either, both. For 'either', a 'Y' on either end
-of a paired\-end read will be filtered. For 'both', a 'Y' is required
-on both ends of a paired\-end read (or on the only end of a single\-end read).
-.TP
-\fB\-\-allow\-pe\-name\-mismatch\fR
-Allows accession names of reads to mismatch in paired\-end files
-.PP
-Computation options
-.IP
-Note: GSNAP has an ultrafast algorithm for calculating mismatches up to and including
-.PP
-((readlength+2)/kmer \- 2) ("ultrafast mismatches"). The program will run fastest if
-max\-mismatches (plus suboptimal\-levels) is within that value.
-Also, indels, especially end indels, take longer to compute, although the algorithm
-is still designed to be fast.
-.TP
-\fB\-B\fR, \fB\-\-batch\fR=\fI\,INT\/\fR
- Batch mode (default = 2)
- Mode Offsets Positions Genome Suffix array
- 0 see note mmap mmap mmap
- 1 see note mmap & preload mmap mmap
- (default) 2 see note mmap & preload mmap & preload mmap & preload
- 3 see note allocate mmap & preload mmap & preload
- 4 see note allocate allocate mmap & preload
- 5 see note allocate 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 offsets: Expansion of offsets can be controlled
-independently by the \fB\-\-expand\-offsets\fR flag. However, offsets
-are accessed relatively fast in this version of GSNAP.
-.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\-m\fR, \fB\-\-max\-mismatches\fR=\fI\,FLOAT\/\fR
-Maximum number of mismatches allowed (if not specified, then
-defaults to the ultrafast level of ((readlength+index_interval\-1)/kmer \- 2))
-(By default, the genome index interval is 3, but this can be changed
-.TP
-by providing a different value for \fB\-q\fR to gmap_build when processing
-the genome.)
-.TP
-If specified between 0.0 and 1.0, then treated as a fraction
-of each read length. Otherwise, treated as an integral number
-of mismatches (including indel and splicing penalties)
-For RNA\-Seq, you may need to increase this value slightly
-to align reads extending past the ends of an exon.
-.TP
-\fB\-\-query\-unk\-mismatch\fR=\fI\,INT\/\fR
-Whether to count unknown (N) characters in the query as a mismatch
-(0=no (default), 1=yes)
-.TP
-\fB\-\-genome\-unk\-mismatch\fR=\fI\,INT\/\fR
-Whether to count unknown (N) characters in the genome as a mismatch
-(0=no, 1=yes (default))
-.TP
-\fB\-\-maxsearch\fR=\fI\,INT\/\fR
-Maximum number of alignments to find (default 1000).
-Must be larger than \fB\-\-npaths\fR, which is the number to report.
-Keeping this number large will allow for random selection among multiple alignments.
-Reducing this number can speed up the program.
-.TP
-\fB\-\-terminal\-threshold\fR=\fI\,INT\/\fR
-Threshold for computing a terminal alignment (from one end of the
-read to the best possible position at the other end) (default 2)
-For example, if this value is 2, then if GSNAP finds an exact or
-1\-mismatch alignment, it will not try to find a terminal alignment.
-To turn off the computation of terminal alignments, set this to a
-high value, greater than the value for \fB\-\-max\-mismatches\fR. However,
-note hat terminal alignments are needed to help the GMAP algorithm
-find some alignments. Therefore, to avoid getting terminal alignments
-in the output, you should generally set \fB\-\-terminal\-output\-minlength\fR
-instead of this parameter.
-.TP
-\fB\-\-reject\-trimlength\fR=\fI\,INT\/\fR
-Do not print alignments where amount trimmed on both ends totals more than
-.TP
-this amount (default 1000).
-Note that ambiguous splicing does not count
-.IP
-as a trim.
-.TP
-\fB\-i\fR, \fB\-\-indel\-penalty\fR=\fI\,INT\/\fR
-Penalty for an indel (default 2).
-Counts against mismatches allowed. To find indels, make
-indel\-penalty less than or equal to max\-mismatches.
-A value < 2 can lead to false positives at read ends
-.TP
-\fB\-\-indel\-endlength\fR=\fI\,INT\/\fR
-Minimum length at end required for indel alignments (default 4)
-.TP
-\fB\-y\fR, \fB\-\-max\-middle\-insertions\fR=\fI\,INT\/\fR
-Maximum number of middle insertions allowed (default 9)
-.HP
-\fB\-z\fR, \fB\-\-max\-middle\-deletions\fR=\fI\,INT\/\fR Maximum number of middle deletions allowed (default 30)
-.TP
-\fB\-Y\fR, \fB\-\-max\-end\-insertions\fR=\fI\,INT\/\fR
-Maximum number of end insertions allowed (default 3)
-.TP
-\fB\-Z\fR, \fB\-\-max\-end\-deletions\fR=\fI\,INT\/\fR
-Maximum number of end deletions allowed (default 6)
-.TP
-\fB\-M\fR, \fB\-\-suboptimal\-levels\fR=\fI\,INT\/\fR
-Report suboptimal hits beyond best hit (default 0)
-All hits with best score plus suboptimal\-levels are reported
-.TP
-\fB\-a\fR, \fB\-\-adapter\-strip\fR=\fI\,STRING\/\fR
-Method for removing adapters from reads. Currently allowed values: off, paired.
-Default is "off". To turn on, specify "paired", which removes adapters
-from paired\-end reads if they appear to be present.
-.TP
-\fB\-\-trim\-mismatch\-score\fR=\fI\,INT\/\fR
-Score to use for mismatches when trimming at ends (default is \fB\-3\fR;
-to turn off trimming, specify 0). Warning: turning trimming off
-will give false positive mismatches at the ends of reads
-.TP
-\fB\-\-trim\-indel\-score\fR=\fI\,INT\/\fR
-Score to use for indels when trimming at ends (default is \fB\-2\fR;
-to turn off trimming, specify 0). Warning: turning trimming off
-will give false positive indels at the ends of reads
-.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\-\-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\-\-tallydir\fR=\fI\,STRING\/\fR
-Directory for tally IIT file to resolve concordant multiple results (default is
-location of genome index files specified using \fB\-D\fR and \fB\-d\fR). Note: can
-just give full path name to \fB\-\-use\-tally\fR instead.
-.TP
-\fB\-\-use\-tally\fR=\fI\,STRING\/\fR
-Use this tally IIT file to resolve concordant multiple results
-.TP
-\fB\-\-runlengthdir\fR=\fI\,STRING\/\fR
-Directory for runlength IIT file to resolve concordant multiple results (default is
-location of genome index files specified using \fB\-D\fR and \fB\-d\fR). Note: can
-just give full path name to \fB\-\-use\-runlength\fR instead.
-.TP
-\fB\-\-use\-runlength\fR=\fI\,STRING\/\fR
-Use this runlength IIT file to resolve concordant multiple results
-.TP
-\fB\-t\fR, \fB\-\-nthreads\fR=\fI\,INT\/\fR
-Number of worker threads
-.PP
-Options for GMAP alignment within GSNAP
-.TP
-\fB\-\-gmap\-mode\fR=\fI\,STRING\/\fR
-Cases to use GMAP for complex alignments containing multiple splices or indels
-Allowed values: none, all, pairsearch, indel_knownsplice, terminal, improve
-.TP
-(or multiple values, separated by commas).
-Default: all, i.e., pairsearch,indel_knownsplice,terminal,improve
-.TP
-\fB\-\-trigger\-score\-for\-gmap\fR=\fI\,INT\/\fR
-Try GMAP pairsearch on nearby genomic regions if best score (the total
-of both ends if paired\-end) exceeds this value (default 5)
-.TP
-\fB\-\-gmap\-min\-match\-length\fR=\fI\,INT\/\fR
-Keep GMAP hit only if it has this many consecutive matches (default 20)
-.TP
-\fB\-\-gmap\-allowance\fR=\fI\,INT\/\fR
-Extra mismatch/indel score allowed for GMAP alignments (default 3)
-.TP
-\fB\-\-max\-gmap\-pairsearch\fR=\fI\,INT\/\fR
-Perform GMAP pairsearch on nearby genomic regions up to this many
-many candidate ends (default 50). Requires pairsearch in \fB\-\-gmap\-mode\fR
-.TP
-\fB\-\-max\-gmap\-terminal\fR=\fI\,INT\/\fR
-Perform GMAP terminal on nearby genomic regions up to this many
-candidate ends (default 50). Requires terminal in \fB\-\-gmap\-mode\fR
-.TP
-\fB\-\-max\-gmap\-improvement\fR=\fI\,INT\/\fR
-Perform GMAP improvement on nearby genomic regions up to this many
-candidate ends (default 5). Requires improve in \fB\-\-gmap\-mode\fR
-.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)
-.PP
-Splicing options for RNA\-Seq
-.TP
-\fB\-N\fR, \fB\-\-novelsplicing\fR=\fI\,INT\/\fR
-Look for novel splicing (0=no (default), 1=yes)
-.TP
-\fB\-\-splicingdir\fR=\fI\,STRING\/\fR
-Directory for splicing involving known sites or known introns,
-as specified by the \fB\-s\fR or \fB\-\-use\-splicing\fR flag (default is
-directory computed from \fB\-D\fR and \fB\-d\fR flags). Note: can
-just give full pathname to the \fB\-s\fR flag instead.
-.TP
-\fB\-s\fR, \fB\-\-use\-splicing\fR=\fI\,STRING\/\fR
-Look for splicing involving known sites or known introns
-(in <STRING>.iit), at short or long distances
-See README instructions for the distinction between known sites
-and known introns
-.TP
-\fB\-\-ambig\-splice\-noclip\fR
-For ambiguous known splicing at ends of the read, do not clip at the
-splice site, but extend instead into the intron. This flag makes
-sense only if you provide the \fB\-\-use\-splicing\fR flag, and you are trying
-to eliminate all soft clipping with \fB\-\-trim\-mismatch\-score\fR=\fI\,0\/\fR
-.TP
-\fB\-w\fR, \fB\-\-localsplicedist\fR=\fI\,INT\/\fR
-Definition of local novel splicing event (default 200000)
-.TP
-\fB\-\-novelend\-splicedist\fR=\fI\,INT\/\fR
-Distance to look for novel splices at the ends of reads (default 50000)
-.TP
-\fB\-e\fR, \fB\-\-local\-splice\-penalty\fR=\fI\,INT\/\fR
-Penalty for a local splice (default 0). Counts against mismatches allowed
-.TP
-\fB\-E\fR, \fB\-\-distant\-splice\-penalty\fR=\fI\,INT\/\fR
-Penalty for a distant splice (default 1). A distant splice is one where
-the intron length exceeds the value of \fB\-w\fR, or \fB\-\-localsplicedist\fR, or is an
-inversion, scramble, or translocation between two different chromosomes
-Counts against mismatches allowed
-.TP
-\fB\-K\fR, \fB\-\-distant\-splice\-endlength\fR=\fI\,INT\/\fR
-Minimum length at end required for distant spliced alignments (default 20, min
-allowed is the value of \fB\-k\fR, or kmer size)
-.TP
-\fB\-l\fR, \fB\-\-shortend\-splice\-endlength\fR=\fI\,INT\/\fR
-Minimum length at end required for short\-end spliced alignments (default 2,
-but unless known splice sites are provided with the \fB\-s\fR flag, GSNAP may still
-need the end length to be the value of \fB\-k\fR, or kmer size to find a given splice
-.TP
-\fB\-\-distant\-splice\-identity\fR=\fI\,FLOAT\/\fR
-Minimum identity at end required for distant spliced alignments (default 0.95)
-.TP
-\fB\-\-antistranded\-penalty\fR=\fI\,INT\/\fR
-(Not currently implemented, since it leads to poor results)
-Penalty for antistranded splicing when using stranded RNA\-Seq protocols.
-A positive value, such as 1, expects antisense on the first read
-and sense on the second read. Default is 0, which treats sense and antisense
-equally well
-.TP
-\fB\-\-merge\-distant\-samechr\fR
-Report distant splices on the same chromosome as a single splice, if possible.
-Will produce a single SAM line instead of two SAM lines, which is also done
-for translocations, inversions, and scramble events
-.PP
-Options for paired\-end reads
-.TP
-\fB\-\-pairmax\-dna\fR=\fI\,INT\/\fR
-Max total genomic length for DNA\-Seq paired reads, or other reads
-without splicing (default 1000). Used if \fB\-N\fR or \fB\-s\fR is not specified.
-.TP
-\fB\-\-pairmax\-rna\fR=\fI\,INT\/\fR
-Max total genomic length for RNA\-Seq paired reads, or other reads
-that could have a splice (default 200000). Used if \fB\-N\fR or \fB\-s\fR is specified.
-Should probably match the value for \fB\-w\fR, \fB\-\-localsplicedist\fR.
-.TP
-\fB\-\-pairexpect\fR=\fI\,INT\/\fR
-Expected paired\-end length, previously used for calling splices in medial part
-of paired\-end reads (default 200). Currently not used.
-.TP
-\fB\-\-pairdev\fR=\fI\,INT\/\fR
-Allowable deviation from expected paired\-end length, previously used for
-calling splices in medial part of paired\-end reads (default 100). Currently not used.
-.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 customize this behavior with these flags:
-.TP
-\fB\-J\fR, \fB\-\-quality\-zero\-score\fR=\fI\,INT\/\fR
-FASTQ quality scores are zero at this ASCII value
-(default is 33 for sanger protocol; for Illumina, select 64)
-.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
-Output options
-.TP
-\fB\-n\fR, \fB\-\-npaths\fR=\fI\,INT\/\fR
-Maximum number of paths to print (default 100).
-.TP
-\fB\-Q\fR, \fB\-\-quiet\-if\-excessive\fR
-If more than maximum number of paths are found,
-then nothing is printed.
-.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\-\-show\-refdiff\fR
-For GSNAP output in SNP\-tolerant alignment, shows all differences
-relative to the reference genome as lower case (otherwise, it shows
-all differences relative to both the reference and alternate genome)
-.TP
-\fB\-\-clip\-overlap\fR
-For paired\-end reads whose alignments overlap, clip the overlapping region.
-.TP
-\fB\-\-merge\-overlap\fR
-For paired\-end reads whose alignments overlap, merge the two ends into a single end (beta implementation)
-.TP
-\fB\-\-print\-snps\fR
-Print detailed information about SNPs in reads (works only if \fB\-v\fR also selected)
-(not fully implemented yet)
-.TP
-\fB\-\-failsonly\fR
-Print only failed alignments, those with no results
-.TP
-\fB\-\-nofails\fR
-Exclude printing of failed alignments
-.TP
-\fB\-A\fR, \fB\-\-format\fR=\fI\,STRING\/\fR
-Another format type, other than default.
-Currently implemented: sam, m8 (BLAST tabular format)
-Also allowed, but not installed at compile\-time: goby
-(To install, need to re\-compile with appropriate options)
-.TP
-\fB\-\-split\-output\fR=\fI\,STRING\/\fR
-Basename for multiple\-file output, separately for nomapping,
-halfmapping_uniq, halfmapping_mult, unpaired_uniq, unpaired_mult,
-paired_uniq, paired_mult, concordant_uniq, and concordant_mult results
-.TP
-\fB\-\-failed\-input\fR=\fI\,STRING\/\fR
-Print completely failed alignments as input FASTA or FASTQ format,
-to the given file, appending .1 or .2, for paired\-end data.
-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\-\-failed\-input\fR is given, this flag will append output
-to the existing files. Otherwise, the default is to create new files.
-.TP
-\fB\-\-order\-among\-best\fR=\fI\,STRING\/\fR
-Among alignments tied with the best score, order those alignments in this order.
-Allowed values: genomic, random (default)
-.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
-.PP
-Options for SAM output
-.TP
-\fB\-\-no\-sam\-headers\fR
-Do not print headers beginning with '@'
-.TP
-\fB\-\-sam\-headers\-batch\fR=\fI\,INT\/\fR
-Print headers only for this batch, as specified by \fB\-q\fR
-.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\-\-sam\-multiple\-primaries\fR
-Allows multiple alignments to be marked as primary if they
-have equally good mapping scores
-.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\-\-extend\-soft\-clips\fR
-Extends alignments through soft clipped regions
-.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
-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), \fBgmap\fR(1)
-.br
-http://research-pub.gene.com/gmap/
diff --git a/debian/manpages b/debian/manpages
index d3aa4ba..e0f0a2d 100644
--- a/debian/manpages
+++ b/debian/manpages
@@ -1,2 +1 @@
debian/gmap_build.1
-debian/gsnap.1
diff --git a/debian/rules b/debian/rules
index 54d8c86..18fd4f6 100755
--- a/debian/rules
+++ b/debian/rules
@@ -6,7 +6,8 @@ export DH_OPTIONS
pkg := $(shell dpkg-parsechangelog --show-field=Source)
version := $(shell dpkg-parsechangelog --show-field=Version)
mandir := $(CURDIR)/debian/$(pkg)/usr/share/man/man1
-bindir := $(CURDIR)/util
+utildir := $(CURDIR)/util
+bindir := $(CURDIR)/src
DEB_HOST_ARCH ?= $(shell dpkg-architecture -qDEB_HOST_ARCH)
EXTRA_CONFIGURE_ARGS =
@@ -14,19 +15,21 @@ ifeq ($(DEB_HOST_ARCH), i386)
EXTRA_CONFIGURE_ARGS += --enable-sse4.1=no --disable-simd
endif
-HELP2MAN = help2man --no-info --help-option="''" --version-string="$(version)"
+HELP2MAN = /usr/bin/help2man --no-info --help-option="''" --version-string="$(version)"
%:
- dh $@ --with autotools_dev
+ dh $@ --parallel --with autotools_dev
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 -p $(mandir)
-
- $(HELP2MAN) --name='Genomic Mapping and Alignment Program'\
+ $(HELP2MAN) --name='Genomic Mapping and Alignment Program' \
$(bindir)/gmap |debian/filter.pl >$(mandir)/gmap.1;
+ $(HELP2MAN) --name='Genomic Short-read Nucleotide Alignment Program' \
+ $(bindir)/gsnap |debian/filter.pl >$(mandir)/gsnap.1;
+ dh_auto_install
override_dh_install:
dh_install
--
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