[med-svn] [ea-utils] 01/02: Add missing manpages
Andreas Tille
tille at debian.org
Sat Jul 25 10:41:56 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository ea-utils.
commit 744afd8f5c0e0e9708f9db0750a15eaf8c38ad5a
Author: Andreas Tille <tille at debian.org>
Date: Sat Jul 25 12:18:58 2015 +0200
Add missing manpages
---
debian/createmanpages | 12 ++++++
debian/man/randomFQ.1 | 31 ++++++++++++++
debian/man/sam-stats.1 | 111 +++++++++++++++++++++++++++++++++++++++++++++++++
debian/man/varcall.1 | 73 ++++++++++++++++++++++++++++++++
4 files changed, 227 insertions(+)
diff --git a/debian/createmanpages b/debian/createmanpages
index 6f2851d..c917c7a 100755
--- a/debian/createmanpages
+++ b/debian/createmanpages
@@ -37,6 +37,18 @@ LC_ALL=C help2man --no-info --no-discard-stderr --help-option="-h" \
--version-string="$VERSION" fastx-graph \
| sed -e '/^Loading/d' -e '/Attaching package/d' -e '/^The following objects are masked from/d' -e '/^format.pval/d' > $MANDIR/fastx-graph.1
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='ea-utils: return random entries from the input fastq' \
+ --version-string="$VERSION" randomFQ > $MANDIR/randomFQ.1
+
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='ea-utils: produce digested statistics' \
+ --version-string="$VERSION" sam-stats > $MANDIR/sam-stats.1
+
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='ea-utils: output summry stats or perform variant calling' \
+ --version-string="$VERSION" varcall > $MANDIR/varcall.1
+
cat <<EOT
Please enhance the help2man output.
The following web page might be helpful in doing so:
diff --git a/debian/man/randomFQ.1 b/debian/man/randomFQ.1
new file mode 100644
index 0000000..33a516b
--- /dev/null
+++ b/debian/man/randomFQ.1
@@ -0,0 +1,31 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH RANDOMFQ "1" "July 2015" "randomFQ 1.1.2" "User Commands"
+.SH NAME
+randomFQ \- ea-utils: return random entries from the input fastq
+.SH DESCRIPTION
+Unknown option: h
+usage: ./randomFQ (\fB\-c\fR <count> | \fB\-p\fR <pct>) [\-fasta] [\-out <prefix>] [\-seed <int>] <input\-fastq> [<input\-2> [<index\-3>] ]
+.PP
+Returns <count> number of random entries from the input fastq.
+.PP
+Output is fastq, unless you specify \fB\-fasta\fR
+.PP
+If the \fB\-out\fR parameter ends in .gz, the result is gzipped in\-place.
+.PP
+\fB\-p\fR returns a % of total reads, \fB\-c\fR returns a fixed count.
+.PP
+SINGLE END:
+.PP
+Outputs to standard output, unless \fB\-out\fR <file> is specified.
+.PP
+PAIRED END:
+.PP
+Pass 2 (or 3) files as input, \fB\-out\fR is required.
+.PP
+If the paired\-end output contains a "%" sign, it is replaced with the 1 & 2 for paired\-end.
+.PP
+IE: \fB\-o\fR output_%.fastq.gz
+.PP
+Otherwise it's jsut output_1 and output_2
+.PP
+*** If one file is an indexed read, it has to be the 3rd file (for now).
diff --git a/debian/man/sam-stats.1 b/debian/man/sam-stats.1
new file mode 100644
index 0000000..d1f2094
--- /dev/null
+++ b/debian/man/sam-stats.1
@@ -0,0 +1,111 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH SAM-STATS "1" "July 2015" "sam-stats 1.1.2" "User Commands"
+.SH NAME
+sam-stats \- ea-utils: produce digested statistics
+.SH SYNOPSIS
+.B sam-stats
+[\fI\,options\/\fR] [\fI\,file1\/\fR] [\fI\,file2\/\fR...\fI\,filen\/\fR]
+.SH DESCRIPTION
+Version: 1.38.681
+.PP
+Produces lots of easily digested statistics for the files listed
+.PP
+Options (default in parens):
+.PP
+\fB\-D\fR Keep track of multiple alignments
+\fB\-O\fR PREFIX Output prefix enabling extended output (see below)
+\fB\-R\fR FIL Coverage/RNA output (coverage, 3' bias, etc, implies \fB\-A\fR)
+\fB\-A\fR Report all chr sigs, even if there are more than 1000
+\fB\-b\fR INT Number of reads to sample for per\-base stats (1M)
+\fB\-S\fR INT Size of ascii\-signature (30)
+\fB\-x\fR FIL File extension for handling multiple files (stats)
+\fB\-M\fR Only overwrite if newer (requires \fB\-x\fR, or multiple files)
+\fB\-B\fR Input is bam, don't bother looking at magic
+\fB\-z\fR Don't fail when zero entries in sam
+.PP
+OUTPUT:
+.PP
+If one file is specified, then the output is to standard out. If
+multiple files are specified, or if the \fB\-x\fR option is supplied,
+the output file is <filename>.<ext>. Default extension is 'stats'.
+.PP
+Complete Stats:
+.TP
+<STATS>
+: mean, max, stdev, median, Q1 (25 percentile), Q3
+.TP
+reads
+: # of entries in the sam file, might not be # reads
+.TP
+phred
+: phred scale used
+.TP
+bsize
+: # reads used for qual stats
+.TP
+mapped reads
+: number of aligned reads (unique probe id sequences)
+.TP
+mapped bases
+: total of the lengths of the aligned reads
+.TP
+forward
+: number of forward\-aligned reads
+.TP
+reverse
+: number of reverse\-aligned reads
+.TP
+snp rate
+: mismatched bases / total bases (snv rate)
+.TP
+ins rate
+: insert bases / total bases
+.TP
+del rate
+: deleted bases / total bases
+.TP
+pct mismatch
+: percent of reads that have mismatches
+.TP
+pct align
+: percent of reads that aligned
+.TP
+len <STATS>
+: read length stats, ignored if fixed\-length
+.TP
+mapq <STATS>
+: stats for mapping qualities
+.TP
+insert <STATS>
+: stats for insert sizes
+.TP
+%<CHR>
+: percentage of mapped bases per chr, followed by a signature
+.SS "Subsampled stats (1M reads max):"
+.IP
+base qual <STATS> : stats for base qualities
+%A,%T,%C,%G : base percentages
+.SS "Meaning of the per-chromosome signature:"
+.IP
+A ascii\-histogram of mapped reads by chromosome position.
+It is only output if the original SAM/BAM has a header. The values
+are the log2 of the # of mapped reads at each position + ascii '0'.
+.SS "Extended output mode produces a set of files:"
+.TP
+\&.stats
+: primary output
+.TP
+\&.fastx
+: fastx\-toolkit compatible output
+.TP
+\&.rcov
+: per\-reference counts & coverage
+.TP
+\&.xdist
+: mismatch distribution
+.TP
+\&.ldist
+: length distribution (if applicable)
+.TP
+\&.mqdist
+: mapping quality distribution
diff --git a/debian/man/varcall.1 b/debian/man/varcall.1
new file mode 100644
index 0000000..6d87cc2
--- /dev/null
+++ b/debian/man/varcall.1
@@ -0,0 +1,73 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH VARCALL "1" "July 2015" "varcall 1.1.2" "User Commands"
+.SH NAME
+varcall \- ea-utils: output summry stats or perform variant calling
+.SH SYNOPSIS
+.B varcall
+\fI\,<-s|-v> <-f REF> \/\fR[\fI\,options\/\fR] \fI\,bam1 \/\fR[\fI\,bam2\/\fR...]
+.SH DESCRIPTION
+Version: 0.9.632 (BETA)
+.PP
+Either outputs summry stats for the list of files, or performs variant calling
+.PP
+Options (later options override earlier):
+.PP
+\fB\-s\fR Calculate statistics
+\fB\-v\fR Calculate variants bases on supplied parameters (see \fB\-S\fR)
+\fB\-f\fR Reference fasta (required if using bams, ignored otherwise)
+\fB\-m\fR Min locii depth (0)
+\fB\-a\fR Min allele depth (0)
+\fB\-p\fR Min allele pct by quality (0)
+\fB\-q\fR Min qual (3)
+\fB\-Q\fR Min mapping quality (0)
+\fB\-b\fR Min pct balance (strand/total) (0)
+\fB\-D\fR FLOAT Max duplicate read fraction (depth/length per position) (1)
+\fB\-B\fR Turn off BAQ correction (false)
+\fB\-R\fR Homopolymer repeat indel filtering (8)
+\fB\-e\fR FLOAT Alpha filter to use, requires \fB\-l\fR or \fB\-S\fR (.05)
+\fB\-g\fR FLOAT Global minimum error rate (default: assume phred is ok)
+\fB\-l\fR INT Number of locii in total pileup used for bonferroni (1 mil)
+\fB\-x\fR CHR:POS Output this pos only, then quit
+\fB\-N\fR FIL Output noise stats to FIL
+\fB\-S\fR FIL Read in statistics and params from a previous run with \fB\-s\fR (do this!)
+\fB\-A\fR ANNOT Calculate in\-target stats using the annotation file (requires \fB\-o\fR)
+\fB\-o\fR PREFIX Output prefix (note: overlaps with \fB\-N\fR)
+.PP
+Input files
+.PP
+Files must be sorted bam files with bai index files available. Alternatively,
+a single pileup file can be supplied.
+.PP
+Output files
+.PP
+Varcalls go to stdout. Stats go to stdout, or stderr if varcalling too
+.SS "If an output prefix is used, files are created as follows:"
+.TP
+PREFIX.var
+Variant calls in tab delimited 'varcall' format
+.TP
+PREFIX.eav
+Variant calls in tab delimited 'ea\-var' format
+.TP
+PREFIX.vcf
+Variant calls, in vcf format
+.TP
+PREFIX.varsum
+Summary of variant calls
+.TP
+PREFIX.tgt
+On\-target stats detail
+.TP
+PREFIX.tgtsum
+Summary of on\-target stats
+.TP
+PREFIX.noise
+Noise stats detail
+.PP
+Stats Output:
+.PP
+Contains mean, median, quartile information for depth, base quality, read len,
+mapping quality, indel levels. Also estimates parameters suitable for
+variant calls, and can be passed directly to this program for variant calls
+.PP
+Filtering Details:
--
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