`hisat-3n-table` can not parse base quality correctly

DaehwanKimLab / hisat2

Graph-based alignment (Hierarchical Graph FM index)

GNU General Public License v3.0

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`hisat-3n-table` can not parse base quality correctly #392

Closed y9c closed 1 year ago

y9c commented 1 year ago

Some alignment files can not parsed by hisat-3n-table correctly, Although the number of converted and unconverted counts is correct, the baseQuality columns are not. An example for debugging is attracted.

hisat-3n-table -p 12 --alignments test.sam --ref ./ref.fa --output-name /dev/stdout --base-change C,T

test.zip

imzhangyun commented 1 year ago

Hello @y9c ,

I am sorry for the bug. I just fixed the problem. Please pull & make again.

Best, Leo