[med-svn] [snpomatic] 04/15: add manpage sources

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
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commit c9e917f53a57ea14e214dd5f24a5b4f394133cdf
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Sat Dec 12 21:09:00 2015 +0000

    add manpage sources
---
 debian/findknownsnps.1.ronn | 167 ++++++++++++++++++++++++++++++++++++++++++++
 debian/snpomatic.manpages   |   1 +
 2 files changed, 168 insertions(+)

diff --git a/debian/findknownsnps.1.ronn b/debian/findknownsnps.1.ronn
new file mode 100644
index 0000000..43e6507
--- /dev/null
+++ b/debian/findknownsnps.1.ronn
@@ -0,0 +1,167 @@
+findknownsnps(1) -- main executable for snpomatic
+=================================================
+
+## SYNOPSIS
+
+`findknownsnps` <options>
+
+## DESCRIPTION
+
+findknownsnps is the main executable for the **snpomatic** software.
+
+## OPTIONS
+
+These options control whether output is written to file(s), standard output, or
+directly to a man pager.
+
+  * `--genome=GENOME_FILE`:
+    FASTA file with chromosomes (mandatory)
+
+  * `--fasta=FASTA_FILE`:
+    FASTA file with Solexa reads (mandatory, except when --fastq or --index is
+    used)
+
+  * `--fasta=FASTA_FILE`:
+    FASTA file with Solexa reads (mandatory, except when --fastq or --index is
+    used)
+
+  * `--fastq=FASTQ_FILE`:
+    FASTQ file with Solexa reads (mandatory, except when --fasta or --index is
+    used)
+
+  * `--fastq2=FASTQ_FILE2`:
+    FASTQ file with Solexa reads (optional; read mate)
+
+  * `--nono=FILENAME`:
+    File with list of read names (!) to ignore (optional)
+
+  * `--regions=REGION_FILE`:
+    Region file for finding new SNPs (optional) [DEPRECATED]
+
+  * `--snps=SNP_FILE`:
+    Simple SNP file (optional)
+
+  * `--gff=GFF_FILE`:
+    GFF file with SNPs (optional)
+
+  * `--uniqueness=FILE`:
+    Output a uniqueness data file for the reference; no Solexa reads needed;
+    implies `--noshortcuts` (optional)
+
+  * `--pileup=FILE`:
+    Outputs complete pileup into that file (optional)
+
+  * `--cigar=FILE`:
+    Outputs alignment in CIGAR format (optional)
+
+  * `--gffout=FILE`:
+    Outputs reads in GFF format (optional)
+
+  * `--coverage=FILENAME`:
+    Outputs (high depth) coverage data (optional)
+
+  * `--wobble=FILENAME`:
+    Outputs a list of possible variations (optional; paired reads only)
+    [UNDER CONSTRUCTION]
+
+  * `--fragmentplot=FILENAME`:
+    Outputs a plot of fragment size distribution to a file (optional)
+
+  * `--snpsinreads=FILENAME`:
+    Outputs a list of reads containing known SNPs to a file (optional)
+
+  * `--indelplot=FILENAME`:
+    Outputs indel data to a file (optional)
+
+  * `--inversions=FILENAME`:
+    For paired reads, writes read matches indicating inversions into a file (optional)
+
+  * `--faceaway=FILENAME`:
+    For paired reads, writes read matches that "face away" from each other into a file (optional)
+
+  * `--sqlite=FILENAME`:
+    Creates a sqlite text file with alignment data [EXPERIMENTAL] (optional)
+
+  * `--sam=FILENAME`:
+    Creates a SAM alignment file (optional)
+
+  * `--spancontigs=FILENAME`:
+    Outputs read pairs where "half" reads map uniquely to different
+    contigs (optional)
+
+  * `--bins=FILE_PREFIX`:
+    Outputs no-match, single-match and multi-match Solexa reads into prefixed
+    files (optional)
+
+  * `--binmask=MASK`:
+    Mask of 1s and 0s to turn off individual bins. Order: No match, single
+    match, multi-match, IUPAC. Example: 0100 creates only single-match bin.
+    (optional; default:1111)
+
+  * `--pair=NUMBER`:
+    For paired reads, the length of the first part of the read (mandatory for
+    paired reads)
+
+  * `--fragment=NUMBER`:
+    For paired reads, the average fragment length (mandatory for paired reads)
+
+  * `--variance=NUMBER`:
+    For paired reads, the variance of the fragment length to either side (optional; default: 1/4 of fragment size)
+
+  * `--wobblemax=NUMBER`:
+    Maximum number of mismatches for wobble (optional; default 2; see --wobble)
+
+  * `--mspi=NUMBER`:
+    Maximum number of SNPs per chromosomal index (optional; default:8)
+
+  * `--index=FILENAME`:
+    Index filename (index will be created if it does not exist; optional)
+
+  * `--noshortcuts`:
+    Will process all chrososomal regions, even those with lots'o'repeats (optional;
+    no value)
+
+  * `--snpsonly`:
+    Only lists found SNPs in the pileup (optional; no value)
+
+  * `--chromosome=NAME`:
+    Discards all chromosomes but NAME prior to run (optional)
+
+  * `--index_from=NUMBER`:
+    Starts indexing at this position on all chromosomes (optional)
+
+  * `--index_to=NUMBER`:
+    Stops indexing at this position on all chromosomes (optional)
+
+  * `--chop=NUMBER`:
+    For paired reads, if one but not the other matches, shorten the other by
+    `NUMBER` bases (optional)
+
+  * `--index1=NUMBER` :
+    Length of internal index 1 (optional; default:10)
+
+  * `--index2=NUMBER`:
+    Length of internal index 2 (optional; default:16)
+
+  * `--memory_save=NUMBER`:
+    Indexes the genome every NUMBER of positions; saves memory and runtime, but
+    can have strange side effects (optional)
+
+  * `--multimatch`:
+    Puts a multiple-matching read to a random position (optional) [currently
+    paired reads only]
+
+  * `--singlematch`:
+    Only performs additional output functions for single matches (optional)
+    [currently paired reads only]
+
+  * `--foum`:
+    For paired reads, at least one read has to match uniquely in the genome
+    (force one unique match) (optional)
+
+  * `--mismatch`:
+    The number of mismatches allowed outside the index (index1+index2)
+    (optional)
+
+  * `--rpa=FILENAME`:
+    Writes all read pair alignments into a file (optional)
diff --git a/debian/snpomatic.manpages b/debian/snpomatic.manpages
new file mode 100644
index 0000000..7f4ba27
--- /dev/null
+++ b/debian/snpomatic.manpages
@@ -0,0 +1 @@
+debian/findknownsnps.1

-- 
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