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commit 744afd8f5c0e0e9708f9db0750a15eaf8c38ad5a Author: Andreas Tille <[email protected]> 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: -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ea-utils.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
