BAM, Zlib and BGZF library

[xinwu]

Hi all,
There is few information in SAMTools website and the published paper about BAM. In the paper, the author said BAM is based on the Zlib and used BGZF library. I just wonder where can I find the customized Zlib algorithm and BGZF library? I've search it with google but found nothing.
Thanks in advance.

[maubp]

See http://samtools.sourceforge.net/SAM1.pdf

[jkbonfield]

The code for implementing bgzf is in the samtools C distribution (bgzf.c), although the API seems a bit unstable. I noticed bgzf_tell vanished in 0.1.8 but was in 0.1.7.

It's a reasonable interface though, essentially allowing some pretence at randomly seeking to notional file offsets as if the data was uncompressed. I assume the Java Picard class has a similar API to bgzf too.

[lh3]

bgzf_tell becomes a macro in 0.1.8

[jkbonfield]

Ah thanks Heng. My mistake - having rechecked my build environment somehow I was picking up include files from one version with the library from another. Oops.

Cheers.