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@pjotrp pjotrp released this Nov 30, 2020 · 3 commits to master since this release

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-0.8.0
Assets 3

@pjotrp pjotrp released this Nov 28, 2019 · 32 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 · 45 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 · 53 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 · 79 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 · 108 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 · 300 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 · 346 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 · 388 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