Releases: biod/sambamba
Sambamba 1.0.1 (stable)
Sambamba 1.0.0 (stable)
ChangeLog v1.0.0 (20230119)
A minor fix and a major release. After 10 years and over one thousand citations we can announce sambamba 1.0 stable!
For now use the static binary of the previous release - it is essentially the same.
Sambamba 0.8.2
Maintenance release aligns with D compiler updates which had sambamba breaking in Debian. Notably lz4 got removed from the source tree and the meson build system is close to becoming the default. Again some free speed improvement thanks to the latest ldc2+LLVM toolchain. Amazing work by these groups!
- Slightly faster (approx 5%) static sambamba with ldc2 1.27+LLVM 11.
- Purged lz4 sources in favour of using the lz4 dependency (the Debian
library appears to be complete) - Fixed meson builds for Debian, see #484
(thanks @atille) - Optimized meson build so it is close to static build times
- Removed most ldc2 deprecation warnings
- Moved Python scripts 2->3 (following the Debian patch)
- Fix ldc 1.27.1 build by using get to unwrap Nullable
- Merged PR #480 (thanks @dukc)
Contributors
Assets 3
Sambamba 0.8.1
ChangeLog v0.8.1 (20210731)
- Some FASTA unittests break when they write to disk and read after -
marked withversion(Broken) - Fix build for LDC 1.26.0 and LLVM 9.0.1 - some speed improvement
Sambamba 0.8.0
ChangeLog v0.8.0 (20201130)
Maintainance release and bug fixes: this is a special release where we
removed all CRAM support. The added value of CRAM in sambamba was
limited because it was using essentially the same htslib backend as
samtools. Removing the htslib dependency removes one maintenance
headache. See also #425.
BioD was also moved back into the main trunk. We separated it in the
past, but as there is no development there we might as well have it in
Sambamba (again).
- Removed CRAM support and htslib dependency with ec78eab
- Removed BioD source tree back into Sambamba
- Sambamba builds on ARM64 (see Travis-CI)
- Changed github issue tracker template to report bugs only
- Added FASTA handlers, indexing and slicing (thanks @NickRoz1)
- Updated slice.d (thanks @NickRoz1)
- Fixed FASTA file handlers not closing cdc5f84
- Added badges to the top of README
- Added Meson build system for Debian (thanks Matthias @ximion)
- Fixed Python2 -> Python3 stuff (thanks Matthias @ximion)
penguin2:~$ /usr/bin/time --verbose ./sambamba-0.8.0 markdup HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.
20130415.bam test.bam
sambamba 0.8.0
by Artem Tarasov and Pjotr Prins (C) 2012-2020
LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4)
finding positions of the duplicate reads in the file...
sorted 3969781 end pairs
and 73839 single ends (among them 22397 unmatched pairs)
collecting indices of duplicate reads... done in 616 ms
found 239673 duplicates
collected list of positions in 0 min 10 sec
marking duplicates...
collected list of positions in 0 min 17 sec
Command being timed: "./sambamba-0.8.0 markdup HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.bam test.bam"
User time (seconds): 196.01
System time (seconds): 69.92
Percent of CPU this job got: 1392%
Elapsed (wall clock) time (h:mm:ss or m:ss): 0:19.09
Average shared text size (kbytes): 0
Average unshared data size (kbytes): 0
Average stack size (kbytes): 0
Average total size (kbytes): 0
Maximum resident set size (kbytes): 1732640
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 0
Minor (reclaiming a frame) page faults: 687925
Voluntary context switches: 4157903
Involuntary context switches: 6964
Swaps: 0
File system inputs: 1720752
File system outputs: 1967384
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0
Download and unzip sambamba-0.8.0.gz:
md5sum sambamba-0.8.0-linux-amd64-static.gz
7895d6d73f9d931525aa4fd709450803 sambamba-0.8.0-linux-amd64-static.gz
chmod u+x sambamba-0.8.0
./sambamba-0.8.0Sambamba 0.7.1
ChangeLog v0.7.1 (20191128)
- Fixed major segfault problem that got introduced after ldc 1.10, see #393
- make error message more informative - see https://github.com/biod/sambamba/pull/411/files, thanks https://github.com/EwaMarek
penguin2:~$ /usr/bin/time --verbose ./sambamba-0.7.1-linux-static markdup HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.bam test.bam
sambamba 0.7.1
by Artem Tarasov and Pjotr Prins (C) 2012-2019
LDC 1.17.0 / DMD v2.087.1 / LLVM8.0.1 / bootstrap LDC - the LLVM D compiler (1.17.0)
finding positions of the duplicate reads in the file...
sorted 3969781 end pairs
and 73839 single ends (among them 22397 unmatched pairs)
collecting indices of duplicate reads... done in 642 ms
found 239673 duplicates
collected list of positions in 0 min 8 sec
marking duplicates...
collected list of positions in 0 min 18 sec
Command being timed: "./sambamba-0.7.1-linux-static markdup HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.bam test.bam"
User time (seconds): 177.73
System time (seconds): 45.90
Percent of CPU this job got: 1097%
Elapsed (wall clock) time (h:mm:ss or m:ss): 0:20.38
Average shared text size (kbytes): 0
Average unshared data size (kbytes): 0
Average stack size (kbytes): 0
Average total size (kbytes): 0
Maximum resident set size (kbytes): 1343524
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 0
Minor (reclaiming a frame) page faults: 436841
Voluntary context switches: 4610690
Involuntary context switches: 11696
Swaps: 0
File system inputs: 48
File system outputs: 1967368
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0
Static file was built on Debian testing. Md5sum:
a47932d27f92a2639d4b228eb7847e04 /home/wrk/sambamba-0.7.1-linux-static.gz
Sambamba 0.7.0
Sambamba 0.6.9
ChangeLog v0.6.9 (20190313)
-
Added support for Picard style sorting, see #369 - thanks https://github.com/TimurIs
-
Add a new sorting option to pull together mates when sorting by read name, see #380 - thanks https://github.com/emi80
-
Many module renames to build a BioD for the future - thanks https://github.com/george-githinji
sambamba 0.6.9 by Artem Tarasov and Pjotr Prins (C) 2012-2019 LDC 1.14.0 / DMD v2.084.1 / LLVM7.0.1 / bootstrap LDC - the LLVM D compiler (0.17.6)
2e1c46f4627a00f85a248b0941cbd37f bin/sambamba-0.6.9-linux-static.gz
Sambamba 0.6.8
ChangeLog v0.6.8 (20181004)
Pre-release with a much faster statically compiled binary. 10-20% faster than v0.6.6, due to ldc and LLVM improvements. Fixes speed regression of v0.6.7 for large files due to singleobj compilation. See also #345 and performance
64-bit compilation should be fine on ldc 1.10+. i386 target is still a problem.
- Fix mark duplicates in files with many contigs, see #361 (thanks Devon Ryan @dpryan79)
- Fix missing PM tag in #356 (thanks Kurt Hetrick @Kurt-Hetrick)
- Fix Bcftools version checking #352 (thanks Nathan S. Watson-Haigh @nathanhaigh)
- Fixate version info in BAM output headers for reproducibility. See #357
- Fixed Makefile for general use, see #332
- Started benchmarking, see #283 and https://github.com/biod/sambamba/blob/master/test/benchmark/stats.org
- Readded Travis-ci support for Linux (and MacOS #338)
- Fixed MacOS build in Travis with ae269cf
- Updated BioD to latest biod/BioD@5e56b2b
- Bug fixes:
- Documentation updates
- Updated lz4 to latest (still source in tree because Debian dropped frame support in liblz4-dev)
- Added support for GNU Guix and build containers
- Added shunit2 to the source tree for testing
- Update python build dependencies to use python3.x
- Fixed a number of D compiler messages on deprecated features (ldc 1.11)
To install the image, download and
md5sum sambamba-0.6.8.gz
ee61000bcb33a82013c284bac8feb91f sambamba-0.6.8.gz
gzip -d sambamba-0.6.8.gz
chmod a+x sambamba-0.6.8
./sambamba-0.8.6
sambamba 0.6.8 by Artem Tarasov and Pjotr Prins (C) 2012-2018
LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4)The binary images were built on x86_64 with
~/.config/guix/current/bin/guix pull -l
Generation 3 Sep 25 2018 09:39:08
guix 932839f
repository URL: https://git.savannah.gnu.org/git/guix.git
branch: origin/master
commit: 932839ff124ff3b0dd3070914fb1c5beec69bf32
guix environment -C guix --ad-hoc gcc gdb bash ld-wrapper ldc which python git
make clean && make -j 16 && make check
for x in `ldd bin/sambamba|cut -d ' ' -f 3` ; do realpath $x ; done
/gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libpthread-2.27.so
/gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libm-2.27.so
/gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/librt-2.27.so
/gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libdl-2.27.so
/gnu/store/bmaxmigwnlbdpls20px2ipq1fll36ncd-gcc-8.2.0-lib/lib/libgcc_s.so.1
/gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libc-2.27.so
# build static image
make clean && make static -j 16 && make checkGit submodule versions were
git submodule status
2f0634b187e0f454809432093238cf31e9fbfee6 BioD (v0.2.0-5-g2f0634b)
2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5 htslib (0.2.0-rc10-271-g2f3c3ea)
b3692db46d2b23a7c0af2d5e69988c94f126e10a lz4 (v1.8.2)
9be93876982b5f14fcca60832563b3cd767dd84d undeaD (v1.0.1-49-g9be9387)
0.6.8-pre3
This is a pre-release of sambamba, please test.
ChangeLog v0.6.8-pre3 (20180910)
Pre-release with a much faster statically compiled binary. 10-20%
faster than v0.6.6, due to ldc and LLVM improvements. Fixes speed
regression of v0.6.7 for large files due to singleobj compilation. See
also #345 and
performance
64-bit compilation should be fine on ldc 1.10. i386 target is still a problem.
- Fix mark duplicates in files with many contigs, see #361 (thanks Devon Ryan @dpryan79)
- Fix Bcftools version checking #352 (thanks Nathan S. Watson-Haigh @nathanhaigh)
- Fixate version info in BAM output headers for reproducibility. See #357
- Fixed Makefile for general use, see #332
- Started benchmarking, see #283 and https://github.com/biod/sambamba/blob/master/test/benchmark/stats.org
- Readded Travis-ci support for Linux (MacOS is disabled #338)
- Updated BioD to latest biod/BioD@5e56b2b
- Bug fixes:
- Documentation updates
- Updated lz4 to latest