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  • Biodescartes
    Junior Member
    • Apr 2014
    • 1
    #1

    How to write parallel bai files in C

    Hello everybody !
    I'm a newbie in this site and I'm happy to be a part of the seqancers community.
    I have to precise that I'm french and my english could be bad sometimes and I'm sorry for that. So please let me know if I'm not enough understandable.

    I'm a computer science sophomore, and I have a programming project.
    This using C langage with SamTools and MPI.

    Basically we will receive chromosom reads under String type and we have to write those in Bam files (using bgzf) and Bai corresponding files.
    After hours of research in google, I can't find the right information for my case.

    My question is:
    How can I write .bai corresponding files in C ? What are the steps to make this done ?

    Thank you
    Tags: None
    • dpryan
      Devon Ryan
      • Jul 2011
      • 3478
      #2
      I think one of your classmates has also been asking for help.

      In the samtools C API, the function you want is bam_index_build(), which accepts the name of a BAM file (char *) as an argument. If you really must write your own method then I'd recommend just looking through that function for implementation details (the format is mentioned in the SAM specification, but I recall reading recently that some details are missing).

        Comment

        • maubp
          Peter (Biopython etc)
          • Jul 2009
          • 1544
          #3
          There is an open pull request to add the missing BIN and index information to the official specification:
          Describe BAI changes for 'samtools idxstats' and details of BIN value by peterjc · Pull Request #2 · samtools/hts-specs
          https://github.com/samtools/hts-specs/pull/2
          Pull request as requested on mailing list: http://sourceforge.net/mailarchive/message.php?msg_id=29006056

            Comment

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