Loading debian/createmanpages 0 → 100755 +26 −0 Original line number Diff line number Diff line #!/bin/sh MANDIR=debian/mans mkdir -p $MANDIR VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'` NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1` PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1` AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and can be used for any other usage of the program. " progname=bcalm help2man --no-info --no-discard-stderr --help-option="-h" \ --name="$NAME" \ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 echo $AUTHOR >> $MANDIR/${progname}.1 echo "$MANDIR/*.1" > debian/manpages cat <<EOT Please enhance the help2man output. The following web page might be helpful in doing so: http://liw.fi/manpages/ EOT debian/manpages 0 → 100644 +1 −0 Original line number Diff line number Diff line debian/mans/*.1 debian/mans/bcalm.1 0 → 100644 +139 −0 Original line number Diff line number Diff line .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8. .TH BCALM "1" "September 2019" "bcalm 2.2.1" "User Commands" .SH NAME bcalm \- de Bruijn compaction in low memory .SH DESCRIPTION Bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data. .PP [bcalm_1 options] .TP \fB\-nb\-cores\fR (1 arg) : number of cores [default '0'] .TP \fB\-verbose\fR (1 arg) : verbosity level [default '1'] .TP \fB\-version\fR (0 arg) : version .TP \fB\-help\fR (0 arg) : help .IP [graph options] .TP \fB\-no\-mphf\fR (0 arg) : don't construct the MPHF .IP [kmer count options] .TP \fB\-in\fR (1 arg) : reads file [default ''] .TP \fB\-kmer\-size\fR (1 arg) : size of a kmer [default '31'] .TP \fB\-abundance\-min\fR (1 arg) : min abundance threshold for solid kmers [default '2'] .TP \fB\-abundance\-max\fR (1 arg) : max abundance threshold for solid kmers [default '2147483647'] .TP \fB\-solidity\-custom\fR (1 arg) : when solidity\-kind is custom, specifies list of files where kmer must be present [default ''] .TP \fB\-max\-memory\fR (1 arg) : max memory (in MBytes) [default '5000'] .TP \fB\-max\-disk\fR (1 arg) : max disk (in MBytes) [default '0'] .TP \fB\-out\fR (1 arg) : output file [default ''] .TP \fB\-out\-dir\fR (1 arg) : output directory [default '.'] .TP \fB\-out\-tmp\fR (1 arg) : output directory for temporary files [default '.'] .TP \fB\-out\-compress\fR (1 arg) : h5 compression level (0:none, 9:best) [default '0'] .TP \fB\-storage\-type\fR (1 arg) : storage type of kmer counts ('hdf5' or 'file') [default 'hdf5'] .TP \fB\-histo2D\fR (1 arg) : compute the 2D histogram (with first file = genome, remaining files = reads) [default '0'] .TP \fB\-histo\fR (1 arg) : output the kmer abundance histogram [default '0'] .IP [kmer count, advanced performance tweaks options] .TP \fB\-minimizer\-type\fR (1 arg) : minimizer type (0=lexi, 1=freq) [default '1'] .TP \fB\-minimizer\-size\fR (1 arg) : size of a minimizer [default '10'] .TP \fB\-repartition\-type\fR (1 arg) : minimizer repartition (0=unordered, 1=ordered) [default '1'] .IP [bloom options] .TP \fB\-bloom\fR (1 arg) : bloom type ('basic', 'cache', 'neighbor') [default 'neighbor'] .TP \fB\-debloom\fR (1 arg) : debloom type ('none', 'original' or 'cascading') [default 'cascading'] .TP \fB\-debloom\-impl\fR (1 arg) : debloom impl ('basic', 'minimizer') [default 'minimizer'] .IP [branching options] .TP \fB\-branching\-nodes\fR (1 arg) : branching type ('none' or 'stored') [default 'stored'] .TP \fB\-topology\-stats\fR (1 arg) : topological information level (0 for none) [default '0'] .IP [general options] .TP \fB\-config\-only\fR (0 arg) : dump config only .TP \fB\-nb\-cores\fR (1 arg) : number of cores [default '0'] .TP \fB\-verbose\fR (1 arg) : verbosity level [default '1'] .TP \fB\-integer\-precision\fR (1 arg) : integers precision (0 for optimized value) [default '0'] .TP [debug options] .TP \fB\-redo\-bcalm\fR (0 arg) : debug function, redo the bcalm algo .TP \fB\-skip\-bcalm\fR (0 arg) : same, but skip bcalm .TP \fB\-redo\-bglue\fR (0 arg) : same, but redo bglue .TP \fB\-skip\-bglue\fR (0 arg) : same, but skip bglue .TP \fB\-redo\-links\fR (0 arg) : same, but redo links .TP \fB\-skip\-links\fR (0 arg) : same, but skip links .TP \fB\-nb\-glue\-partitions\fR (1 arg) : number of glue partitions (automatically calculated by default) [default '0'] .SH AUTHOR This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program. Loading
debian/createmanpages 0 → 100755 +26 −0 Original line number Diff line number Diff line #!/bin/sh MANDIR=debian/mans mkdir -p $MANDIR VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'` NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1` PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1` AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and can be used for any other usage of the program. " progname=bcalm help2man --no-info --no-discard-stderr --help-option="-h" \ --name="$NAME" \ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 echo $AUTHOR >> $MANDIR/${progname}.1 echo "$MANDIR/*.1" > debian/manpages cat <<EOT Please enhance the help2man output. The following web page might be helpful in doing so: http://liw.fi/manpages/ EOT
debian/mans/bcalm.1 0 → 100644 +139 −0 Original line number Diff line number Diff line .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8. .TH BCALM "1" "September 2019" "bcalm 2.2.1" "User Commands" .SH NAME bcalm \- de Bruijn compaction in low memory .SH DESCRIPTION Bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data. .PP [bcalm_1 options] .TP \fB\-nb\-cores\fR (1 arg) : number of cores [default '0'] .TP \fB\-verbose\fR (1 arg) : verbosity level [default '1'] .TP \fB\-version\fR (0 arg) : version .TP \fB\-help\fR (0 arg) : help .IP [graph options] .TP \fB\-no\-mphf\fR (0 arg) : don't construct the MPHF .IP [kmer count options] .TP \fB\-in\fR (1 arg) : reads file [default ''] .TP \fB\-kmer\-size\fR (1 arg) : size of a kmer [default '31'] .TP \fB\-abundance\-min\fR (1 arg) : min abundance threshold for solid kmers [default '2'] .TP \fB\-abundance\-max\fR (1 arg) : max abundance threshold for solid kmers [default '2147483647'] .TP \fB\-solidity\-custom\fR (1 arg) : when solidity\-kind is custom, specifies list of files where kmer must be present [default ''] .TP \fB\-max\-memory\fR (1 arg) : max memory (in MBytes) [default '5000'] .TP \fB\-max\-disk\fR (1 arg) : max disk (in MBytes) [default '0'] .TP \fB\-out\fR (1 arg) : output file [default ''] .TP \fB\-out\-dir\fR (1 arg) : output directory [default '.'] .TP \fB\-out\-tmp\fR (1 arg) : output directory for temporary files [default '.'] .TP \fB\-out\-compress\fR (1 arg) : h5 compression level (0:none, 9:best) [default '0'] .TP \fB\-storage\-type\fR (1 arg) : storage type of kmer counts ('hdf5' or 'file') [default 'hdf5'] .TP \fB\-histo2D\fR (1 arg) : compute the 2D histogram (with first file = genome, remaining files = reads) [default '0'] .TP \fB\-histo\fR (1 arg) : output the kmer abundance histogram [default '0'] .IP [kmer count, advanced performance tweaks options] .TP \fB\-minimizer\-type\fR (1 arg) : minimizer type (0=lexi, 1=freq) [default '1'] .TP \fB\-minimizer\-size\fR (1 arg) : size of a minimizer [default '10'] .TP \fB\-repartition\-type\fR (1 arg) : minimizer repartition (0=unordered, 1=ordered) [default '1'] .IP [bloom options] .TP \fB\-bloom\fR (1 arg) : bloom type ('basic', 'cache', 'neighbor') [default 'neighbor'] .TP \fB\-debloom\fR (1 arg) : debloom type ('none', 'original' or 'cascading') [default 'cascading'] .TP \fB\-debloom\-impl\fR (1 arg) : debloom impl ('basic', 'minimizer') [default 'minimizer'] .IP [branching options] .TP \fB\-branching\-nodes\fR (1 arg) : branching type ('none' or 'stored') [default 'stored'] .TP \fB\-topology\-stats\fR (1 arg) : topological information level (0 for none) [default '0'] .IP [general options] .TP \fB\-config\-only\fR (0 arg) : dump config only .TP \fB\-nb\-cores\fR (1 arg) : number of cores [default '0'] .TP \fB\-verbose\fR (1 arg) : verbosity level [default '1'] .TP \fB\-integer\-precision\fR (1 arg) : integers precision (0 for optimized value) [default '0'] .TP [debug options] .TP \fB\-redo\-bcalm\fR (0 arg) : debug function, redo the bcalm algo .TP \fB\-skip\-bcalm\fR (0 arg) : same, but skip bcalm .TP \fB\-redo\-bglue\fR (0 arg) : same, but redo bglue .TP \fB\-skip\-bglue\fR (0 arg) : same, but skip bglue .TP \fB\-redo\-links\fR (0 arg) : same, but redo links .TP \fB\-skip\-links\fR (0 arg) : same, but skip links .TP \fB\-nb\-glue\-partitions\fR (1 arg) : number of glue partitions (automatically calculated by default) [default '0'] .SH AUTHOR This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.
