[med-svn] [Git][med-team/bamkit][master] 4 commits: Use 2to3
Andreas Tille
gitlab at salsa.debian.org
Mon Jun 1 21:17:37 BST 2020
Andreas Tille pushed to branch master at Debian Med / bamkit
Commits:
658e9ec4 by Andreas Tille at 2020-06-01T21:52:24+02:00
Use 2to3
- - - - -
9d4ddd09 by Andreas Tille at 2020-06-01T21:53:41+02:00
No test for the moment
- - - - -
d8fac94e by Andreas Tille at 2020-06-01T22:03:07+02:00
Use python scripts as links
- - - - -
fbe24971 by Andreas Tille at 2020-06-01T22:16:40+02:00
Add manpages
- - - - -
18 changed files:
- − debian/README.test
- + debian/createmanpages
- debian/install
- − debian/lintian-overrides
- + debian/man/bamcleanheader.py.1
- + debian/man/bamfilterrg.py.1
- + debian/man/bamfixflags.py.1
- + debian/man/bamgroupreads.py.1
- + debian/man/bamheadrg.py.1
- + debian/man/bamlibs.py.1
- + debian/man/bamtofastq.py.1
- + debian/manpages
- + debian/patches/2to3.patch
- + debian/patches/series
- debian/rules
- − debian/tests/control
- − debian/tests/run-unit-test
- debian/upstream/metadata
Changes:
=====================================
debian/README.test deleted
=====================================
@@ -1,8 +0,0 @@
-Notes on how this package can be tested.
-────────────────────────────────────────
-
-This package can be tested by running the provided test:
-
- sh run-unit-test
-
-in order to confirm its integrity.
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,64 @@
+#!/bin/sh
+MANDIR=debian/man
+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 $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=bamcleanheader.py
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name="remove illegal and malformed fields from a BAM file's header" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=bamfilterrg.py
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name="filter readgroup(s) from a BAM file" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=bamfixflags.py
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name="filter readgroup(s) from a BAM file" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=bamgroupreads.py
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name="Group BAM file by read IDs without sorting" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=bamheadrg.py
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name="Inject readgroup info" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=bamlibs.py
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name="output comma delimited string of read group IDs for each library" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=bamtofastq.py
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name="Convert a coordinate sorted BAM file to FASTQ" \
+ --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/install
=====================================
@@ -1,2 +1,2 @@
-*.py usr/bin
+*.py usr/share/bamkit
sectosupp usr/bin
=====================================
debian/lintian-overrides deleted
=====================================
@@ -1,2 +0,0 @@
-# see https://lists.debian.org/debian-med/2018/06/msg00043.html
-bamkit: script-with-language-extension usr/bin/*.*
=====================================
debian/man/bamcleanheader.py.1
=====================================
@@ -0,0 +1,24 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH BAMCLEANHEADER.PY "1" "June 2020" "bamcleanheader.py 0.0.1+git20170413.ccd079d" "User Commands"
+.SH NAME
+bamcleanheader.py \- remove illegal and malformed fields from a BAM file's header
+.SH SYNOPSIS
+.B bamcleanheader.py
+[\-h] [\-S] [input [input ...]]
+.SH DESCRIPTION
+remove illegal and malformed fields from a BAM file's header
+.SH OPTIONS
+.SS "positional arguments:"
+.TP
+input
+SAM/BAM file to inject header lines into. If '\-' or absent then defaults to stdin.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-S\fR, \fB\-\-is_sam\fR
+input is SAM
+.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/man/bamfilterrg.py.1
=====================================
@@ -0,0 +1,35 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH BAMFILTERRG.PY "1" "June 2020" "bamfilterrg.py 0.0.1+git20170413.ccd079d" "User Commands"
+.SH NAME
+bamfilterrg.py \- filter readgroup(s) from a BAM file
+.SH SYNOPSIS
+.B bamfilterrg.py
+[\-h] [\-i BAM] [\-r STR] [\-n INT] [\-S] [\-b] [\-u]
+.SH DESCRIPTION
+filter readgroup(s) from a BAM file
+.SH OPTIONS
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-i\fR BAM, \fB\-\-input\fR BAM
+Input BAM file
+.TP
+\fB\-r\fR STR, \fB\-\-readgroup\fR STR
+Read group(s) to extract (comma separated)
+.TP
+\fB\-n\fR INT
+Output first n alignments and quit
+.TP
+\fB\-S\fR
+Input is SAM format
+.TP
+\fB\-b\fR
+Output BAM format
+.TP
+\fB\-u\fR
+Output uncompressed BAM format (implies \fB\-b\fR)
+.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/man/bamfixflags.py.1
=====================================
@@ -0,0 +1,35 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH BAMFIXFLAGS.PY "1" "June 2020" "bamfixflags.py 0.0.1+git20170413.ccd079d" "User Commands"
+.SH NAME
+bamfixflags.py \- filter readgroup(s) from a BAM file
+.SH SYNOPSIS
+.B bamfixflags.py
+[\-h] [\-i BAM] \fB\-l\fR FILE [\-n INT] [\-S] [\-b] [\-u]
+.SH DESCRIPTION
+filter readgroup(s) from a BAM file
+.SH OPTIONS
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-i\fR BAM, \fB\-\-input\fR BAM
+Input BAM file
+.TP
+\fB\-l\fR FILE, \fB\-\-lib_info\fR FILE
+SVTyper JSON file of library information
+.TP
+\fB\-n\fR INT
+Output first n alignments and quit
+.TP
+\fB\-S\fR
+Input is SAM format
+.TP
+\fB\-b\fR
+Output BAM format
+.TP
+\fB\-u\fR
+Output uncompressed BAM format (implies \fB\-b\fR)
+.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/man/bamgroupreads.py.1
=====================================
@@ -0,0 +1,41 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH BAMGROUPREADS.PY "1" "June 2020" "bamgroupreads.py 0.0.1+git20170413.ccd079d" "User Commands"
+.SH NAME
+bamgroupreads.py \- Group BAM file by read IDs without sorting
+.SH SYNOPSIS
+.B bamgroupreads.py
+[\-h] [\-i BAM] [\-r STR] [\-d] [\-f] [\-S] [\-b] [\-u] [\-M]
+.SH DESCRIPTION
+Group BAM file by read IDs without sorting
+.SH OPTIONS
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-i\fR BAM, \fB\-\-input\fR BAM
+Input BAM file
+.TP
+\fB\-r\fR STR, \fB\-\-readgroup\fR STR
+Read group(s) to extract (comma separated)
+.TP
+\fB\-d\fR, \fB\-\-reset_dups\fR
+Reset duplicate flags
+.TP
+\fB\-f\fR, \fB\-\-fix_flags\fR
+Fix mate flags for secondary reads
+.TP
+\fB\-S\fR
+Input is SAM format
+.TP
+\fB\-b\fR
+Output BAM format
+.TP
+\fB\-u\fR
+Output uncompressed BAM format (implies \fB\-b\fR)
+.TP
+\fB\-M\fR
+split reads are flagged as secondary, not supplementary. For compatibility with legacy BWA\-MEM "\-M" flag
+.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/man/bamheadrg.py.1
=====================================
@@ -0,0 +1,30 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH BAMHEADRG.PY "1" "June 2020" "bamheadrg.py 0.0.1+git20170413.ccd079d" "User Commands"
+.SH NAME
+bamheadrg.py \- Inject readgroup info
+.SH SYNOPSIS
+.B bamheadrg.py
+[\-h] [\-r READGROUP] \fB\-d\fR DONOR [\-S] [recipient]
+.SH DESCRIPTION
+Inject readgroup info
+.SH OPTIONS
+.SS "positional arguments:"
+.TP
+recipient
+SAM file to inject header lines into. If '\-' or absent then defaults to stdin.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-r\fR READGROUP, \fB\-\-readgroup\fR READGROUP
+Read group(s) to extract (comma separated)
+.TP
+\fB\-d\fR DONOR, \fB\-\-donor\fR DONOR
+Donor BAM/SAM file to extract read group info
+.TP
+\fB\-S\fR, \fB\-\-donor_is_sam\fR
+Donor file is SAM
+.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/man/bamlibs.py.1
=====================================
@@ -0,0 +1,24 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH BAMLIBS.PY "1" "June 2020" "bamlibs.py 0.0.1+git20170413.ccd079d" "User Commands"
+.SH NAME
+bamlibs.py \- output comma delimited string of read group IDs for each library
+.SH SYNOPSIS
+.B bamlibs.py
+[\-h] [\-S] [input]
+.SH DESCRIPTION
+output comma delimited string of read group IDs for each library
+.SH OPTIONS
+.SS "positional arguments:"
+.TP
+input
+SAM/BAM file to inject header lines into. If '\-' or absent then defaults to stdin.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-S\fR, \fB\-\-is_sam\fR
+input is SAM
+.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/man/bamtofastq.py.1
=====================================
@@ -0,0 +1,34 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH BAMTOFASTQ.PY "1" "June 2020" "bamtofastq.py 0.0.1+git20170413.ccd079d" "User Commands"
+.SH NAME
+bamtofastq.py \- Convert a coordinate sorted BAM file to FASTQ
+.SH SYNOPSIS
+.B bamtofastq.py
+[\-h] [\-r STR] [\-n] [\-S] [\-H FILE] [BAM [BAM ...]]
+.SH DESCRIPTION
+Convert a coordinate sorted BAM file to FASTQ
+(ignores unpaired reads)
+.SH OPTIONS
+.SS "positional arguments:"
+.TP
+BAM
+Input BAM file(s). If absent then defaults to stdin.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-r\fR STR, \fB\-\-readgroup\fR STR
+Read group(s) to extract (comma separated)
+.TP
+\fB\-n\fR, \fB\-\-rename\fR
+Rename reads
+.TP
+\fB\-S\fR, \fB\-\-is_sam\fR
+Input is SAM format
+.TP
+\fB\-H\fR FILE, \fB\-\-header\fR FILE
+Write BAM header to file
+.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/man/*.1
=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,256 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 26 May 2020 15:07:58 +0200
+Description: Use 2to3 t port to Python3
+
+--- a/bamcleanheader.py
++++ b/bamcleanheader.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+
+ import argparse, sys
+ from argparse import RawTextHelpFormatter
+@@ -107,11 +107,11 @@ def bam_clean(bam, is_sam, header_only):
+
+ # out_bam = pysam.Samfile('-', 'w', template=in_bam)
+
+- print get_clean_header(in_bam)
++ print(get_clean_header(in_bam))
+
+ if not header_only:
+ for al in in_bam:
+- print al
++ print(al)
+
+ # # this code leads to pipeing errors
+ # if not header_only:
+@@ -140,6 +140,6 @@ def main():
+ if __name__ == '__main__':
+ try:
+ sys.exit(main())
+- except IOError, e:
++ except IOError as e:
+ if e.errno != 32: # ignore SIGPIPE
+ raise
+--- a/bamfilterrg.py
++++ b/bamfilterrg.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+
+ # for tgi cluster:
+ #/gapp/x64linux/opt/pythonbrew/venvs/Python-2.7.6/gemini/bin/python
+@@ -125,7 +125,7 @@ def main():
+ if __name__ == "__main__":
+ try:
+ sys.exit(main())
+- except IOError, e:
++ except IOError as e:
+ if e.errno != 32: # ignore SIGPIPE
+ raise
+
+--- a/bamfixflags.py
++++ b/bamfixflags.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+
+ # for tgi cluster:
+ #/gapp/x64linux/opt/pythonbrew/venvs/Python-2.7.6/gemini/bin/python
+@@ -121,16 +121,16 @@ def bamfixflags(bamfile,
+ for sample in lib_info:
+ # print lib_info[sample]['libraryArray'][0]
+ for lib in lib_info[sample]['libraryArray']:
+- lib_hist = {int(k):int(v) for k,v in lib['histogram'].items()}
++ lib_hist = {int(k):int(v) for k,v in list(lib['histogram'].items())}
+ p25 = percentile(lib_hist, 25)
+ p75 = percentile(lib_hist, 75)
+ lib_mean = mean(lib_hist)
+ lib_sd = stdev(lib_hist)
+
+- print 'p25', p25
+- print 'p75', p75
+- print 'mean', lib_mean
+- print 'sd', lib_sd
++ print('p25', p25)
++ print('p75', p75)
++ print('mean', lib_mean)
++ print('sd', lib_sd)
+
+ low = int(p25 - mapping_bound * (p75 - p25) + .499)
+ high = int(p75 + mapping_bound * (p75 - p25) + .499)
+@@ -171,49 +171,49 @@ def bamfixflags(bamfile,
+ else:
+ out_bam = pysam.Samfile('-', 'wh', template=in_bam)
+
+- print proper
++ print(proper)
+ for al in in_bam:
+ # out_bam.write(al)
+- print al
++ print(al)
+
+ if al.is_supplementary:
+ pass
+
+ elif al.is_unmapped or al.mate_is_unmapped:
+ if al.is_proper_pair:
+- print 'mismarked proper (unmapped)'
++ print('mismarked proper (unmapped)')
+ al.is_proper_pair = False
+
+ elif al.reference_id != al.next_reference_id:
+ if al.is_proper_pair:
+- print 'mismarked proper (chrom)'
++ print('mismarked proper (chrom)')
+ al.is_proper_pair = False
+
+ elif (al.reference_start < al.next_reference_start
+ and (al.is_reverse or not al.mate_is_reverse)):
+ if al.is_proper_pair:
+- print 'mismarked proper (orient +)'
++ print('mismarked proper (orient +)')
+ al.is_proper_pair = False
+
+ elif (al.reference_start > al.next_reference_start
+ and (not al.is_reverse or al.mate_is_reverse)):
+ if al.is_proper_pair:
+- print 'mismarked proper (orient -)'
++ print('mismarked proper (orient -)')
+ al.is_proper_pair = False
+
+ # if al.supp
+ elif (al.template_length >= proper[al.opt('RG')][0]
+ and al.template_length <= proper[al.opt('RG')][1]):
+ if not al.is_proper_pair:
+- print 'mismarked improper (insert size)'
++ print('mismarked improper (insert size)')
+ al.is_proper_pair = True
+ else:
+ if al.is_proper_pair:
+- print 'mismarked proper (insert size)'
++ print('mismarked proper (insert size)')
+ al.is_proper_pair = False
+
+ # out_bam.write(al)
+- print al
++ print(al)
+ # print proper[al.opt('RG')], al.template_length
+ # print al
+ # # must be in a user specified readgroup
+@@ -301,7 +301,7 @@ def main():
+ if __name__ == "__main__":
+ try:
+ sys.exit(main())
+- except IOError, e:
++ except IOError as e:
+ if e.errno != 32: # ignore SIGPIPE
+ raise
+
+--- a/bamgroupreads.py
++++ b/bamgroupreads.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+
+ # for tgi cluster:
+ #/gapp/x64linux/opt/pythonbrew/venvs/Python-2.7.6/gemini/bin/python
+@@ -169,7 +169,7 @@ def main():
+ if __name__ == "__main__":
+ try:
+ sys.exit(main())
+- except IOError, e:
++ except IOError as e:
+ if e.errno != 32: # ignore SIGPIPE
+ raise
+
+--- a/bamheadrg.py
++++ b/bamheadrg.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+
+ import argparse, sys
+ from argparse import RawTextHelpFormatter
+@@ -71,9 +71,9 @@ def bamheadrg(recipient, rg_out):
+ if in_header:
+ if line[0] != '@':
+ for readgroup in rg_out:
+- print '@RG\t' + '\t'.join([':'.join((t,readgroup[t])) for t in readgroup])
++ print('@RG\t' + '\t'.join([':'.join((t,readgroup[t])) for t in readgroup]))
+ in_header = False
+- print line.rstrip()
++ print(line.rstrip())
+ return
+
+ # --------------------------------------
+@@ -101,6 +101,6 @@ def main():
+ if __name__ == '__main__':
+ try:
+ sys.exit(main())
+- except IOError, e:
++ except IOError as e:
+ if e.errno != 32: # ignore SIGPIPE
+ raise
+--- a/bamlibs.py
++++ b/bamlibs.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+
+ import argparse, sys
+ from argparse import RawTextHelpFormatter
+@@ -58,7 +58,7 @@ def get_libs(bam, is_sam, header_only):
+
+ # print
+ for lib in lib_rg:
+- print ','.join(lib_rg[lib])
++ print(','.join(lib_rg[lib]))
+ in_bam.close()
+
+ return
+@@ -77,6 +77,6 @@ def main():
+ if __name__ == '__main__':
+ try:
+ sys.exit(main())
+- except IOError, e:
++ except IOError as e:
+ if e.errno != 32: # ignore SIGPIPE
+ raise
+--- a/bamtofastq.py
++++ b/bamtofastq.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+
+ # for tgi cluster:
+ #/gapp/x64linux/opt/pythonbrew/venvs/Python-2.7.6/gemini/bin/python
+@@ -131,15 +131,15 @@ description: Convert a coordinate sorted
+
+ def printfastq(al,read):
+ if(al.is_reverse):
+- print "@" + str(al.qname) + "/" + str(read) + "\n" + str(revcomp(al.seq)) + "\n" + "+" + "\n" + str(al.qual[::-1])
++ print("@" + str(al.qname) + "/" + str(read) + "\n" + str(revcomp(al.seq)) + "\n" + "+" + "\n" + str(al.qual[::-1]))
+ else:
+- print "@" + str(al.qname) + "/" + str(read) + "\n" + str(al.seq) + "\n" + "+" + "\n" + str(al.qual)
++ print("@" + str(al.qname) + "/" + str(read) + "\n" + str(al.seq) + "\n" + "+" + "\n" + str(al.qual))
+
+ def printfastq_rg(al,read, rg):
+ if(al.is_reverse):
+- print "@" + str(al.qname) + "/" + str(read) + " " + "RG:Z:" + str(rg) + "\n" + str(revcomp(al.seq)) + "\n" + "+" + "\n" + str(al.qual[::-1])
++ print("@" + str(al.qname) + "/" + str(read) + " " + "RG:Z:" + str(rg) + "\n" + str(revcomp(al.seq)) + "\n" + "+" + "\n" + str(al.qual[::-1]))
+ else:
+- print "@" + str(al.qname) + "/" + str(read) + " " + "RG:Z:" + str(rg) + "\n" + str(al.seq) + "\n" + "+" + "\n" + str(al.qual)
++ print("@" + str(al.qname) + "/" + str(read) + " " + "RG:Z:" + str(rg) + "\n" + str(al.seq) + "\n" + "+" + "\n" + str(al.qual))
+
+ def revcomp(seq):
+ seq1 = seq.translate(maketrans("AGCTagct", "TCGAtcga"))
+@@ -166,7 +166,7 @@ def main():
+ if __name__ == "__main__":
+ try:
+ sys.exit(main())
+- except IOError, e:
++ except IOError as e:
+ if e.errno != 32: # ignore SIGPIPE
+ raise
+
=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+2to3.patch
=====================================
debian/rules
=====================================
@@ -8,6 +8,15 @@ include /usr/share/dpkg/default.mk
%:
dh $@ --with python3
+override_dh_link:
+ dh_link
+ for py in debian/$(DEB_SOURCE)/usr/share/$(DEB_SOURCE)/*.py ; do \
+ dh_link `echo $${py} | sed 's:^debian/$(DEB_SOURCE)::'` usr/bin/`basename $${py}` ; \
+ done
+
+override_dh_installman:
+ dh_installman --language=C
+
### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
#override_dh_auto_test:
#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
=====================================
debian/tests/control deleted
=====================================
@@ -1,3 +0,0 @@
-Tests: run-unit-test
-Depends: @
-Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test deleted
=====================================
@@ -1,19 +0,0 @@
-#!/bin/bash
-set -e
-
-pkg=#PACKAGENAME#
-
-export LC_ALL=C.UTF-8
-if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
- AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
- # Double quote below to expand the temporary directory variable now versus
- # later is on purpose.
- # shellcheck disable=SC2064
- trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
-fi
-
-cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
-
-cd "${AUTOPKGTEST_TMP}"
-
-#do_stuff_to_test_package#
=====================================
debian/upstream/metadata
=====================================
@@ -1,15 +1,3 @@
-Reference:
- Author:
- Title:
- Journal:
- Year:
- Volume:
- Number:
- Pages:
- DOI:
- PMID:
- URL:
- eprint:
Registry:
- Name: conda:bioconda
- Entry:
+ Entry: NA
View it on GitLab: https://salsa.debian.org/med-team/bamkit/-/compare/e92c0a3e1f1591a597cfd69a51f9d0fa916e1014...fbe2497195abd1060c69dcf00fe56558cd93d154
--
View it on GitLab: https://salsa.debian.org/med-team/bamkit/-/compare/e92c0a3e1f1591a597cfd69a51f9d0fa916e1014...fbe2497195abd1060c69dcf00fe56558cd93d154
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