[med-svn] [Git][med-team/allelecount][master] 6 commits: New upstream version 4.2.0

[Nilesh Patra]

Nilesh Patra pushed to branch master at Debian Med / allelecount


Commits:
385b4b73 by Nilesh Patra at 2020-10-03T20:36:21+05:30
New upstream version 4.2.0
- - - - -
abc39e75 by Nilesh Patra at 2020-10-03T20:36:21+05:30
routine-update: New upstream version

- - - - -
aec5af90 by Nilesh Patra at 2020-10-03T20:36:26+05:30
Update upstream source from tag 'upstream/4.2.0'

Update to upstream version '4.2.0'
with Debian dir f768b94517fe5f4dbd1a5d5dabaf3c1858915a6f
- - - - -
1c5e7e18 by Nilesh Patra at 2020-10-03T20:36:26+05:30
routine-update: debhelper-compat 13

- - - - -
41da495c by Nilesh Patra at 2020-10-03T20:36:32+05:30
routine-update: Ready to upload to unstable

- - - - -
1192ebec by Nilesh Patra at 2020-10-03T20:59:48+05:30
Add autopkgtests

- - - - -


7 changed files:

- CHANGES.md
- debian/changelog
- debian/control
- + debian/tests/control
- + debian/tests/run-unit-test
- perl/lib/Sanger/CGP/AlleleCount.pm
- setup.sh


Changes:

=====================================
CHANGES.md
=====================================
@@ -1,5 +1,9 @@
 # CHANGES
 
+## v4.2.0
+
+* Updated to hstlib 1.11
+
 ## v4.1.0
 
 * Created Docker file and build scripts to generate a containeraized code


=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+allelecount (4.2.0-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * debhelper-compat 13 (routine-update)
+  * Add autopkgtests
+
+ -- Nilesh Patra <npatra974 at gmail.com>  Sat, 03 Oct 2020 20:36:32 +0530
+
 allelecount (4.1.0-3) unstable; urgency=medium
 
   * Just use Build-Depends to enable build time testing


=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
 Testsuite: autopkgtest-pkg-perl
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
                libhts-dev,
                libbz2-dev,
                libconst-fast-perl <!nocheck>,


=====================================
debian/tests/control
=====================================
@@ -0,0 +1,4 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
+


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,26 @@
+#!/bin/bash
+set -e
+
+CUR_DIR=`pwd`
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cd "${AUTOPKGTEST_TMP}"
+cp -a ${CUR_DIR}/testData/* .
+
+echo "Testing C binary"
+alleleCounter -l test10X.loci -b test10X.bam -o test1 -m 2 -r test10X.bam.bai
+echo "PASS"
+
+echo "Test Perl counterpart"
+alleleCounter.pl -l test10X.loci -b test10X.bam -o test2 -m 2 -r test10X.bam.bai
+echo "PASS"
+
+echo "Check if both are same"
+diff -u test1 test2
+rm -f ./test1 ./test2
+echo "PASS"
+


=====================================
perl/lib/Sanger/CGP/AlleleCount.pm
=====================================
@@ -25,7 +25,7 @@ package Sanger::CGP::AlleleCount;
 use strict;
 
 use base 'Exporter';
-our $VERSION = '4.1.0';
+our $VERSION = '4.2.0';
 our @EXPORT = qw($VERSION);
 
 1;


=====================================
setup.sh
=====================================
@@ -21,7 +21,7 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 ##########LICENCE##########
 
-SOURCE_HTSLIB="https://github.com/samtools/htslib/releases/download/1.7/htslib-1.7.tar.bz2"
+SOURCE_HTSLIB="https://github.com/samtools/htslib/releases/download/1.11/htslib-1.11.tar.bz2"
 
 EXP_SAMV="1.3.1"
 



View it on GitLab: https://salsa.debian.org/med-team/allelecount/-/compare/de01c3599424c27358cb4daac8540b34c967ea3a...1192ebec65645b291a8ea20b305137bb63edce80

-- 
View it on GitLab: https://salsa.debian.org/med-team/allelecount/-/compare/de01c3599424c27358cb4daac8540b34c967ea3a...1192ebec65645b291a8ea20b305137bb63edce80
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