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replacing read id in bam file

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  • replacing read id in bam file

    Hi everybody,

    I'd like to replace the sequence id for a huge alignment file in .bam format.
    I'd rather avoid using the sam format as it would be around 250GB of data, instead I'd like to use samtools c api (writesam/writebam).

    I couldn't find much documentation on how to use this library, does anyone know if there is any quick way to replace the read id? I know that the read id is stored in a bam1_t->data array but I cannot understand how to set/replace it.

    Any help is much appreciated. Thanks in advance

  • #2
    Originally posted by blu78 View Post
    Hi everybody,

    I'd like to replace the sequence id for a huge alignment file in .bam format.
    I'd rather avoid using the sam format as it would be around 250GB of data, instead I'd like to use samtools c api (writesam/writebam).

    I couldn't find much documentation on how to use this library, does anyone know if there is any quick way to replace the read id? I know that the read id is stored in a bam1_t->data array but I cannot understand how to set/replace it.

    Any help is much appreciated. Thanks in advance
    Modifying that portion is a bit of a pain using the C API since you have to resize the array etc. I would suggest using the Java API (or PERL or Python API) to replace the read name. It will be much easier, and with Java, almost as fast.

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    • #3
      Originally posted by nilshomer View Post
      Modifying that portion is a bit of a pain using the C API since you have to resize the array etc. I would suggest using the Java API (or PERL or Python API) to replace the read name. It will be much easier, and with Java, almost as fast.

      OK I will try and do that. Thanks a lot for the help

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