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10XGenomics / bamtofastq

Convert 10x BAM files to the original FASTQs compatible with 10x pipelines
MIT License
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`head_suffix` missing index information #17

Open wflynny opened 4 years ago

wflynny commented 4 years ago

Besides sort order, I would expect that FASTQs generated from the bam should be identical to the original FASTQs. However, the head_suffix is hardcoded as :N:0:0 rather than the format :N:0:{index}. E.g.:

@A00739:209:HNTY3DMXX:2:1101:1090:1000 1:N:0:AGTGGAAC
...
@A00739:209:HNTY3DMXX:2:1101:4291:1000 1:N:0:AGTGGAAC
...
@A00739:209:HNTY3DMXX:2:1101:5195:1000 1:N:0:AGTGGAAC

Is it possible to include this information?