[med-svn] r23625 - in trunk/packages/seqprep/trunk/debian: . patches tests

Andreas Tille tille at moszumanska.debian.org
Tue Jan 17 18:09:02 UTC 2017 

Author: tille
Date: 2017-01-17 18:09:00 +0000 (Tue, 17 Jan 2017)
New Revision: 23625

Modified:
   trunk/packages/seqprep/trunk/debian/changelog
   trunk/packages/seqprep/trunk/debian/compat
   trunk/packages/seqprep/trunk/debian/control
   trunk/packages/seqprep/trunk/debian/copyright
   trunk/packages/seqprep/trunk/debian/patches/fix_unused_variable_errors.patch
   trunk/packages/seqprep/trunk/debian/patches/replace-float-with-double.patch
   trunk/packages/seqprep/trunk/debian/tests/run-unit-test
Log:
  * New upstream version
  * debhelper 10
  * d/watch: version=4


Modified: trunk/packages/seqprep/trunk/debian/changelog
===================================================================
--- trunk/packages/seqprep/trunk/debian/changelog	2017-01-17 10:39:34 UTC (rev 23624)
+++ trunk/packages/seqprep/trunk/debian/changelog	2017-01-17 18:09:00 UTC (rev 23625)
@@ -1,3 +1,11 @@
+seqprep (1.3.2-1) unstable; urgency=medium
+
+  * New upstream version
+  * debhelper 10
+  * d/watch: version=4
+
+ -- Andreas Tille <tille at debian.org>  Tue, 17 Jan 2017 18:24:59 +0100
+
 seqprep (1.2-1) unstable; urgency=medium
 
   * New upstream version

Modified: trunk/packages/seqprep/trunk/debian/compat
===================================================================
--- trunk/packages/seqprep/trunk/debian/compat	2017-01-17 10:39:34 UTC (rev 23624)
+++ trunk/packages/seqprep/trunk/debian/compat	2017-01-17 18:09:00 UTC (rev 23625)
@@ -1 +1 @@
-9
+10

Modified: trunk/packages/seqprep/trunk/debian/control
===================================================================
--- trunk/packages/seqprep/trunk/debian/control	2017-01-17 10:39:34 UTC (rev 23624)
+++ trunk/packages/seqprep/trunk/debian/control	2017-01-17 18:09:00 UTC (rev 23625)
@@ -4,7 +4,7 @@
            Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 10),
                python,
                python-markdown,
                ruby-ronn,

Modified: trunk/packages/seqprep/trunk/debian/copyright
===================================================================
--- trunk/packages/seqprep/trunk/debian/copyright	2017-01-17 10:39:34 UTC (rev 23624)
+++ trunk/packages/seqprep/trunk/debian/copyright	2017-01-17 18:09:00 UTC (rev 23625)
@@ -1,14 +1,15 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: SeqPrep
 Upstream-Contact: jstjohn at soe.ucsc.edu
 Source: https://github.com/jstjohn/SeqPrep
 
 Files: *
-Copyright: (C) 2011 by John St. John
+Copyright: (C) 2011-2017 by John St. John
 License: MIT
 
 Files: debian/*
 Copyright: (C) 2015 Tim Booth <tbooth at ceh.ac.uk>
+               2015-2017 Andreas Tille <tille at debian.org>
 License: MIT
 
 License: MIT

Modified: trunk/packages/seqprep/trunk/debian/patches/fix_unused_variable_errors.patch
===================================================================
--- trunk/packages/seqprep/trunk/debian/patches/fix_unused_variable_errors.patch	2017-01-17 10:39:34 UTC (rev 23624)
+++ trunk/packages/seqprep/trunk/debian/patches/fix_unused_variable_errors.patch	2017-01-17 18:09:00 UTC (rev 23625)
@@ -5,7 +5,7 @@
 
 --- a/SeqPrep.c
 +++ b/SeqPrep.c
-@@ -68,7 +68,7 @@ void help ( char *prog_name ) {
+@@ -69,7 +69,7 @@ void help ( char *prog_name ) {
    fprintf(stderr, "\t-z <use mask; N will replace adapters>\n");
    fprintf(stderr, "Optional Arguments for Merging:\n" );
    fprintf(stderr, "\t-y <maximum quality score in output ((phred 33) default = '%c' )>\n", maximum_quality );
@@ -14,7 +14,7 @@
    fprintf(stderr, "\t-s <perform merging and output the merged reads to this file>\n" );
    fprintf(stderr, "\t-E <write pretty alignments to this file for visual Examination>\n" );
    fprintf(stderr, "\t-x <max number of pretty alignments to write (if -E provided); default = %d>\n", DEF_MAX_PRETTY_PRINT );
-@@ -120,7 +120,7 @@ int main( int argc, char* argv[] ) {
+@@ -121,7 +121,7 @@ int main( int argc, char* argv[] ) {
    char reverse_discard_fn[MAX_FN_LEN];
    char merged_out_fn[MAX_FN_LEN];
    bool do_read_merging = false;
@@ -23,7 +23,7 @@
    bool write_discard=false;
    bool use_mask=false;
    char forward_primer[MAX_SEQ_LEN+1];
-@@ -261,7 +261,8 @@ int main( int argc, char* argv[] ) {
+@@ -266,7 +266,8 @@ int main( int argc, char* argv[] ) {
        maximum_quality = optarg[0];
        break;
      case 'g' :

Modified: trunk/packages/seqprep/trunk/debian/patches/replace-float-with-double.patch
===================================================================
--- trunk/packages/seqprep/trunk/debian/patches/replace-float-with-double.patch	2017-01-17 10:39:34 UTC (rev 23624)
+++ trunk/packages/seqprep/trunk/debian/patches/replace-float-with-double.patch	2017-01-17 18:09:00 UTC (rev 23625)
@@ -5,7 +5,7 @@
 
 --- a/SeqPrep.c
 +++ b/SeqPrep.c
-@@ -138,12 +138,12 @@ int main( int argc, char* argv[] ) {
+@@ -139,12 +139,12 @@ int main( int argc, char* argv[] ) {
    int min_ol_adapter = DEF_OL2MERGE_ADAPTER;
    int min_ol_reads = DEF_OL2MERGE_READS;
    unsigned short int min_read_len =DEF_MIN_READ_LEN;
@@ -23,7 +23,7 @@
    unsigned short max_mismatch_adapter[MAX_SEQ_LEN+1];
    unsigned short max_mismatch_reads[MAX_SEQ_LEN+1];
    unsigned short min_match_adapter[MAX_SEQ_LEN+1];
-@@ -307,10 +307,10 @@ int main( int argc, char* argv[] ) {
+@@ -312,10 +312,10 @@ int main( int argc, char* argv[] ) {
  
    //Calculate table matching overlap length to min matches and max mismatches
    for(i=0;i<MAX_SEQ_LEN+1;i++){

Modified: trunk/packages/seqprep/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/seqprep/trunk/debian/tests/run-unit-test	2017-01-17 10:39:34 UTC (rev 23624)
+++ trunk/packages/seqprep/trunk/debian/tests/run-unit-test	2017-01-17 18:09:00 UTC (rev 23625)
@@ -3,6 +3,7 @@
 pkg=seqprep
 if [ "$ADTTMP" = "" ] ; then
   ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+  trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
 fi
 cd $ADTTMP
 cp -a /usr/share/doc/${pkg}/examples/* .
@@ -15,5 +16,3 @@
     echo "Test failed"
     exit 1
 fi
-
-rm -fr $ADTTMP/*

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