[med-svn] [Git][med-team/lumpy-sv][master] 4 commits: Leave other test options for some later point in time
Andreas Tille
gitlab at salsa.debian.org
Wed Jun 3 10:49:22 BST 2020
Andreas Tille pushed to branch master at Debian Med / lumpy-sv
Commits:
d947718e by Andreas Tille at 2020-06-03T08:48:38+02:00
Leave other test options for some later point in time
- - - - -
1bfed267 by Andreas Tille at 2020-06-03T08:49:13+02:00
Upload to new
- - - - -
b06d0b1e by Andreas Tille at 2020-06-03T11:42:18+02:00
Add manpages
- - - - -
5b82acc7 by Andreas Tille at 2020-06-03T11:44:19+02:00
Fix more scripts
- - - - -
8 changed files:
- debian/changelog
- + debian/createmanpages
- + debian/lumpy.1
- + debian/lumpy_filter.1
- + debian/lumpyexpress.1
- + debian/manpages
- debian/patches/fix_shebang.patch
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
-lumpy-sv (0.3.0+dfsg-1) UNRELEASED; urgency=medium
+lumpy-sv (0.3.0+dfsg-1) unstable; urgency=medium
* Initial release (Closes: #961998)
- -- Andreas Tille <tille at debian.org> Mon, 01 Jun 2020 21:58:38 +0200
+ -- Andreas Tille <tille at debian.org> Wed, 03 Jun 2020 08:49:09 +0200
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,40 @@
+#!/bin/sh
+MANDIR=debian
+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\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=lumpy
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="Automated breakpoint detection for standard analyses" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=lumpy_filter
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="filter for lumpy(1) usage" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=lumpyexpress
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="Automated breakpoint detection for standard analyses" \
+ --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/lumpy.1
=====================================
@@ -0,0 +1,92 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH LUMPY "1" "June 2020" "lumpy 0.3.0" "User Commands"
+.SH NAME
+lumpy \- Automated breakpoint detection for standard analyses
+.SH SYNOPSIS
+.B lumpy
+[\fI\,OPTIONS\/\fR]
+.SH DESCRIPTION
+LUMPY, a novel SV discovery framework that naturally integrates multiple
+SV signals jointly across multiple samples. LUMPY yields improved
+sensitivity, especially when SV signal is reduced owing to either low
+coverage data or low intra-sample variant allele frequency.
+.SH OPTIONS
+.TP
+\fB\-g\fR
+Genome file (defines chromosome order)
+.TP
+\fB\-e\fR
+Show evidence for each call
+.TP
+\fB\-w\fR
+File read windows size (default 1000000)
+.TP
+\fB\-mw\fR
+minimum weight for a call
+.TP
+\fB\-msw\fR
+minimum per\-sample weight for a call
+.TP
+\fB\-tt\fR
+trim threshold
+.TP
+\fB\-x\fR
+exclude file bed file
+.TP
+\fB\-t\fR
+temp file prefix, must be to a writeable directory
+.TP
+\fB\-P\fR
+output probability curve for each variant
+.TP
+\fB\-b\fR
+output BEDPE instead of VCF
+.TP
+\fB\-sr\fR
+bam_file:<file name>,
+.IP
+id:<sample name>,
+.IP
+back_distance:<distance>,
+.IP
+min_mapping_threshold:<mapping quality>,
+.IP
+weight:<sample weight>,
+.IP
+min_clip:<minimum clip length>,
+.IP
+read_group:<string>
+.TP
+\fB\-pe\fR
+bam_file:<file name>,
+.IP
+id:<sample name>,
+.IP
+histo_file:<file name>,
+.IP
+mean:<value>,
+.IP
+stdev:<value>,
+.IP
+read_length:<length>,
+.IP
+min_non_overlap:<length>,
+.IP
+discordant_z:<z value>,
+.IP
+back_distance:<distance>,
+.IP
+min_mapping_threshold:<mapping quality>,
+.IP
+weight:<sample weight>,
+.IP
+read_group:<string>
+.TP
+\fB\-bedpe\fR
+bedpe_file:<bedpe file>,
+.IP
+id:<sample name>,
+weight:<sample weight>
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/lumpy_filter.1
=====================================
@@ -0,0 +1,10 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH LUMPY_FILTER "1" "June 2020" "lumpy_filter 0.3.0" "User Commands"
+.SH NAME
+lumpy_filter \- filter for lumpy(1) usage
+.SH SYNOPSIS
+.B lumpy_filter
+\fB\-f\fR <optional\-reference> <bam> <split out> <discord out> (optional #threads)
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/lumpyexpress.1
=====================================
@@ -0,0 +1,60 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH LUMPYEXPRESS "1" "June 2020" "lumpyexpress 0.3.0" "User Commands"
+.SH NAME
+lumpyexpress \- Automated breakpoint detection for standard analyses
+.SH SYNOPSIS
+.B lumpyexpress
+[options]
+.SH OPTIONS
+.TP
+\fB\-B\fR FILE
+full BAM or CRAM file(s) (comma separated) (required)
+.TP
+\fB\-S\fR FILE
+split reads BAM file(s) (comma separated)
+.TP
+\fB\-D\fR FILE
+discordant reads BAM files(s) (comma separated)
+.TP
+\fB\-R\fR FILE
+indexed reference genome fasta file (recommended for CRAMs)
+.TP
+\fB\-d\fR FILE
+bedpe file of depths (comma separated and prefixed by sample:)
+e.g sample_x:/path/to/sample_x.bedpe,sample_y:/path/to/sample_y.bedpe
+.TP
+\fB\-o\fR FILE
+output file [fullBam.bam.vcf]
+.TP
+\fB\-x\fR FILE
+BED file to exclude
+.TP
+\fB\-P\fR
+output probability curves for each variant
+.TP
+\fB\-m\fR INT
+minimum sample weight for a call [4]
+.HP
+\fB\-r\fR FLOAT trim threshold [0]
+.TP
+\fB\-T\fR DIR
+temp directory [./output_prefix.XXXXXXXXXXXX]
+.TP
+\fB\-k\fR
+keep temporary files
+.TP
+\fB\-K\fR FILE
+path to lumpyexpress.config file
+.IP
+(default: same directory as lumpyexpress)
+.TP
+\fB\-v\fR
+verbose
+.TP
+\fB\-h\fR
+show this message
+.PP
+Error: \fB\-B\fR is required
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1
=====================================
debian/patches/fix_shebang.patch
=====================================
@@ -34,3 +34,27 @@ Description: Remove additional hash sign
if [ -z $7 ]
then
+--- a/lumpy_tests/orig/bp_pesr.sh
++++ b/lumpy_tests/orig/bp_pesr.sh
+@@ -1,4 +1,4 @@
+-##!/bin/bash
++#!/bin/bash
+
+ if [ -z $6 ]
+ then
+--- a/lumpy_tests/orig/bp_sr.sh
++++ b/lumpy_tests/orig/bp_sr.sh
+@@ -1,4 +1,4 @@
+-##!/bin/bash
++#!/bin/bash
+
+ if [ -z $4 ]
+ then
+--- a/test/bp_sr.sh
++++ b/test/bp_sr.sh
+@@ -1,4 +1,4 @@
+-##!/bin/bash
++#!/bin/bash
+
+ if [ -z $5 ]
+ then
=====================================
debian/tests/run-unit-test
=====================================
@@ -26,5 +26,9 @@ sed -i -e 's:\.\./scripts:/usr/share/lumpy-sv/scripts:' \
# Testing lumpy paired-end
# ./bp_pe_pl.sh: line 26 refers to /usr/share/lumpy-sv/scripts/pairend_distro.pl
# but there is only /usr/share/lumpy-sv/scripts/pairend_distro.py ... but with different options
-./test_pl.sh
-# --> contact upstream
\ No newline at end of file
+# ./test_pl.sh
+# FIXME: contact upstream
+
+# FIXME: needs more work
+# cd ../lumpy_tests
+# sh test.sh
View it on GitLab: https://salsa.debian.org/med-team/lumpy-sv/-/compare/3a44f943ef37ae1ee666ff7a9e966adfd2c0e5c5...5b82acc7527a6fbdc763bcc450230fe3822930da
--
View it on GitLab: https://salsa.debian.org/med-team/lumpy-sv/-/compare/3a44f943ef37ae1ee666ff7a9e966adfd2c0e5c5...5b82acc7527a6fbdc763bcc450230fe3822930da
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200603/63315a5f/attachment-0001.html>
More information about the debian-med-commit
mailing list