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@pjotrp pjotrp released this Nov 28, 2019 · 9 commits to master since this release

ChangeLog v0.7.1 (20191128)

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
Assets 3

@pjotrp pjotrp released this May 29, 2019 · 22 commits to master since this release

  • Release avoids crashing problem by building with ldc-1.10.0, see #393
  • Merge pull request #396 from joelmartin/flagstat-return returning 0
Assets 3

@pjotrp pjotrp released this Mar 14, 2019 · 30 commits to master since this release

ChangeLog v0.6.9 (20190313)

2e1c46f4627a00f85a248b0941cbd37f bin/sambamba-0.6.9-linux-static.gz

Assets 3
Jan 12, 2019
Merge pull request #383 from emi80/master
Add tests for the new '--match-mates' sort option

@pjotrp pjotrp released this Oct 4, 2018 · 56 commits to master since this release

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)
Assets 3
Pre-release
Pre-release

@pjotrp pjotrp released this Sep 10, 2018 · 85 commits to master since this release

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
Assets 3

@pjotrp pjotrp released this Nov 23, 2017 · 277 commits to master since this release

  • 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
Assets 3

@lomereiter lomereiter released this Mar 5, 2017 · 323 commits to master since this release

  • 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)
Assets 4

@lomereiter lomereiter released this Oct 24, 2016 · 365 commits to master since this release

  • 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)
Assets 4

@lomereiter lomereiter released this Sep 10, 2016 · 380 commits to master since this release

  • 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
Assets 4
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