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cancerit / telomerecat

Telomerecat: The telomere computational analysis tool
GNU General Public License v3.0
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Does Telomerecat accepts CRAM file as input instead of BAM file? #21

Closed Ramanandan closed 3 years ago

Ramanandan commented 4 years ago

Hi,

I would like to use CRAM files instead of BAM files.

Does it accept CRAM files?

keiranmraine commented 3 years ago

All the pysam calls are actually in the parabam layer. They are hardcoded to r/w BAM currently.

It may be possible, but I'm aware of a few places where seek is called on the alignment files which would take some investigation to determine why.

keiranmraine commented 3 years ago

See 4.0.0