[med-svn] [ea-utils] 02/02: Add several help2man generated manpages
Andreas Tille
tille at debian.org
Sat Jul 25 07:08:39 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 998408fe954cccc2f48d4c244a7ab66903e88900
Author: Andreas Tille <tille at debian.org>
Date: Sat Jul 25 09:08:18 2015 +0200
Add several help2man generated manpages
---
debian/createmanpages | 35 +++++++++-
debian/man/alc.1 | 14 ++++
debian/man/determine-phred.1 | 11 ++++
debian/man/fastq-clipper.1 | 38 +++++++++++
debian/man/fastq-join.1 | 34 ++++++++++
debian/man/fastq-mcf.1 | 148 +++++++++++++++++++++++++++++++++++++++++++
debian/man/fastq-multx.1 | 50 +++++++++++++++
debian/man/fastq-stats.1 | 66 +++++++++++++++++++
debian/man/fastx-graph.1 | 23 +++++++
debian/manpages | 1 +
10 files changed, 417 insertions(+), 3 deletions(-)
diff --git a/debian/createmanpages b/debian/createmanpages
index febcd91..6f2851d 100755
--- a/debian/createmanpages
+++ b/debian/createmanpages
@@ -1,12 +1,41 @@
#!/bin/sh
-MANDIR=debian
+MANDIR=debian/man
mkdir -p $MANDIR
VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
help2man --no-info --no-discard-stderr --help-option=" " \
- --name='<optional description of the program>' \
- --version-string="$VERSION" <programname> > $MANDIR/<programname>.1
+ --name='ea-utils: Approximate line counts for each file.' \
+ --version-string="$VERSION" alc > $MANDIR/alc.1
+
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='ea-utils: read sam, fastq or pileup and return the phred-scale' \
+ --version-string="$VERSION" determine-phred > $MANDIR/determine-phred.1
+
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='ea-utils: removes one or more adapter sequences from the fastq file' \
+ --version-string="$VERSION" fastq-clipper > $MANDIR/fastq-clipper.1
+
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='ea-utils: join two paired-end reads on the overlapping ends' \
+ --version-string="$VERSION" fastq-join > $MANDIR/fastq-join.1
+
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='ea-utils: detect levels of adapter presence, compute likelihoods and locations of the adapters' \
+ --version-string="$VERSION" fastq-mcf > $MANDIR/fastq-mcf.1
+
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='ea-utils: replace '%' with the barcode id in the barcodes file' \
+ --version-string="$VERSION" fastq-multx > $MANDIR/fastq-multx.1
+
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='ea-utils: produce lots of easily digested statistics' \
+ --version-string="$VERSION" fastq-stats > $MANDIR/fastq-stats.1
+
+LC_ALL=C help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='ea-utils: R script to process fastq-stats output' \
+ --version-string="$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
cat <<EOT
Please enhance the help2man output.
diff --git a/debian/man/alc.1 b/debian/man/alc.1
new file mode 100644
index 0000000..c34d808
--- /dev/null
+++ b/debian/man/alc.1
@@ -0,0 +1,14 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH ALC "1" "July 2015" "alc 1.1.2" "User Commands"
+.SH NAME
+alc \- ea-utils: Approximate line counts for each file.
+.SH SYNOPSIS
+.B alc
+[\fI\,-o\/\fR] \fI\,<file1> \/\fR[\fI\,<file2>\/\fR] ...
+.SH DESCRIPTION
+Approximate line counts for each file. Attempts to be
+somewhat compatible with "wc \fB\-l\fR" by default.
+.PP
+\fB\-o\fR|\-\-only Output line count only for a single file.
+\fB\-w\fR|\-\-window <int> Read <int> bytes from head, mid, and tail.
+\fB\-s\fR|\-\-segs <int> Divide file & window into <int> segments.
diff --git a/debian/man/determine-phred.1 b/debian/man/determine-phred.1
new file mode 100644
index 0000000..61e47d6
--- /dev/null
+++ b/debian/man/determine-phred.1
@@ -0,0 +1,11 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH DETERMINE-PHRED "1" "July 2015" "determine-phred 1.1.2" "User Commands"
+.SH NAME
+determine-phred \- ea-utils: read sam, fastq or pileup and return the phred-scale
+.SH SYNOPSIS
+.B determine-phred
+\fI\,FILE\/\fR
+.SH DESCRIPTION
+Reads a sam, fastq or pileup, possibly gzipped and returns the phred\-scale,
+.IP
+either 64 or 33, based on a quick scan of the data in the file.
diff --git a/debian/man/fastq-clipper.1 b/debian/man/fastq-clipper.1
new file mode 100644
index 0000000..c2e705d
--- /dev/null
+++ b/debian/man/fastq-clipper.1
@@ -0,0 +1,38 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH FASTQ-CLIPPER "1" "July 2015" "fastq-clipper 1.1.2" "User Commands"
+.SH NAME
+fastq-clipper \- ea-utils: removes one or more adapter sequences from the fastq file
+.SH DESCRIPTION
+usage: fastq\-clipper [options] <fastq\-file> <adapters>
+.PP
+Removes one or more adapter sequences from the fastq file.
+Adapter sequences are colon\-delimited.
+Stats go to stderr, unless \fB\-o\fR is specified.
+.SH OPTIONS
+.TP
+\fB\-h\fR
+This help
+.TP
+\fB\-o\fR FIL
+Output file (stats to stdout)
+.TP
+\fB\-p\fR N
+Maximum difference percentage (10)
+.TP
+\fB\-m\fR N
+Minimum clip length (1)
+.TP
+\fB\-l\fR N
+Minimum remaining sequence length (15)
+.TP
+\fB\-x\fR [N]
+Extra match length past adapter length,
+.IP
+N =\-1 : search all
+N = 0 : search only up to adapter length
+.TP
+\fB\-e\fR
+End\-of\-line (default)
+.TP
+\fB\-b\fR
+Beginning\-of\-line (not supported yet)
diff --git a/debian/man/fastq-join.1 b/debian/man/fastq-join.1
new file mode 100644
index 0000000..b311344
--- /dev/null
+++ b/debian/man/fastq-join.1
@@ -0,0 +1,34 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH FASTQ-JOIN "1" "July 2015" "fastq-join 1.1.2" "User Commands"
+.SH NAME
+fastq-join \- ea-utils: join two paired-end reads on the overlapping ends
+.SH SYNOPSIS
+.B fastq-join
+[\fI\,options\/\fR] \fI\,<read1.fq> <read2.fq> \/\fR[\fI\,mate.fq\/\fR] \fI\,-o <read.%.fq>\/\fR
+.SH DESCRIPTION
+fastq\-join: invalid option \fB\-\-\fR 'h'
+Unknown option `\-h'.
+.PP
+Joins two paired\-end reads on the overlapping ends.
+.SH OPTIONS
+\fB\-o\fR FIL See 'Output' below
+\fB\-v\fR C Verifies that the 2 files probe id's match up to char C
+.IP
+use ' ' (space) for Illumina reads
+.PP
+\fB\-p\fR N N\-percent maximum difference (8)
+\fB\-m\fR N N\-minimum overlap (6)
+\fB\-r\fR FIL Verbose stitch length report
+\fB\-R\fR No reverse complement
+\fB\-x\fR Allow insert < read length
+.PP
+Output:
+.IP
+You can supply 3 \fB\-o\fR arguments, for un1, un2, join files, or one
+.PP
+argument as a file name template. The suffix 'un1, un2, or join' is
+appended to the file, or they replace a %\-character if present.
+.IP
+If a 'mate' input file is present (barcode read), then the files
+.PP
+\&'un3' and 'join2' are also created.
diff --git a/debian/man/fastq-mcf.1 b/debian/man/fastq-mcf.1
new file mode 100644
index 0000000..ea04561
--- /dev/null
+++ b/debian/man/fastq-mcf.1
@@ -0,0 +1,148 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH FASTQ-MCF "1" "July 2015" "fastq-mcf 1.1.2" "User Commands"
+.SH NAME
+fastq-mcf \- ea-utils: detect levels of adapter presence, compute likelihoods and locations of the adapters
+.SH SYNOPSIS
+.B fastq-mcf
+[\fI\,options\/\fR] \fI\,<adapters.fa> <reads.fq> \/\fR[\fI\,mates1.fq \/\fR...]
+.SH DESCRIPTION
+Version: 1.04.676
+.PP
+Detects levels of adapter presence, computes likelihoods and
+locations (start, end) of the adapters. Removes the adapter
+sequences from the fastq file(s).
+.PP
+Stats go to stderr, unless \fB\-o\fR is specified.
+.PP
+Specify \fB\-0\fR to turn off all default settings
+.PP
+If you specify multiple 'paired\-end' inputs, then a \fB\-o\fR option is
+required for each. IE: \fB\-o\fR read1.clip.q \fB\-o\fR read2.clip.fq
+.SH OPTIONS
+.TP
+\fB\-h\fR
+This help
+.TP
+\fB\-o\fR FIL
+Output file (stats to stdout)
+.TP
+\fB\-s\fR N.N
+Log scale for adapter minimum\-length\-match (2.2)
+.TP
+\fB\-t\fR N
+% occurance threshold before adapter clipping (0.25)
+.TP
+\fB\-m\fR N
+Minimum clip length, overrides scaled auto (1)
+.TP
+\fB\-p\fR N
+Maximum adapter difference percentage (10)
+.TP
+\fB\-l\fR N
+Minimum remaining sequence length (19)
+.TP
+\fB\-L\fR N
+Maximum remaining sequence length (none)
+.TP
+\fB\-D\fR N
+Remove duplicate reads : Read_1 has an identical N bases (0)
+.TP
+\fB\-k\fR N
+sKew percentage\-less\-than causing cycle removal (2)
+.TP
+\fB\-x\fR N
+\&'N' (Bad read) percentage causing cycle removal (20)
+.TP
+\fB\-q\fR N
+quality threshold causing base removal (10)
+.TP
+\fB\-w\fR N
+window\-size for quality trimming (1)
+.TP
+\fB\-H\fR
+remove >95% homopolymer reads (no)
+.TP
+\fB\-X\fR
+remove low complexity reads (no)
+.TP
+\fB\-0\fR
+Set all default parameters to zero/do nothing
+.TP
+\fB\-U\fR|u
+Force disable/enable Illumina PF filtering (auto)
+.TP
+\fB\-P\fR N
+Phred\-scale (auto)
+.TP
+\fB\-R\fR
+Don't remove N's from the fronts/ends of reads
+.TP
+\fB\-n\fR
+Don't clip, just output what would be done
+.TP
+\fB\-C\fR N
+Number of reads to use for subsampling (300k)
+.TP
+\fB\-S\fR
+Save all discarded reads to '.skip' files
+.TP
+\fB\-d\fR
+Output lots of random debugging stuff
+.SS "Quality adjustment options:"
+.TP
+\fB\-\-cycle\-adjust\fR
+CYC,AMT Adjust cycle CYC (negative = offset from end) by amount AMT
+.TP
+\fB\-\-phred\-adjust\fR
+SCORE,AMT Adjust score SCORE by amount AMT
+.TP
+\fB\-\-phred\-adjust\-max\fR
+SCORE Adjust scores > SCORE to SCOTE
+.SS "Filtering options*:"
+.TP
+\fB\-\-[mate\-]qual\-mean\fR
+NUM Minimum mean quality score
+.TP
+\fB\-\-[mate\-]qual\-gt\fR
+NUM,THR At least NUM quals > THR
+.TP
+\fB\-\-[mate\-]max\-ns\fR
+NUM Maxmium N\-calls in a read (can be a %)
+.TP
+\fB\-\-[mate\-]min\-len\fR
+NUM Minimum remaining length (same as \fB\-l\fR)
+.TP
+\fB\-\-homopolymer\-pct\fR
+PCT Homopolymer filter percent (95)
+.TP
+\fB\-\-lowcomplex\-pct\fR
+PCT Complexity filter percent (95)
+.PP
+If mate\- prefix is used, then applies to second non\-barcode read only
+.PP
+Adapter files are 'fasta' formatted:
+.PP
+Specify n/a to turn off adapter clipping, and just use filters
+.PP
+Increasing the scale makes recognition\-lengths longer, a scale
+of 100 will force full\-length recognition of adapters.
+.PP
+Adapter sequences with _5p in their label will match 'end's,
+and sequences with _3p in their label will match 'start's,
+otherwise the 'end' is auto\-determined.
+.PP
+Skew is when one cycle is poor, 'skewed' toward a particular base.
+If any nucleotide is less than the skew percentage, then the
+whole cycle is removed. Disable for methyl\-seq, etc.
+.PP
+Set the skew (\fB\-k\fR) or N\-pct (\fB\-x\fR) to 0 to turn it off (should be done
+for miRNA, amplicon and other low\-complexity situations!)
+.PP
+Duplicate read filtering is appropriate for assembly tasks, and
+never when read length < expected coverage. \fB\-D\fR 50 will use
+4.5GB RAM on 100m DNA reads \- be careful. Great for RNA assembly.
+.PP
+*Quality filters are evaluated after clipping/trimming
+.PP
+Homopolymer filtering is a subset of low\-complexity, but will not
+be separately tracked unless both are turned on.
diff --git a/debian/man/fastq-multx.1 b/debian/man/fastq-multx.1
new file mode 100644
index 0000000..04a12e7
--- /dev/null
+++ b/debian/man/fastq-multx.1
@@ -0,0 +1,50 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH FASTQ-MULTX "1" "July 2015" "fastq-multx 1.1.2" "User Commands"
+.SH NAME
+fastq-multx \- ea-utils: replace % with the barcode id in the barcodes file
+.SH SYNOPSIS
+.B fastq-multx
+[\fI\,-g|-l|-B\/\fR] \fI\,<barcodes.fil> <read1.fq> -o r1.%.fq \/\fR[\fI\,mate.fq -o r2.%.fq\/\fR] ...
+.SH DESCRIPTION
+fastq\-multx: invalid option \fB\-\-\fR 'h'
+Unknown option `\-h'.
+.PP
+Version: 1.02.684
+.PP
+Output files must contain a '%' sign which is replaced with the barcode id in the barcodes file.
+Output file can be n/a to discard the corresponding data (use this for the barcode read)
+.PP
+Barcodes file (\fB\-B\fR) looks like this:
+.PP
+<id1> <sequence1>
+<id2> <sequence2> ...
+.PP
+Default is to guess the \fB\-bol\fR or \fB\-eol\fR based on clear stats.
+.PP
+If \fB\-g\fR is used, then it's parameter is an index lane, and frequently occuring sequences are used.
+.PP
+If \fB\-l\fR is used then all barcodes in the file are tried, and the *group* with the *most* matches is chosen.
+.PP
+Grouped barcodes file (\fB\-l\fR or \fB\-L\fR) looks like this:
+.PP
+<id1> <sequence1> <group1>
+<id1> <sequence1> <group1>
+<id2> <sequence2> <group2>...
+.PP
+Mated reads, if supplied, are kept in\-sync
+.SH OPTIONS
+\fB\-o\fR FIL1 Output files (one per input, required)
+\fB\-g\fR SEQFIL Determine barcodes from indexed read SEQFIL
+\fB\-l\fR BCFIL Determine barcodes from any read, using BCFIL as a master list
+\fB\-L\fR BCFIL Determine barcodes from <read1.fq>, using BCFIL as a master list
+\fB\-B\fR BCFIL Use barcodes from the specified file, don't run a determination step
+\fB\-b\fR Force beginning of line (5') for barcode matching
+\fB\-e\fR Force end of line (3') for batcode matching
+\fB\-t\fR NUM Divide threshold for auto\-determine by factor NUM (1), > 1 = more sensitive
+\fB\-G\fR NAME Use group(s) matching NAME only
+\fB\-x\fR Don't trim barcodes off before writing out destination
+\fB\-n\fR Don't execute, just print likely barcode list
+\fB\-v\fR C Verify that mated id's match up to character C (Use ' ' for illumina)
+\fB\-m\fR N Allow up to N mismatches, as long as they are unique (1)
+\fB\-d\fR N Require a minimum distance of N between the best and next best (2)
+\fB\-q\fR N Require a minimum phred quality of N to accept a barcode base (0)
diff --git a/debian/man/fastq-stats.1 b/debian/man/fastq-stats.1
new file mode 100644
index 0000000..9836370
--- /dev/null
+++ b/debian/man/fastq-stats.1
@@ -0,0 +1,66 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH FASTQ-STATS "1" "July 2015" "fastq-stats 1.1.2" "User Commands"
+.SH NAME
+fastq-stats \- ea-utils: produce lots of easily digested statistics
+.SH SYNOPSIS
+.B fastq-stats
+[\fI\,options\/\fR] \fI\,<fastq-file>\/\fR
+.SH DESCRIPTION
+Version: 1.01 $Id: fastq\-stats.cpp 652 2013\-09\-17 17:40:32Z earonesty $
+.PP
+Produces lots of easily digested statistics for the files listed
+.PP
+Options
+.PP
+\fB\-c\fR cyclemax: max cycles for which following quality stats are produced [35]
+\fB\-w\fR INT window: max window size for generating duplicate read statistics [2000000]
+\fB\-d\fR debug: prints out debug statements
+\fB\-D\fR don't do duplicate read statistics
+\fB\-s\fR INT number of top duplicate reads to display
+\fB\-x\fR FIL output fastx statistics (requires an output filename)
+\fB\-b\fR FIL output base breakdown by per phred quality at every cycle.
+.IP
+It sets cylemax to longest read length
+.PP
+\fB\-L\fR FIL Output length counts
+.PP
+The following data are printed to stdout:
+.TP
+reads
+: #reads in the fastq file
+.TP
+len
+: read length. mean and stdev are provided for variable read lengths
+.TP
+phred
+: phred scale used
+.TP
+window\-size
+: Number of reads used to generate duplicate read statistics
+.TP
+cycle\-max
+: Number of bases to assess for duplicity
+.TP
+dups
+: Number of reads that are duplicates
+.TP
+%dup
+: Pct reads that are duplcate
+.TP
+unique\-dup seq
+: Number sequences that are duplicated
+.TP
+min dup count
+: Smallest duplicate tally for any duplicate sequence
+.TP
+dup seq <rank> <count> <sequence>
+: Lists top 10 most frequent duplicate reads along with count mean and stdev
+.TP
+qual
+: Base Quality min, max and mean
+.TP
+%A,%T,%C,%G
+: base percentages
+.TP
+total bases
+: total number of bases
diff --git a/debian/man/fastx-graph.1 b/debian/man/fastx-graph.1
new file mode 100644
index 0000000..117cd19
--- /dev/null
+++ b/debian/man/fastx-graph.1
@@ -0,0 +1,23 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH FASTX-GRAPH "1" "July 2015" "fastx-graph 1.1.2" "User Commands"
+.SH NAME
+fastx-graph \- ea-utils: R script to process fastq-stats output
+.SH SYNOPSIS
+.B fastx-graph
+[\fI\,-\/\fR[\fI\,-input|i\/\fR] \fI\,<character>\/\fR] [\fI\,-\/\fR[\fI\,-gc|G\/\fR] \fI\,<character>\/\fR] [\fI\,-\/\fR[\fI\,-out|o\/\fR] \fI\,<character>\/\fR] [\fI\,-\/\fR[\fI\,-help|h\/\fR]]
+.SH DESCRIPTION
+.PP
+.PP
+.IP
+.TP
+\fB\-i\fR|\-\-input
+file from fastq\-stats \fB\-x\fR (required)
+.TP
+\fB\-G\fR|\-\-gc
+input gc content file (optional)
+.TP
+\fB\-o\fR|\-\-out
+output filename (optional)
+.TP
+\fB\-h\fR|\-\-help
+this help
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..13cdaf4
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/man/*.1
--
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