[med-svn] [Git][med-team/bamtools][master] small fixes to 2.5.3 and upload to unstable
Dominique Belhachemi (@domibel)
gitlab at salsa.debian.org
Sat Sep 27 04:45:50 BST 2025
Dominique Belhachemi pushed to branch master at Debian Med / bamtools
Commits:
aa133d88 by Dominique Belhachemi at 2025-09-26T23:45:39-04:00
small fixes to 2.5.3 and upload to unstable
- - - - -
11 changed files:
- debian/bamtools.1
- debian/changelog
- debian/control
- debian/patches/0001-ignore-thirdparty-and-fix-jsoncpp.patch
- − debian/patches/do_not_corrupt_output.patch
- + debian/patches/doxyfile_version.patch
- − debian/patches/filter_script.patch
- − debian/patches/fix_soversion.patch
- debian/patches/series
- debian/patches/shared_and_static.patch
- − debian/patches/typo.patch
Changes:
=====================================
debian/bamtools.1
=====================================
@@ -1,4 +1,4 @@
-.TH BAMTOOLS "1" "April 2014" "bamtools 2.3.0+dfsg" "User Commands"
+.TH BAMTOOLS "1" "September 2025" "bamtools 2.5.3+dfsg" "User Commands"
.SH NAME
bamtools \- toolkit for manipulating BAM (genome alignment) files
.SH SYNOPSIS
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+bamtools (2.5.3+dfsg-1) unstable; urgency=medium
+
+ * Team upload
+ * New upstream version
+ * Fix FTBFS with CMake 4 (Closes: #1112718)
+ * Standards-Version: 4.7.2 (routine-update)
+ * Drop outdated patches
+ * Add Doxyfile version patch
+
+ -- Dominique Belhachemi <domibel at debian.org> Fri, 26 Sep 2025 21:59:11 -0400
+
bamtools (2.5.2+dfsg-6) unstable; urgency=medium
* Fix output data on bigendian architectures (Thanks a lot for the
=====================================
debian/control
=====================================
@@ -14,7 +14,7 @@ Build-Depends: debhelper-compat (= 13),
help2man,
doxygen,
pkgconf
-Standards-Version: 4.7.0
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/bamtools
Vcs-Git: https://salsa.debian.org/med-team/bamtools.git
Homepage: https://github.com/pezmaster31/bamtools/wiki
@@ -57,7 +57,7 @@ Package: libbamtools-dev
Architecture: any
Multi-Arch: same
Section: libdevel
-Depends: libbamtools2.5.2 (= ${binary:Version}),
+Depends: libbamtools2.5.3 (= ${binary:Version}),
${misc:Depends},
${devlibs:Depends}
Suggests: libbamtools-doc (= ${binary:Version})
@@ -75,7 +75,7 @@ Description: C++ API for manipulating BAM (genome alignment) files
.
This is the developers API package.
-Package: libbamtools2.5.2
+Package: libbamtools2.5.3
Architecture: any
Multi-Arch: same
Section: libs
=====================================
debian/patches/0001-ignore-thirdparty-and-fix-jsoncpp.patch
=====================================
@@ -1,7 +1,7 @@
-From: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Date: Wed, 7 Nov 2012 18:44:06 -0700
-Subject: ignore-thirdparty-and-fix-jsoncpp
+Description: ignore-thirdparty-and-fix-jsoncpp
+Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Forwarded: not-needed
+Last-Update: 2012-11-07
---
src/CMakeLists.txt | 2 +-
=====================================
debian/patches/do_not_corrupt_output.patch deleted
=====================================
@@ -1,36 +0,0 @@
-Description: bamtools crashes/corrupts output data on s390x
- The issue was detected in Ubuntu autopkgtests. The call to
- bamtools revert -in sam_spec_example.bam -out out.bam
- fails due to the buffer overflow detected
- This is due to the write loop in
- src/api/internal/bam/BamWriter_p.cpp
- using single byte instead of sizeof(uint32_t) increment to
- swap bytes in the integer data.
- The output file on s390x is corrupted by the write operation.
- bamtools crash with the hardening flags enabled.
-Author: Vladimir Petko <vladimir.petko at canonical.com>
-Bug: https://github.com/pezmaster31/bamtools/issues/235
-Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/bamtools/+bug/2072463
-Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075990
-Last-Update: 2024-07-09
-
---- a/src/api/internal/bam/BamWriter_p.cpp
-+++ b/src/api/internal/bam/BamWriter_p.cpp
-@@ -349,7 +349,7 @@
- char* cigarData = new char[packedCigarLength]();
- std::memcpy(cigarData, packedCigar.data(), packedCigarLength);
- if (m_isBigEndian) {
-- for (size_t i = 0; i < packedCigarLength; ++i) {
-+ for (size_t i = 0; i < packedCigarLength; i+= sizeof(uint32_t)) {
- BamTools::SwapEndian_32p(&cigarData[i]);
- }
- }
-@@ -501,7 +501,7 @@
- std::memcpy(cigarData, packedCigar.data(), packedCigarLength);
- if (m_isBigEndian) {
- for (size_t i = 0; i < packedCigarLength;
-- ++i) { // FIXME: similarly, this should be "i += 4", not "++i"
-+ i+= sizeof(uint32_t)) { // FIXME: similarly, this should be "i += 4", not "++i"
- BamTools::SwapEndian_32p(&cigarData[i]);
- }
- }
=====================================
debian/patches/doxyfile_version.patch
=====================================
@@ -0,0 +1,16 @@
+Description: Fix the project version
+Author: Dominique Belhachemi <domibel at debian.org>
+Forwarded: yes
+Last-Update: 2025-09-26
+
+--- bamtools-2.5.3+dfsg.orig/docs/Doxyfile
++++ bamtools-2.5.3+dfsg/docs/Doxyfile
+@@ -31,7 +31,7 @@ PROJECT_NAME = BamTools
+ # This could be handy for archiving the generated documentation or
+ # if some version control system is used.
+
+-PROJECT_NUMBER = 2.5.2
++PROJECT_NUMBER = 2.5.3
+
+ # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
+ # base path where the generated documentation will be put.
=====================================
debian/patches/filter_script.patch deleted
=====================================
@@ -1,43 +0,0 @@
-Description: fix infinite loop on s390x, arm, ppc64el
- const std::string FilterTool::FilterToolPrivate::GetScriptContents()
- loops indefinitely due to fgets() not setting eof flag if
- the call returns data on those platforms.
- The fgetc/ungetc calls then set/clear eof flag indefinitely.
-Author: Vladimir Petko <vladimir.petko at canonical.com>
-Bug: https://github.com/pezmaster31/bamtools/issues/237
-Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=992143
-Last-Update: 2024-07-09
-
-diff --git a/src/toolkit/bamtools_filter.cpp b/src/toolkit/bamtools_filter.cpp
-index 16a1b0d..9c2ea44 100644
---- a/src/toolkit/bamtools_filter.cpp
-+++ b/src/toolkit/bamtools_filter.cpp
-@@ -540,22 +540,18 @@ const std::string FilterTool::FilterToolPrivate::GetScriptContents()
- // read in entire script contents
- char buffer[1024];
- std::ostringstream docStream;
-- while (true) {
--
-- // peek ahead, make sure there is data available
-- char ch = fgetc(inFile);
-- ungetc(ch, inFile);
-- if (feof(inFile)) {
-+ while (!feof(inFile)) {
-+ // read next block of data
-+ char *data = fgets(buffer, 1024, inFile);
-+ if (data == 0) {
- break;
- }
--
-- // read next block of data
-- if (fgets(buffer, 1024, inFile) == 0) {
-+ if (ferror(inFile)) {
- std::cerr << "bamtools filter ERROR: could not read script contents" << std::endl;
- return std::string();
- }
-
-- docStream << buffer;
-+ docStream << data;
- }
-
- // close script file
=====================================
debian/patches/fix_soversion.patch deleted
=====================================
@@ -1,17 +0,0 @@
-Description: SONAME is only MAJOR.MINOR
- Ist turned out that this patch is not really a good idea and its
- better to stick with upstream soname
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 15 Oct 2021 15:08:32 +0200
-
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -120,7 +120,7 @@ add_library(
- # as Bamtools does not yet guarantee a stable ABI
- set_target_properties(
- BamTools PROPERTIES
-- SOVERSION ${BamTools_VERSION}
-+ SOVERSION "${BamTools_VERSION_MAJOR}.${BamTools_VERSION_MINOR}"
- OUTPUT_NAME bamtools
- CXX_STANDARD 11
- CXX_STANDARD_REQUIRED ON
=====================================
debian/patches/series
=====================================
@@ -1,6 +1,3 @@
0001-ignore-thirdparty-and-fix-jsoncpp.patch
shared_and_static.patch
-#fix_soversion.patch
-typo.patch
-filter_script.patch
-do_not_corrupt_output.patch
+doxyfile_version.patch
=====================================
debian/patches/shared_and_static.patch
=====================================
@@ -1,6 +1,7 @@
Description: Build additional static lib
Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 27 May 2020 09:59:29 +0200
+Forwarded: not-needed
+Last-Update: 2020-05-27
--- bamtools.orig/src/CMakeLists.txt
+++ bamtools/src/CMakeLists.txt
=====================================
debian/patches/typo.patch deleted
=====================================
@@ -1,17 +0,0 @@
-Description: fix typo caught by lintian.
-Author: Étienne Mollier <emollier at debian.org>
-Forwarded: https://github.com/pezmaster31/bamtools/pull/231
-Last-Update: 2023-12-15
----
-This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- bamtools.orig/src/toolkit/bamtools_filter.cpp
-+++ bamtools/src/toolkit/bamtools_filter.cpp
-@@ -1020,7 +1020,7 @@
- const std::string isFirstMateDesc = "keep only alignments marked as first mate?";
- const std::string isMappedDesc = "keep only alignments that were mapped?";
- const std::string isMateMappedDesc = "keep only alignments with mates that mapped";
-- const std::string isMateReverseDesc = "keep only alignments with mate on reverese strand?";
-+ const std::string isMateReverseDesc = "keep only alignments with mate on reverse strand?";
- const std::string isPairedDesc = "keep only alignments that were sequenced as paired?";
- const std::string isPrimaryDesc = "keep only alignments marked as primary?";
- const std::string isProperPairDesc = "keep only alignments that passed PE resolution?";
View it on GitLab: https://salsa.debian.org/med-team/bamtools/-/commit/aa133d88d554c6ac60ae35cf929321f42e90bb4c
--
View it on GitLab: https://salsa.debian.org/med-team/bamtools/-/commit/aa133d88d554c6ac60ae35cf929321f42e90bb4c
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