Releases: biod/sambamba
Releases · biod/sambamba
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 inview
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
insambamba 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
andflagstat
when running multiple threads. -
index
tool collects statistics readable bysamtools 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
)