[med-svn] [Git][med-team/bbmap][master] 3 commits: Create another manpage
Andreas Tille
gitlab at salsa.debian.org
Tue Mar 26 14:54:33 GMT 2019
Andreas Tille pushed to branch master at Debian Med / bbmap
Commits:
fd6ce4ac by Andreas Tille at 2019-03-26T14:45:52Z
Create another manpage
- - - - -
dfd9d0d7 by Andreas Tille at 2019-03-26T14:46:16Z
Add docs
- - - - -
134de0f9 by Andreas Tille at 2019-03-26T14:54:10Z
Add manpage for bloomfilter.sh
- - - - -
5 changed files:
- + debian/bbmap.docs
- + debian/bloomfilter.sh.1
- debian/createmanpages
- debian/lintian-overrides
- debian/rules
Changes:
=====================================
debian/bbmap.docs
=====================================
@@ -0,0 +1 @@
+docs/*
=====================================
debian/bloomfilter.sh.1
=====================================
@@ -0,0 +1,108 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.
+.TH BLOOMFILTER.SH "1" "March 2019" "bloomfilter.sh 38.43" "User Commands"
+.SH NAME
+bloomfilter.sh \- Filters reads potentially sharing a kmer with a reference
+.SH SYNOPSIS
+.B bloomfilter.sh
+\fI\,in=<input file> out=<nonmatches> outm=<matches> ref=<reference>\/\fR
+.SH DESCRIPTION
+Filters reads potentially sharing a kmer with a reference.
+The more memory, the higher the accuracy. Reads going to outu are guaranteed
+to not match the reference, but reads going to outm might may or may not
+match the reference.
+.SH EXAMPLES
+bloomfilter.sh in=reads.fq outm=nonhuman.fq outm=human.fq k=31 minhits=3 ref=human.fa
+.PP
+Error correction and depth filtering can be done simultaneously.
+.SH OPTIONS
+.SS File parameters:
+.TP
+in=<file>
+Primary input, or read 1 input.
+.TP
+in2=<file>
+Read 2 input if reads are in two files.
+.TP
+outm=<file>
+(out) Primary matched read output.
+.TP
+outm2=<file>
+(out2) Matched read 2 output if reads are in two files.
+.TP
+outu=<file>
+Primary unmatched read output.
+.TP
+outu2=<file>
+Unmatched read 2 output if reads are in two files.
+.TP
+ref=<file>
+Reference sequence file, or a comma\-delimited list.
+.IP
+For depth\-based filtering, set this to the same as the input.
+.TP
+overwrite=t
+(ow) Set to false to force the program to abort rather than
+overwrite an existing file.
+.SS Hashing parameters:
+.TP
+k=31
+Kmer length.
+.TP
+hashes=2
+Number of hashes per kmer. Higher generally reduces
+false positives at the expense of speed.
+.TP
+minprob=0.5
+Ignore reference kmers with probability of being correct
+below this (affects fastq references only).
+.TP
+memmult=1.0
+Fraction of free memory to use for Bloom filter. 1.0 should
+generally work; if the program crashes with an out of memory
+error, set this lower. Higher increases specificity.
+.TP
+cells=
+Option to set the number of cells manually. By default this
+will be autoset to use all available memory.
+The only reason
+to set this is to ensure deterministic output.
+.TP
+seed=0
+This will change the hash function used.
+.SS Reference\-matching parameters:
+.TP
+minhits=3
+Consecutive kmer hits for a read to be considered matched.
+.IP
+Higher reduces false positives at the expense of sensitivity.
+.TP
+mincount=1
+Minimum number of times a read kmer must occur in the
+reference to be considered a match.
+.TP
+requireboth=f
+Require both reads in a pair to match the ref in order to go
+to outm.
+.IP
+By default, pairs go to outm if either matches.
+.SS Java Parameters
+.TP
+\fB\-Xmx\fR
+This will set Java's memory usage, overriding autodetection.
+.IP
+\fB\-Xmx20g\fR will specify 20 gigs of RAM, and \fB\-Xmx200m\fR will
+specify 200 megs. The max is typically 85% of physical memory.
+.TP
+\fB\-eoom\fR
+This flag will cause the process to exit if an out\-of\-memory
+exception occurs.
+Requires Java 8u92+.
+.TP
+\fB\-da\fR
+Disable assertions.
+.SH AUTHOR
+Written by Brian Bushnell
+.P
+Please contact Brian Bushnell at bbushnell at lbl.gov if you encounter any problems.
+.P
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
=====================================
debian/createmanpages
=====================================
@@ -12,12 +12,18 @@ can be used for any other usage of the program.
# If program name is different from package name or title should be
# different from package short description change this here
-progname=${PROGNAME}
+progname=${PROGNAME}.sh
help2man --no-info --no-discard-stderr --help-option=" " \
--name="$NAME" \
--version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
echo $AUTHOR >> $MANDIR/${progname}.1
+progname=bloomfilter.sh
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="Filters reads potentially sharing a kmer with a reference" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
echo "$MANDIR/*.1" > debian/manpages
cat <<EOT
=====================================
debian/lintian-overrides
=====================================
@@ -1,2 +1,2 @@
# see https://lists.debian.org/debian-med/2018/06/msg00043.html
-bbmap: script-with-language-extension usr/bin/*.*
+bbmap: script-with-language-extension usr/bin/*
=====================================
debian/rules
=====================================
@@ -29,7 +29,7 @@ override_dh_install:
dh_install
mkdir -p $(PKGSHAREDIR)
mkdir -p $(PKGBINDIR)
- cp -a calcmem.sh $(PKGSHAREDIR)/calcmem
+ # cp -a calcmem.sh $(PKGSHAREDIR)/calcmem # we don't have any name space collision when keeping .sh extension
for scr in *.sh ; do \
if [ "$${scr}" != "calcmem.sh" ] ; then \
sed -e 's:^CP=".DIR""current/":CP=/usr/share/java/bbmap.jar:' \
View it on GitLab: https://salsa.debian.org/med-team/bbmap/compare/8f5d9517e9395ffec2c29fa0c49818e8e8e7d722...134de0f9d1e3b25709f11849352dfdc5fa89426b
--
View it on GitLab: https://salsa.debian.org/med-team/bbmap/compare/8f5d9517e9395ffec2c29fa0c49818e8e8e7d722...134de0f9d1e3b25709f11849352dfdc5fa89426b
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