BamM is a c library, wrapped in python, that parses BAM files.

BamM is a c library, wrapped in python, that parses BAM files. The code is intended to provide a faster, more stable interface to parsing BAM files than PySam, but doesn’t implement all / any of PySam’s features.

Do you want all the links that join two contigs in a BAM?
Do you need to get coverage?
Would you like to just work out the insert size and orientation of some mapped reads?

Then BamM is for you!
$ bamm make -d -c read1.R1.fq.gz read1.R2.fq.gz …
$ bamm parse -c covs.tsv -l links.tsv -i inserts.tsv -b mapping.bam
$ bamm extract -g BIN_1.fna -b mapping.bam

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