@pjotrp pjotrp released this Oct 4, 2018 · 17 commits to master since this release

Assets 3

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:
    • #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 check

Git 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)
Pre-release

@pjotrp pjotrp released this Sep 10, 2018 · 46 commits to master since this release

Assets 3

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:
    • #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

@pjotrp pjotrp released this Nov 23, 2017 · 238 commits to master since this release

Assets 3
  • Adding ability to provide bed file for sambamba slice (#307) by Brett T. Hannigan
  • Adding ability to slice multiple regions at once by Brett T. Hannigan
  • markdup: use uint type for read scores; fixes #137

@lomereiter lomereiter released this Mar 5, 2017 · 284 commits to master since this release

Assets 4
  • view tool --num-filter option (#264), the syntax is x/y (x, /y), meaning samtools -f x -F y
  • filtering bug fix: enable [mate_]ref_name =~ /regex/ matching (#265)

@lomereiter lomereiter released this Oct 24, 2016 · 326 commits to master since this release

Assets 4
  • mpileup:
    • fix hanging issues (#247, thanks @nosepy)
    • queue length based on total data size (#253)
  • A few more warnings are printed (#251, #254)
  • Sort is more robust when memory can't be allocated (#254 by @sambrightman)

@lomereiter lomereiter released this Sep 10, 2016 · 341 commits to master since this release

Assets 4
  • mpileup:
    • Parallellization improvements by @sambrightman (#238)
    • Fixed a bug with splitting at chromosome ends (#244)
  • view adds a 'PG' record to the header (#206)
  • Tool awareness of the new AH ('alternate haplotype') SAM header tag (thanks @indraniel)
  • Binary builds on Linux are now done with LLVM 3.8 and LDC 0.17.1 which should improve both performance and stability
  • Added YAML file generator for updating the bioconda package

@lomereiter lomereiter released this Jun 21, 2016 · 354 commits to master since this release

Assets 4
  • Fixed handling zero-coverage bases in depth base (#225)
  • Option -z/--report-zero-coverageis now deprecated, use -c 0/--min-coverage=0 instead

@lomereiter lomereiter released this Jun 16, 2016 · 360 commits to master since this release

Assets 4
  • Updated lz4 library to fix occasional mpileup/markdup failures (#214, #224)
  • Fixed a minor bug in depth window (c228c63)

@lomereiter lomereiter released this May 1, 2016 · 365 commits to master since this release

Assets 4
  • depth tool:
    • new option -m (--fix-mate-overlaps) for proper counting of overlapping read pairs (#204)
    • fixed a rare bug occurring when two consecutive records have same position but different reference (#193)
  • filtering (all tools):
    • empty string is now accepted (#191)
    • new string fields are recognized: strand (+/-), ref_name, and mate_ref_name (#203)

@lomereiter lomereiter released this Mar 6, 2016 · 385 commits to master since this release

Assets 4
  • Fixed segfaults with PacBio reads (#182, #190)
  • Implemented external sort in markdup command, its memory usage should be much lower now (#123)
  • Added chimeric flag to filtering (#185), which selects paired reads mapped to different reference sequences