v0.4.7

Yet another bugfixing release.

• Use random subdirectories for temporary files in both sort and markdup utilities (allows to run multiple processes in parallel) (#74)
• Fixed bug in slice tool: when slicing last reference, unmapped reads were written too (#76)
• Fixed a bug in uncompressed BAM output (#78)
• Fixed a bug in BED intersection routine (#79)

v0.4.6

• fixed a bug in duplicate marking tool
• fixed handling empty BAM files in sort tool
• repeated subsampling now works correctly

v0.4.5

• New -L option in view tool which allows to intersect sorted BAM file with a BED file
• Aborting if output filename clashes with one of input filenames
• Improved performance of conversion to SAM

v0.4.4

Fixed sorting by name — it was broken in the recent releases.

v0.4.3

• improved sort performance
• bug fixes in sort (it previously failed to merge files without -p flag due to miscompilation)
• view supports '*' region instead of --unmapped option which is removed now

v0.4.2

• new option --unmapped in sambamba view which works only for indexed BAM files
  
  (for unindexed SAM/BAM use --filter 'ref_id == -1')
• fixed epic bug in random access code which was introduced in 0.4.1 :(

v0.4.1

• Integrated new BAM reader (less use of garbage collector => better scaling on multicore).

  The effect is most visible on view -c and flagstat when running multiple threads.

• index tool collects statistics readable by samtools idxstats

• Optional check during indexing that bins are computed correctly

• Fixed a long-standing bug: -f json outputted SAM instead of JSON

sambamba_v0.4.1_centos5.tar.bz2 was built with LDC 0.11.0 while
sambamba_v0.4.1b_centos5.tar.bz2 was built with LDC 0.12.0

v0.4.0

Added tool for marking duplicates, which uses Picard criteria.

v0.3.3

• bugfix: reduced buffer size for uncompressed BAM output (it was more than pipe buffer size)
• added subsampling option to sambamba view

v0.3.2

• fixed bug in flagstat parameter parsing
• consistent name of option for specifying number of threads (-t)