debian/changelog

+sambamba (0.7.1-2) UNRELEASED; urgency=medium
+
+  * Use 2to3 to port from Python2 to Python3
+    Closes: #938431
+  * Set upstream metadata fields: Repository, Repository-Browse.
+
+ -- Andreas Tille <tille@debian.org>  Tue, 17 Dec 2019 21:03:13 +0100
+
 sambamba (0.7.1-1) unstable; urgency=medium
 
   [ Andreas Tille ]

debian/patches/02_disable-assert.patch

@@ -4,9 +4,9 @@ Author: Gianfranco Costamagna <locutusofborg@debian.org>
 Bug-Debian: https://bugs.debian.org/893664
 Last-Update: 2018-03-21
 
---- sambamba-0.6.7.orig/sambamba/markdup.d
-+++ sambamba-0.6.7/sambamba/markdup.d
-@@ -606,7 +606,7 @@ struct PairedEndsInfo {
+--- a/sambamba/markdup.d
++++ b/sambamba/markdup.d
+@@ -610,7 +610,7 @@ struct PairedEndsInfo {
      }
  }
  

debian/patches/2to3.patch

+Description: Use 2to3 to port from Python2 to Python3
+Bug-Debian: https://bugs.debian.org/938431 
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Tue, 17 Dec 2019 21:03:13 +0100
+
+--- a/INSTALL.md
++++ b/INSTALL.md
+@@ -15,12 +15,12 @@
+ After checking out the source from github with git submodules is is
+ possibleto install the build tools with GNU Guix
+ 
+-    guix package -i gcc-toolchain gdb bash ld-wrapper ldc which python2 git
++    guix package -i gcc-toolchain gdb bash ld-wrapper ldc which python3 git
+ 
+ Even better, with Guix, you can create a light-weight container in the source tree
+ and run our development setup (gold was added lately by ldc)
+ 
+-    guix environment -C guix --ad-hoc gcc-toolchain gdb bash ld-wrapper ldc which python git binutils-gold vim
++    guix environment -C guix --ad-hoc gcc-toolchain gdb bash ld-wrapper ldc which python3 git binutils-gold vim
+     make clean
+     make -j 4
+     make check
+--- a/RELEASE-NOTES.md
++++ b/RELEASE-NOTES.md
+@@ -69,7 +69,7 @@ Generation 3    Sep 25 2018 09:39:08
+     branch: origin/master
+     commit: 932839ff124ff3b0dd3070914fb1c5beec69bf32
+ 
+-guix environment -C guix --ad-hoc gcc gdb bash ld-wrapper ldc which python git
++guix environment -C guix --ad-hoc gcc gdb bash ld-wrapper ldc which python3 git
+ make clean && make -j 16 && make check
+ 
+ for x in `ldd bin/sambamba|cut -d ' ' -f 3` ; do realpath $x ; done
+--- a/gen_ldc_version_info.py
++++ b/gen_ldc_version_info.py
+@@ -1,6 +1,6 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
++
+ 
+-from __future__ import print_function
+ import re, sys, subprocess
+ 
+ if len(sys.argv) < 2:
+@@ -16,7 +16,7 @@ if not match:
+     sys.exit("ERROR: failed to generated LDC version information")
+ 
+ print("module utils.ldc_version_info_;")
+-for component, version in match.groupdict().items():
++for component, version in list(match.groupdict().items()):
+     if version is None:
+         version = "version not available"
+     print("immutable {0}_VERSION_STRING = \"{1}\";".format(component, version))
+--- a/scripts/bioconda_push.sh
++++ b/scripts/bioconda_push.sh
+@@ -2,7 +2,7 @@ RECIPES=~/github/bioconda-recipes # loca
+ REMOTE=bioconda                   # bioconda/bioconda-recipes remote
+ 
+ UPDATED_RECIPE=/tmp/sambamba.yaml
+-python bioconda_yaml_gen.py > $UPDATED_RECIPE
++python3 bioconda_yaml_gen.py > $UPDATED_RECIPE
+ VERSION=`grep version $UPDATED_RECIPE | cut -d\' -f2`
+ 
+ cd $RECIPES
+--- a/scripts/bioconda_yaml_gen.py
++++ b/scripts/bioconda_yaml_gen.py
+@@ -28,7 +28,7 @@ about:
+   summary: Tools for working with SAM/BAM data"""
+ 
+ import json
+-from urllib2 import urlopen
++from urllib.request import urlopen
+ from hashlib import md5
+ 
+ latest_release = json.loads(urlopen("https://api.github.com/repos/biod/sambamba/releases").read())[0]
+@@ -48,7 +48,7 @@ def md5sum(download):
+ linux_md5 = md5sum(downloads['linux'])
+ osx_md5 = md5sum(downloads['osx'])
+ 
+-print template.format(version=sambamba_version, 
++print(template.format(version=sambamba_version, 
+                 linux_url=downloads['linux'], 
+                 osx_url=downloads['osx'],
+-                linux_md5=linux_md5, osx_md5=osx_md5)
++                linux_md5=linux_md5, osx_md5=osx_md5))
+--- a/test/test_depth.py
++++ b/test/test_depth.py
+@@ -14,7 +14,7 @@ def referenceSequences(bam_fn):
+     return {item['SN']: item['LN'] for item in msgpack.unpackb(header)[2]}
+ 
+ def randomIntervals(ref_seqs, n, max_length=1000):
+-    keys = ref_seqs.keys()
++    keys = list(ref_seqs.keys())
+     result = []
+     for i in range(n):
+         overlap = i > 0 and random.randint(1, 100) <= 20
+@@ -95,14 +95,14 @@ def compareResults(report, expected, pre
+                 fn_expected = prefix + "expected_report.txt"
+                 saveRegionReport(report, fn_failed)
+                 saveRegionReport(expected, fn_expected)
+-                print 'TEST FAILURE'
+-                print "results saved to " + fn_expected + " and " + fn_failed
+-            print "different results:"
+-            print "expected: ", expected_entry
+-            print "got: ", entry
++                print('TEST FAILURE')
++                print("results saved to " + fn_expected + " and " + fn_failed)
++            print("different results:")
++            print("expected: ", expected_entry)
++            print("got: ", entry)
+             n_wrong += 1
+             if n_wrong >= 10:
+-                print "10 or more errors detected, exiting"
++                print("10 or more errors detected, exiting")
+                 break
+         else:
+             n_correct += 1

debian/patches/series

 01_add-meson-build.patch
 02_disable-assert.patch
+2to3.patch

debian/upstream/metadata

 Reference:
- Author: >
-  Artem Tarasov and Albert J. Vilella and Edwin Cuppen and Isaac
-  J. Nijman and Pjotr Prins
- Title: "Sambamba: fast processing of NGS alignment formats"
- Journal: Bioinformatics
- Year: 2015
- Volume: 31
- Number: 12
- Pages: 2032-2034
- DOI: 10.1093/bioinformatics/btv098
- PMID: 25697820
- URL: "https://academic.oup.com/bioinformatics/article-lookup/doi/\
-  10.1093/bioinformatics/btv098"
- eprint: "https://academic.oup.com/bioinformatics/article-pdf/\
-  31/12/2032/568750/btv098.pdf"
+  Author: >
+    Artem Tarasov and Albert J. Vilella and Edwin Cuppen and Isaac
+    J. Nijman and Pjotr Prins
+  Title: 'Sambamba: fast processing of NGS alignment formats'
+  Journal: Bioinformatics
+  Year: 2015
+  Volume: 31
+  Number: 12
+  Pages: 2032-2034
+  DOI: 10.1093/bioinformatics/btv098
+  PMID: 25697820
+  URL: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btv098
+  eprint: https://academic.oup.com/bioinformatics/article-pdf/31/12/2032/568750/btv098.pdf
 Registry:
- - Name: bio.tools
-   Entry: Sambamba
- - Name: OMICtools
-   Entry: OMICS_07586
- - Name: SciCrunch
-   Entry: NA
- - Name: conda:bioconda
-   Entry: sambamba
+- Name: bio.tools
+  Entry: Sambamba
+- Name: OMICtools
+  Entry: OMICS_07586
+- Name: SciCrunch
+  Entry: NA
+- Name: conda:bioconda
+  Entry: sambamba
+Repository: https://github.com/lomereiter/sambamba.git
+Repository-Browse: https://github.com/lomereiter/sambamba