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Ecogenomics / BamM

Metagenomics-focused BAM file manipulation
http://ecogenomics.github.io/BamM/
GNU Lesser General Public License v3.0
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feature/bug request/report: restrict parse output based on ref length #1

Closed wwood closed 10 years ago

wwood commented 10 years ago

Hey,

I've noticed bamm taking a decent amount of memory (100GB+ before I brought down the hammer) when running through a bam file with large numbers of contigs (~8 million), using outlier mode.

One possible fix for this might be to restrict output based on contig size e.g. only print contigs with >2kb length. This would be handy anyway, over and above fixing the RAM issue. Presumably the RAM issue can be fixed since the bam file was created by mapping to those same contigs as references.

ta

minillinim commented 10 years ago

This is now implemented. use --length