Io_lib 1.13.0 released.

Staden io_lib (aka libstaden-read) version 1.13.0 has been released.

The main addition is the inclusion of SAM, BAM and CRAM (both 1.0 and 2.0 specification) support along with a tool called "scramble" to convert between them. For the rest of the package the changes are minimal.

The sam/bam/cram code should be considered as beta quality and subject to changes, both in the code and APIs themselves but also potentially to the cram 2.0 specification which is still in "release candidate" form. The other tools are as stable as before and can be considered production quality.

The primary differences over this C CRAM implementation and the Java CRAM implementation are with speed and memory usage. There is some small speed improvements in the SAM/BAM implementation over Samtools, although definitely not as significant.

Long-term we are unsure if io_lib is the correct location for this code; the inclusion here is simply a migration out of the Gap5 directory which has had sam/bam I/O code for a considerable time.

James

Posted by James Bonfield 2013-03-22

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