CircularMapper does not modify BAM headers correctly: mapDamage and GATK warnings

apeltzer / CircularMapper

A method to improve mappings on circular genomes, using the BWA mapper

GNU General Public License v3.0

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CircularMapper does not modify BAM headers correctly: mapDamage and GATK warnings #1

Closed sc13-bioinf closed 8 years ago

sc13-bioinf commented 8 years ago

The CircularMapper method just modifies the header of the resulting "rewrapped" BAM file to match the original, unmodified reference genome. Apparently, this is not done entirely correct in some cases which is why mapDamage and GATK complain about this.

apeltzer commented 8 years ago

Investigating this, waiting for reply ....

apeltzer commented 8 years ago

Fixed in #2