[med-svn] [Git][med-team/bowtie2][master] Update patches/no_sanity and quilt refresh all

Charles Plessy (@plessy) gitlab at salsa.debian.org
Tue Apr 16 00:58:09 BST 2024 


Charles Plessy pushed to branch master at Debian Med / bowtie2


Commits:
335de96e by Charles Plessy at 2024-04-16T08:57:42+09:00
Update patches/no_sanity and quilt refresh all

- - - - -


10 changed files:

- debian/patches/correct_64bit_test
- debian/patches/do-not-rebuild-during-test.patch
- debian/patches/drop-not-needed-js-from-manual.patch
- debian/patches/hardening.patch
- debian/patches/no_sanity
- debian/patches/reproducible.patch
- debian/patches/simde
- debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch
- debian/patches/use-source-date-epoch-in-Makefile.patch
- debian/patches/wrong-interpreter-path.patch


Changes:

=====================================
debian/patches/correct_64bit_test
=====================================
@@ -3,7 +3,7 @@ Description: Handle -m64 and -msse2 flags better
 Forwarded: not-needed
 --- a/Makefile
 +++ b/Makefile
-@@ -67,10 +67,9 @@ ifneq (,$(findstring Darwin,$(shell unam
+@@ -72,10 +72,9 @@
    endif
  endif
  
@@ -17,7 +17,7 @@ Forwarded: not-needed
    ifeq (1, $(SSE_AVX2))
  	SSE_FLAG := -mavx2 -faligned-new -DSSE_AVX2
    else
-@@ -78,11 +77,8 @@ ifneq (,$(findstring $(ARCH), x86_64 amd
+@@ -83,11 +82,8 @@
    endif
  
    POPCNT_CAPABILITY ?= 1


=====================================
debian/patches/do-not-rebuild-during-test.patch
=====================================
@@ -3,8 +3,8 @@ Description: do not rebuild with default settings during test
  flags, while is needs to be built with the flags in d/rules.
 Author: Sascha Steinbiss <satta at debian.org>
 Forwarded: not-needed
---- bowtie2.orig/scripts/sim/run.sh
-+++ bowtie2/scripts/sim/run.sh
+--- a/scripts/sim/run.sh
++++ b/scripts/sim/run.sh
 @@ -21,17 +21,17 @@
  
  CPUS=$1
@@ -34,8 +34,8 @@ Forwarded: not-needed
  perl scripts/sim/run.pl \
  	--bowtie2=./bowtie2 \
  	--bowtie2-build=./bowtie2-build \
---- bowtie2.orig/scripts/test/simple_tests.sh
-+++ bowtie2/scripts/test/simple_tests.sh
+--- a/scripts/test/simple_tests.sh
++++ b/scripts/test/simple_tests.sh
 @@ -24,19 +24,19 @@
  export ASAN_OPTIONS=halt_on_error=1
  export UBSAN_OPTIONS=halt_on_error=1
@@ -69,8 +69,8 @@ Forwarded: not-needed
  perl scripts/test/simple_tests.pl \
  	--bowtie2=./bowtie2 \
  	--bowtie2-build=./bowtie2-build \
---- bowtie2.orig/scripts/test/simple_tests.pl
-+++ bowtie2/scripts/test/simple_tests.pl
+--- a/scripts/test/simple_tests.pl
++++ b/scripts/test/simple_tests.pl
 @@ -4807,7 +4807,7 @@
  my $tmpfafn = ".simple_tests.pl.fa";
  my $last_ref = undef;
@@ -80,8 +80,8 @@ Forwarded: not-needed
  		for (my $ci = 0; $ci < scalar(@cases); $ci++) {
  			my $c = $cases[$ci];
  			last unless defined($c);
---- bowtie2.orig/scripts/sim/Sim.pm
-+++ bowtie2/scripts/sim/Sim.pm
+--- a/scripts/sim/Sim.pm
++++ b/scripts/sim/Sim.pm
 @@ -423,16 +423,15 @@
  			$argstr .= " ".$args->{$_};
  		}
@@ -171,8 +171,8 @@ Forwarded: not-needed
  	$conf->{tempdir}             = "/tmp"           unless defined($conf->{tempdir});
  	srand(time ^ $$);
  	$conf->{randstr} = randStr(8);
---- bowtie2.orig/scripts/sim/run.pl
-+++ bowtie2/scripts/sim/run.pl
+--- a/scripts/sim/run.pl
++++ b/scripts/sim/run.pl
 @@ -32,8 +32,6 @@
  our %conf = (
  	bowtie2_build       => "bowtie2-build",


=====================================
debian/patches/drop-not-needed-js-from-manual.patch
=====================================
@@ -3,7 +3,7 @@ Author: Alex Mestiashvili <amestia at rsh2.donotuse.de>
 Forwarded: not-needed
 --- a/doc/manual.html
 +++ b/doc/manual.html
-@@ -20,9 +20,6 @@
+@@ -23,9 +23,6 @@
      .display.math{display: block; text-align: center; margin: 0.5rem auto;}
    </style>
    <link rel="stylesheet" href="doc/style.css" />


=====================================
debian/patches/hardening.patch
=====================================
@@ -5,7 +5,7 @@ Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Last-Update: Tue, 2 Jan 2018 16:20:02 +0100
 --- a/Makefile
 +++ b/Makefile
-@@ -313,7 +313,9 @@ DEFS := -fno-strict-aliasing \
+@@ -321,7 +321,9 @@
    $(FILE_FLAGS) \
    $(PREF_DEF) \
    $(MM_DEF) \


=====================================
debian/patches/no_sanity
=====================================
@@ -3,7 +3,7 @@ Description: save resources by not making/testing the -fsantize variants
 Forwarded: not-needed
 --- a/Makefile
 +++ b/Makefile
-@@ -208,15 +208,6 @@ BUILD_CPPS_MAIN := $(BUILD_CPPS) bowtie_
+@@ -216,15 +216,6 @@
  SEARCH_FRAGMENTS := $(wildcard search_*_phase*.c)
  VERSION := $(shell cat BOWTIE2_VERSION)
  
@@ -19,7 +19,7 @@ Forwarded: not-needed
  DEBUG_FLAGS    := -O0 -g3 $(SSE_FLAG)
  RELEASE_FLAGS  := -O3 $(SSE_FLAG) -funroll-loops -g3
  NOASSERT_FLAGS := -DNDEBUG
-@@ -236,15 +227,6 @@ BOWTIE2_BIN_LIST_DBG := bowtie2-build-s-
+@@ -244,15 +235,6 @@
    bowtie2-align-l-debug \
    bowtie2-inspect-s-debug \
    bowtie2-inspect-l-debug
@@ -35,7 +35,7 @@ Forwarded: not-needed
  
  GENERAL_LIST := $(wildcard scripts/*.sh) \
    $(wildcard scripts/*.pl) \
-@@ -296,10 +278,9 @@ endif
+@@ -304,10 +286,9 @@
  .PHONY: all allall both both-debug
  
  all: $(BOWTIE2_BIN_LIST) ;
@@ -47,7 +47,7 @@ Forwarded: not-needed
  
  DEFS := -fno-strict-aliasing \
    -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" \
-@@ -313,17 +294,10 @@ DEFS := -fno-strict-aliasing \
+@@ -321,13 +302,6 @@
    $(CPPFLAGS) \
    $(CFLAGS)
  
@@ -58,71 +58,12 @@ Forwarded: not-needed
 -$(BOWTIE2_BIN_LIST_SAN): $(error "Compiler does not support...")
 -endif
 -
- #
- # bowtie2-build targets
- #
--bowtie2-build-s-sanitized bowtie2-build-s: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
-+bowtie2-build-s: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
- 	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \
- 		$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) -Wall \
- 		$(CPPFLAGS) \
-@@ -331,7 +305,7 @@ bowtie2-build-s-sanitized bowtie2-build-
- 		$(SHARED_CPPS) $(BUILD_CPPS_MAIN) \
- 		$(LDFLAGS) $(LDLIBS)
- 
--bowtie2-build-l-sanitized bowtie2-build-l: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
-+bowtie2-build-l: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
- 	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \
- 		$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) -Wall \
- 		$(CPPFLAGS) \
-@@ -359,7 +333,7 @@ bowtie2-build-l-debug: bt2_build.cpp $(S
- # bowtie2-align targets
- #
- 
--bowtie2-align-s-sanitized bowtie2-align-s: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
-+bowtie2-align-s: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
- 	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \
- 		$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) -Wall \
- 		$(CPPFLAGS) \
-@@ -367,7 +341,7 @@ bowtie2-align-s-sanitized bowtie2-align-
- 		$(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \
- 		$(LDFLAGS) $(LDLIBS)
- 
--bowtie2-align-l-sanitized bowtie2-align-l: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
-+bowtie2-align-l: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
- 	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \
- 		$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) -Wall \
- 		$(CPPFLAGS) \
-@@ -397,7 +371,7 @@ bowtie2-align-l-debug: bt2_search.cpp $(
- # bowtie2-inspect targets
- #
- 
--bowtie2-inspect-s-sanitized bowtie2-inspect-s: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
-+bowtie2-inspect-s: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
- 	$(CXX) $(RELEASE_FLAGS) \
- 		$(RELEASE_DEFS) $(CXXFLAGS) \
- 		$(DEFS) -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \
-@@ -406,7 +380,7 @@ bowtie2-inspect-s-sanitized bowtie2-insp
- 		$(SHARED_CPPS) \
- 		$(LDFLAGS) $(LDLIBS)
- 
--bowtie2-inspect-l-sanitized bowtie2-inspect-l: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
-+bowtie2-inspect-l: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
- 	$(CXX) $(RELEASE_FLAGS) \
- 		$(RELEASE_DEFS) $(CXXFLAGS) \
- 		$(DEFS) -DBOWTIE2 -DBOWTIE_INSPECT_MAIN  -DBOWTIE_64BIT_INDEX -Wall \
-@@ -608,7 +582,7 @@ test: simple-test
- 
- .PHONY: clean
- clean:
--	rm -f $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG) $(BOWTIE2_BIN_LIST_SAN) \
-+	rm -f $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG) \
- 	$(addsuffix .exe,$(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG)) \
- 	bowtie2-*.zip
- 	rm -f core.* .tmp.head
+ bowtie2-build-%: CXXFLAGS += $(BUILD_CXXFLAGS)
+ bowtie2-build-%: LDFLAGS += $(BUILD_LDFLAGS)
+ bowtie2-build-%: LDLIBS += $(BUILD_LDLIBS)
 --- a/bowtie2
 +++ b/bowtie2
-@@ -122,7 +122,6 @@ getBt2Desc(\%desc);
+@@ -122,7 +122,6 @@
  sub isWrapped($) { return defined($wrapped{$_[0]}); }
  
  my $debug = 0;
@@ -130,7 +71,7 @@ Forwarded: not-needed
  my %read_fns = ();
  my %read_compress = ();
  my $cap_out = undef;       # Filename for passthrough
-@@ -184,7 +183,6 @@ GetOptions(
+@@ -184,7 +183,6 @@
          "keep"                          => \$keep,
          "verbose"                       => \$verbose,
          "debug"                         => \$debug,
@@ -138,7 +79,7 @@ Forwarded: not-needed
          "large-index"                   => \$large_idx,
          "no-unal"                       => \$no_unal,
          "un=s"                          => \&handle_un_or_al,
-@@ -473,9 +471,6 @@ my $suffix = "";
+@@ -473,9 +471,6 @@
  if ($debug) {
          $suffix = "-debug";
  }
@@ -150,7 +91,7 @@ Forwarded: not-needed
  quote_params(\@bt2_args);
 --- a/bowtie2-build
 +++ b/bowtie2-build
-@@ -46,7 +46,6 @@ def main():
+@@ -51,7 +51,6 @@
  
      group = parser.add_mutually_exclusive_group()
      group.add_argument('--debug', action='store_true')
@@ -158,7 +99,7 @@ Forwarded: not-needed
  
      logging.basicConfig(level=logging.ERROR,
                          format='%(levelname)s: %(message)s'
-@@ -69,9 +68,9 @@ def main():
+@@ -77,9 +76,9 @@
          build_bin_spec += "-debug"
          build_bin_l += "-debug"
  
@@ -173,7 +114,7 @@ Forwarded: not-needed
      if "-c" not in argv and len(argv) >= 2:
 --- a/bowtie2-inspect
 +++ b/bowtie2-inspect
-@@ -33,7 +33,6 @@ def main():
+@@ -33,7 +33,6 @@
  
      group = parser.add_mutually_exclusive_group()
      group.add_argument('--debug', action='store_true')
@@ -181,7 +122,7 @@ Forwarded: not-needed
  
      parser.add_argument('--verbose', action='store_true')
      parser.add_argument('--large-index', action='store_true')
-@@ -60,10 +59,6 @@ def main():
+@@ -60,10 +59,6 @@
          inspect_bin_spec += '-debug'
          inspect_bin_l += '-debug'
  
@@ -194,7 +135,7 @@ Forwarded: not-needed
      elif len(argv) >= 1:
 --- a/scripts/test/simple_tests.pl
 +++ b/scripts/test/simple_tests.pl
-@@ -4605,7 +4605,7 @@ sub runbowtie2($$$$$$$$$$$$$$$$$$$$$$$$$
+@@ -4605,7 +4605,7 @@
  	close(FA);
  	if($do_build) {
  		my $build_args = "";
@@ -218,7 +159,7 @@ Forwarded: not-needed
  #$MAKE $* bowtie2-align-s \
 --- a/bt2_build.cpp
 +++ b/bt2_build.cpp
-@@ -147,7 +147,6 @@ static void printUsage(ostream& out) {
+@@ -147,7 +147,6 @@
  	out << "    --large-index           force generated index to be 'large', even if ref" << endl
  	    << "                            has fewer than 4 billion nucleotides" << endl
  	    << "    --debug                 use the debug binary; slower, assertions enabled" << endl
@@ -228,7 +169,7 @@ Forwarded: not-needed
  	out << "    -a/--noauto             disable automatic -p/--bmax/--dcv memory-fitting" << endl
 --- a/bt2_inspect.cpp
 +++ b/bt2_inspect.cpp
-@@ -81,7 +81,6 @@ static void printUsage(ostream& out) {
+@@ -81,7 +81,6 @@
  		out << "  --large-index      force inspection of the 'large' index, even if a" << endl
  		    << "                     'small' one is present." << endl
  		    << "  --debug            use the debug binary; slower, assertions enabled" << endl


=====================================
debian/patches/reproducible.patch
=====================================
@@ -6,7 +6,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
 Forwarded: not-needed
 --- a/Makefile
 +++ b/Makefile
-@@ -26,7 +26,7 @@ bindir := $(PREFIX)/bin
+@@ -26,7 +26,7 @@
  
  LDLIBS := -lpthread -lz
  
@@ -15,7 +15,7 @@ Forwarded: not-needed
  BOWTIE_MM := 1
  BOWTIE_SHARED_MEM :=
  
-@@ -225,8 +225,8 @@ DEBUG_FLAGS    := -O0 -g3 $(SSE_FLAG)
+@@ -233,8 +233,8 @@
  RELEASE_FLAGS  := -O3 $(SSE_FLAG) -funroll-loops -g3
  NOASSERT_FLAGS := -DNDEBUG
  FILE_FLAGS     := -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
@@ -28,7 +28,7 @@ Forwarded: not-needed
    bowtie2-build-l \
 --- a/bt2_build.cpp
 +++ b/bt2_build.cpp
-@@ -580,15 +580,15 @@ int bowtie_build(int argc, const char **
+@@ -580,15 +580,15 @@
  			} else {
  				cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl;
  			}
@@ -55,7 +55,7 @@ Forwarded: not-needed
  
 --- a/bt2_inspect.cpp
 +++ b/bt2_inspect.cpp
-@@ -456,15 +456,15 @@ int main(int argc, char **argv) {
+@@ -456,15 +456,15 @@
  			} else {
  				cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl;
  			}
@@ -82,7 +82,7 @@ Forwarded: not-needed
  
 --- a/bt2_search.cpp
 +++ b/bt2_search.cpp
-@@ -5124,15 +5124,15 @@ int bowtie(int argc, const char **argv)
+@@ -5131,15 +5131,15 @@
  			} else {
  				cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl;
  			}
@@ -109,7 +109,7 @@ Forwarded: not-needed
  		{
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -241,7 +241,9 @@ include_directories(${PROJECT_SOURCE_DIR
+@@ -181,7 +181,9 @@
  get_directory_property(COMPILER_DEFS COMPILE_DEFINITIONS)
  string(REPLACE ";" " -D" COMPILER_DEFS "${COMPILER_DEFS}")
  string(REPLACE "\"" "" COMPILER_DEFS "${COMPILER_DEFS}")
@@ -118,5 +118,5 @@ Forwarded: not-needed
 +string(REGEX REPLACE "-ffile-prefix-map=[^ ]* " "" COMP_OPTS ${COMP_OPTS})
 +add_definitions(-DCOMPILER_OPTIONS="${COMP_OPTS}")
  
- add_executable(bowtie2-align-s ${SEARCH_CPPS} ${SHARED_CPPS})
- add_executable(bowtie2-align-l ${SEARCH_CPPS} ${SHARED_CPPS})
+ if (USE_SRA)
+   set(SRA_TOOLS_VER 3.0.9)


=====================================
debian/patches/simde
=====================================
@@ -1,8 +1,8 @@
 Author: Michael R. Crusoe <crusoe at debian.org>
 Description: Enable SIMDE everywhere
 Forwarded: not-needed
---- bowtie2.orig/sse_wrap.h
-+++ bowtie2/sse_wrap.h
+--- a/sse_wrap.h
++++ b/sse_wrap.h
 @@ -27,8 +27,9 @@
  #ifndef SSE_WRAP_H_
  #define SSE_WRAP_H_


=====================================
debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch
=====================================
@@ -16,7 +16,7 @@ Forwarded: not-needed
  use Getopt::Long;
  use List::Util qw(max min);
  
-@@ -105,7 +104,6 @@ $rdlen_min = $rdlen_min || 40;    # min
+@@ -105,7 +104,6 @@
  $frag_av   = $frag_av   || 250;   # mean fragment len
  $frag_sd   = $frag_sd   || 45;    # s.d. when drawing frag len from normal dist
  my @fraglens  = ();     # fragment lengths (for paired)
@@ -24,7 +24,7 @@ Forwarded: not-needed
  
  if($long) {
  	$nreads = 6000;
-@@ -134,77 +132,15 @@ for(0..length($rf)-1) {
+@@ -134,77 +132,15 @@
  }
  
  print STDERR "Adding microindels...\n";
@@ -102,7 +102,7 @@ Forwarded: not-needed
  sub rand_quals($) {
  	my $ret = "";
  	my $upper = (rand() < 0.2 ? 11 : 40);
-@@ -259,61 +195,10 @@ if($paired) {
+@@ -259,61 +195,10 @@
  		}
  		# Possibly reverse complement
  		$fstr = revcomp($fstr) if (int(rand(2)) == 0);
@@ -166,7 +166,7 @@ Forwarded: not-needed
  print STDERR "DONE\n";
 --- a/Makefile
 +++ b/Makefile
-@@ -534,12 +534,12 @@ install: all
+@@ -547,12 +547,12 @@
  	done
  
  .PHONY: simple-test
@@ -181,7 +181,7 @@ Forwarded: not-needed
  	eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
  	sh ./scripts/sim/run.sh $(if $(NUM_CORES), $(NUM_CORES), 2)
  
-@@ -550,8 +550,7 @@ perl-deps:
+@@ -563,8 +563,7 @@
  	fi
  	DL=$$( ( which wget >/dev/null 2>&1 && echo "wget --no-check-certificate -O-" ) || echo "curl -L") ; \
  	$$DL http://cpanmin.us | perl - -l $(CURDIR)/.tmp App::cpanminus local::lib ; \
@@ -191,8 +191,8 @@ Forwarded: not-needed
  
  .PHONY: static-libs
  static-libs:
-@@ -609,7 +608,7 @@ sra-deps:
- 	 fi ;
+@@ -636,7 +635,7 @@
+ 	fi ;
  
  .PHONY: test
 -test: simple-test random-test


=====================================
debian/patches/use-source-date-epoch-in-Makefile.patch
=====================================
@@ -7,7 +7,7 @@ https://reproducible-builds.org/docs/source-date-epoch/
 
 --- a/Makefile
 +++ b/Makefile
-@@ -285,7 +285,7 @@ both-debug: bowtie2-align-s-debug bowtie
+@@ -293,7 +293,7 @@
  DEFS := -fno-strict-aliasing \
    -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" \
    -DBUILD_HOST="\"$${HOSTNAME:-`hostname`}\"" \


=====================================
debian/patches/wrong-interpreter-path.patch
=====================================
@@ -1,88 +1,88 @@
 Description: Use path to interpreter instead of /usr/bin/env
 Author: Alex Mestiashvili <amestia at rsh2.donotuse.de>
 Forwarded: not-needed
---- bowtie2.orig/bowtie2
-+++ bowtie2/bowtie2
+--- a/bowtie2
++++ b/bowtie2
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env perl
 +#!/usr/bin/perl
  
  #
  # Copyright 2011, Ben Langmead <langmea at cs.jhu.edu>
---- bowtie2.orig/bowtie2-build
-+++ bowtie2/bowtie2-build
+--- a/bowtie2-build
++++ b/bowtie2-build
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env python3
 +#!/usr/bin/python3
  
  """
   Copyright 2014, Ben Langmead <langmea at cs.jhu.edu>
---- bowtie2.orig/bowtie2-inspect
-+++ bowtie2/bowtie2-inspect
+--- a/bowtie2-inspect
++++ b/bowtie2-inspect
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env python3
 +#!/usr/bin/python3
  
  """
   Copyright 2014, Ben Langmead <langmea at cs.jhu.edu>
---- bowtie2.orig/example/reads/simulate.pl
-+++ bowtie2/example/reads/simulate.pl
+--- a/example/reads/simulate.pl
++++ b/example/reads/simulate.pl
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env perl
 +#!/usr/bin/perl
  
  ##
  # Copyright 2011, Ben Langmead <langmea at cs.jhu.edu>
---- bowtie2.orig/scripts/sa.py
-+++ bowtie2/scripts/sa.py
+--- a/scripts/sa.py
++++ b/scripts/sa.py
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env python3
 +#!/usr/bin/python3
  
  """
  sa.py
---- bowtie2.orig/scripts/test/benchmark/benchmarks.py
-+++ bowtie2/scripts/test/benchmark/benchmarks.py
+--- a/scripts/test/benchmark/benchmarks.py
++++ b/scripts/test/benchmark/benchmarks.py
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env python3
 +#!/usr/bin/python3
  """
  A few items to deal with sets of benchmarks.
  """
---- bowtie2.orig/scripts/test/benchmark/run.py
-+++ bowtie2/scripts/test/benchmark/run.py
+--- a/scripts/test/benchmark/run.py
++++ b/scripts/test/benchmark/run.py
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env python3
 +#!/usr/bin/python3
  """
     Runs benchmark sets specified in JSON files.
  
---- bowtie2.orig/scripts/test/benchmark/samreader.py
-+++ bowtie2/scripts/test/benchmark/samreader.py
+--- a/scripts/test/benchmark/samreader.py
++++ b/scripts/test/benchmark/samreader.py
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env python3
 +#!/usr/bin/python3
  """
  A reader of SAM format.
  
---- bowtie2.orig/scripts/test/bt2face.py
-+++ bowtie2/scripts/test/bt2face.py
+--- a/scripts/test/bt2face.py
++++ b/scripts/test/bt2face.py
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env python3
 +#!/usr/bin/python3
  
  import os
  import logging
---- bowtie2.orig/scripts/test/btdata.py
-+++ bowtie2/scripts/test/btdata.py
+--- a/scripts/test/btdata.py
++++ b/scripts/test/btdata.py
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env python3
 +#!/usr/bin/python3
  """
  Note: This would look so much better replaced by XML or at least JSON. But
        is not worth to do it for now.
---- bowtie2.orig/scripts/test/dataface.py
-+++ bowtie2/scripts/test/dataface.py
+--- a/scripts/test/dataface.py
++++ b/scripts/test/dataface.py
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env python3
 +#!/usr/bin/python3
@@ -96,16 +96,16 @@ Forwarded: not-needed
 -    
 \ No newline at end of file
 +    
---- bowtie2.orig/scripts/test/large_idx.py
-+++ bowtie2/scripts/test/large_idx.py
+--- a/scripts/test/large_idx.py
++++ b/scripts/test/large_idx.py
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env python3
 +#!/usr/bin/python3
  
  import os
  import gzip
---- bowtie2.orig/scripts/test/regressions.py
-+++ bowtie2/scripts/test/regressions.py
+--- a/scripts/test/regressions.py
++++ b/scripts/test/regressions.py
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env python3
 +#!/usr/bin/python3



View it on GitLab: https://salsa.debian.org/med-team/bowtie2/-/commit/335de96e5e9ba2f2120feecf5354822e8fd19d1d

-- 
View it on GitLab: https://salsa.debian.org/med-team/bowtie2/-/commit/335de96e5e9ba2f2120feecf5354822e8fd19d1d
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