Beta Release 0.1.15 (10 April, 2011)
* Allow to perform variant calling or to extract information in multiple
regions specified by a BED file (`samtools mpileup -l', `samtools view -L'
and `bcftools view -l').
* Added the `depth' command to samtools to compute the per-base depth with a
simpler interface. File `bam2depth.c', which implements this command, is the
recommended example on how to use the mpileup APIs.
* Estimate genotype frequencies with ML; perform chi^2 based Hardy-Weinberg
test using this estimate.
* For `samtools view', when `-R' is specified, drop read groups in the header
that are not contained in the specified file.
* For `samtools flagstat', separate QC-pass and QC-fail reads.
* Improved the command line help of `samtools mpileup' and `bcftools view'.
* Use a global variable to control the verbose level of samtools stderr
output. Nonetheless, it has not been full utilized.
* Fixed an issue in association test which may report false associations,
possibly due to floating point underflow.
(0.1.15: 10 April 2011, r949:203)
Release 0.2.4 (10 April, 2011)
* Give an error if the index file is older than the data file.
* Avoid a segfault given flawed input.
* Added Python APIs contributed by Hyeshik Chang. The new APIs do not bind to
the dynamic library and are reported to be faster. Pysam also comes with a
* Added option "-r" for efficient header replacement.
* Added BED support.
* Synchronized the BGZF library between tabix and samtools.
(0.2.4: 10 April 2011, r949)
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