Depth File contigName Column

[Harrison Ho]

The Depth File contigName column sometimes contains more than just the contig name. When megahit is used as the assembler before running Metabat2, the contigName column will also contain “flag= multi= len= “ after the contig name.

[Rob Egan]

On the premise that these flags are part of the BAM file’s query name for each of these contigs, I modified jgi_summarize_bam_contig_depths.* to trim the comments off of the BAM header target_names before using them.

Harrison, can you test to see if the desired effect is fixed with this version:

f66ce4a68d012d0e