[med-svn] [subread] 03/04: d/changelog: new upstream version d/patches: refresh and remove applied patches d/filter.pl: drop $_ as it is the default anyway

[Alex Mestiashvili]

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malex-guest pushed a commit to branch master
in repository subread.

commit ab3327ceb6e20ff5459841f34f8de159ff2f6be9
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Tue Jan 5 16:01:25 2016 +0100

    d/changelog: new upstream version
    d/patches: refresh and remove applied patches
    d/filter.pl: drop $_ as it is the default anyway
---
 debian/changelog                      |  7 +++++++
 debian/filter.pl                      | 24 ++++++++++++------------
 debian/patches/fix_repair_usage.patch | 13 -------------
 debian/patches/series                 |  1 -
 debian/patches/syntax_err.patch       |  2 +-
 5 files changed, 20 insertions(+), 27 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index a0400cc..df35130 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+subread (1.5.0-p1+dfsg-1) UNRELEASED; urgency=medium
+
+  * Imported Upstream version 1.5.0-p1+dfsg
+  * d/patches: refresh and remove applied patches
+
+ -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Tue, 05 Jan 2016 15:58:47 +0100
+
 subread (1.5.0+dfsg-1) unstable; urgency=medium
 
   * Imported Upstream version 1.5.0+dfsg
diff --git a/debian/filter.pl b/debian/filter.pl
index b4f824d..d87d3ec 100755
--- a/debian/filter.pl
+++ b/debian/filter.pl
@@ -19,23 +19,23 @@ while ( <STDIN> ) {
     #multiline regex
     undef $/;
     # remove colon from the name
-    $_ =~ s/(\.TH\s([\w\d-]*)):/$1/gmxs;
+    s/(\.TH\s([\w\d-]*)):/$1/gmxs;
     # substitude unrecognized version string with the version
-    $_ =~ s/([\w\d]*)\:\sunrecognized\soption\s\'--version\'/$1 $version/g;
-    $_ =~ s/([\w\d]*)\:\sunrecognized\soption\s\'\\-\\-version\'/ $version/g;
+    s/([\w\d]*)\:\sunrecognized\soption\s\'--version\'/$1 $version/g;
+    s/([\w\d]*)\:\sunrecognized\soption\s\'\\-\\-version\'/ $version/g;
     # there are no invalid options
-    $_ =~ s/([\w\d]*)\:\sinvalid\soption\s--\s\'-\'/$1 $version/g;
+    s/([\w\d]*)\:\sinvalid\soption\s--\s\'-\'/$1 $version/g;
     # strip the header or duplicated body of coverageCount
-    $_ =~ s/\.SH\s(DESCRIPTION|SYNOPSIS).*(Usage:\"?|genome\.\n\.PP)/.SH USAGE\n/gmxs;
+    s/\.SH\s(DESCRIPTION|SYNOPSIS).*(Usage:\"?|genome\.\n\.PP)/.SH USAGE\n/gmxs;
     # strip full path
-    $_ =~ s/\\fI\\,\/.*\/bin(\/utilities)?\///gmxs;
+    s/\\fI\\,\/.*\/bin(\/utilities)?\///gmxs;
     # tidy up help2man removeDuP output:
-    $_ =~ s/Repeated\sRead\sRemoval.*accessible:\s\'\'//xms;
-    $_ =~ s/(.SH\sNAME\n[\w\d-]*):/$1/gxms;
+    s/Repeated\sRead\sRemoval.*accessible:\s\'\'//xms;
+    s/(.SH\sNAME\n[\w\d-]*):/$1/gxms;
     # remove "./" from examples 
-    $_ =~ s/(\\\&\.\/)([\w\d-]*)/$2/gxms;
+    s/(\\\&\.\/)([\w\d-]*)/$2/gxms;
     # remove indent and "boldify" the name
-    $_ =~ s/(\.SH\sUSAGE\n*)(\.IP\n|\s|\.TP\n)([\w\d\\-]*)/$1\\fB$3\\fR/xms;
-    $_ =~ s/removeDup\\\\fR\/\\fP/removeDup\\fR/gmxs;
-    print $_;
+    s/(\.SH\sUSAGE\n*)(\.IP\n|\s|\.TP\n)([\w\d\\-]*)/$1\\fB$3\\fR/xms;
+    s/removeDup\\\\fR\/\\fP/removeDup\\fR/gmxs;
+    print;
 }
diff --git a/debian/patches/fix_repair_usage.patch b/debian/patches/fix_repair_usage.patch
deleted file mode 100644
index ea033ef..0000000
--- a/debian/patches/fix_repair_usage.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Description: fix usage string, replace removeDup with repair
-Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
---- subread.orig/src/read-repair.c
-+++ subread/src/read-repair.c
-@@ -16,7 +16,7 @@
- 	SUBREADputs("");
- 	SUBREADputs("Usage:");
- 	SUBREADputs("");
--	SUBREADputs("  ./removeDup [options] -i <input_file> -o <output_file>\n");
-+	SUBREADputs("  ./repair [options] -i <input_file> -o <output_file>\n");
- 	SUBREADputs("");
- 	SUBREADputs("Required arguments:");
- 	SUBREADputs("");
diff --git a/debian/patches/series b/debian/patches/series
index fc3be28..98d6178 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,2 @@
 syntax_err.patch
-fix_repair_usage.patch
 arch_specific_flags.patch
diff --git a/debian/patches/syntax_err.patch b/debian/patches/syntax_err.patch
index ca21aba..41b12ef 100644
--- a/debian/patches/syntax_err.patch
+++ b/debian/patches/syntax_err.patch
@@ -2,7 +2,7 @@ Description: spelling-error-in-binary featureCounts s/requried/required/
 Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 --- subread.orig/src/readSummary.c
 +++ subread/src/readSummary.c
-@@ -3368,7 +3368,7 @@
+@@ -3427,7 +3427,7 @@
  	SUBREADputs("  --largestOverlap    Assign reads to a meta-feature/feature that has the ");
  	SUBREADputs("                      largest number of overlapping bases.");
  	SUBREADputs("");

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