Package: bamtools
Version: 2.5.2+dfsg-5
Followup-For: Bug #1075990
User: ubuntu-de...@lists.ubuntu.com
Usertags: origin-ubuntu oracular ubuntu-patch
Control: tags -1 patch
Dear Maintainer,
Would it be possible to consider adding attached patches to resolve infinite
loop in the filter script loader (non-amd) and the output corruption of S390?
In Ubuntu, the attached patch was applied to achieve the following:
* d/p/do_not_corrupt_output.patch: add patch to avoid corrupting
output on big-endian platforms (LP: #2072463).
* d/p/filter_script.patch: add patch to address Debian bug 992143.
* d/t/run-unit-test: enable filter test on all architectures.
Thanks for considering the patch.
-- System Information:
Debian Release: trixie/sid
APT prefers noble-updates
APT policy: (500, 'noble-updates'), (500, 'noble-security'), (500, 'noble'),
(100, 'noble-backports')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 6.8.0-36-generic (SMP w/32 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE,
TAINT_UNSIGNED_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
diff -Nru bamtools-2.5.2+dfsg/debian/patches/do_not_corrupt_output.patch
bamtools-2.5.2+dfsg/debian/patches/do_not_corrupt_output.patch
--- bamtools-2.5.2+dfsg/debian/patches/do_not_corrupt_output.patch
1970-01-01 12:00:00.000000000 +1200
+++ bamtools-2.5.2+dfsg/debian/patches/do_not_corrupt_output.patch
2024-07-09 15:57:31.000000000 +1200
@@ -0,0 +1,36 @@
+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.pe...@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]);
+ }
+ }
diff -Nru bamtools-2.5.2+dfsg/debian/patches/filter_script.patch
bamtools-2.5.2+dfsg/debian/patches/filter_script.patch
--- bamtools-2.5.2+dfsg/debian/patches/filter_script.patch 1970-01-01
12:00:00.000000000 +1200
+++ bamtools-2.5.2+dfsg/debian/patches/filter_script.patch 2024-07-09
15:57:31.000000000 +1200
@@ -0,0 +1,43 @@
+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.pe...@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
diff -Nru bamtools-2.5.2+dfsg/debian/patches/series
bamtools-2.5.2+dfsg/debian/patches/series
--- bamtools-2.5.2+dfsg/debian/patches/series 2023-12-16 07:09:45.000000000
+1300
+++ bamtools-2.5.2+dfsg/debian/patches/series 2024-07-09 15:57:31.000000000
+1200
@@ -2,3 +2,5 @@
shared_and_static.patch
#fix_soversion.patch
typo.patch
+filter_script.patch
+do_not_corrupt_output.patch
diff -Nru bamtools-2.5.2+dfsg/debian/tests/run-unit-test
bamtools-2.5.2+dfsg/debian/tests/run-unit-test
--- bamtools-2.5.2+dfsg/debian/tests/run-unit-test 2023-12-16
07:09:45.000000000 +1300
+++ bamtools-2.5.2+dfsg/debian/tests/run-unit-test 2024-07-09
15:57:31.000000000 +1200
@@ -21,19 +21,7 @@
bamtools coverage -in sam_spec_example.bam -out out
-# This test fails on ppc64el for whatever reason and is for the moment (see
bug #933505)
-# The test is also problematic for armel (see bug #992143)
-ARCH=$(dpkg --print-architecture)
-if [ "$ARCH" != "ppc64el" -a "$ARCH" != "arm64" -a "$ARCH" != "armel"-a
"$ARCH" != "armhf" -a "$ARCH" != "s390x" ] ; then
- bamtools filter -script filter_script -in sam_spec_example.bam -out out.bam
-else
- if [ "$ARCH" = "ppc64el" ] ; then
- echo "The following test is known to fail on ppc64el architecture (see
bug #933505)"
- else
- echo "The following test is known to time out on $ARCH architecture (see
bug #953939)"
- fi
- echo "bamtools filter -script filter_script -in sam_spec_example.bam -out
out.bam"
-fi
+bamtools filter -script filter_script -in sam_spec_example.bam -out out.bam
bamtools header -in sam_spec_example.bam
