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Sambamba 0.8.0
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@pjotrp pjotrp released this 30 Nov 15:09
· 72 commits to master since this release
v0.8.0
cdc5f84

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