- Fixed the build for recent ldc2 compilers by using a recent msgpack
- Ran benchmarks and optimized meson build
A minor fix and a major release. After 10 years and over one thousand citations we can announce sambamba 1.0 stable!
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)
- Some FASTA unittests break when they write to disk and read after -
marked with
version(Broken) - Fix build for LDC 1.26.0 and LLVM 9.0.1 - some speed improvement
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 ec78eabfbdebd620cf5d4a4d8232692184eacbf7
- 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 cdc5f84c5b6135eedeaf5cba265e3eb9a3c23227
- Added badges to the top of README
- Added Meson build system for Debian (thanks Matthias @ximion)
- Fixed Python2 -> Python3 stuff (thanks Matthias @ximion)
- 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
- Release avoids crashing problem by building with ldc-1.10.0, see #393
- Merge pull request #396 from joelmartin/flagstat-return returning 0
- 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
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 (MacOS is disabled #338)
- Fixed MacOS build in Travis with ae269cfbdf2e78750ce7f8dc70ad32f80a6682df
- Updated BioD to latest https://github.com/biod/BioD/commit/5e56b2bb45324af2194b3339d298fd827c8003ae
- Bug fixes:
- #328 Debug version: SAM output of CRAM file is populated with debug on pipe
- #331 Segmentation fault attempting to view header in json format
- #335 Intel Xeon bug may segfault Sambamba - this was tracked down to an Intel Xeon bug
- #345 sambamba index 0.6.7 takes 4x longer than 0.6.6 on the same files
- 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)