replacing read id in bam file

[blu78]

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

[nilshomer]

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.

[blu78]

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