emtrey (M-2PO, minimap 2 psl output)

SAM to PSL conversion program. Preferably takes a SAM file produced by minimap2 to make a PSL file.

Dependencies

• Go

To compile, use make

Usage

emtrey takes a minimap SAM file and outputs a PSL file.

Options:

-i    Input SAM file
-m    Use to indicate the use of a SAM file that came from minimap2

emtrey will output the PSL file to stdout.

Using a minimap sam file:

./emtrey -m -i minimap_output.sam >out.psl

Otherwise:

./emtrey -i alignment.sam >out.psl

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Notes

• If you aren't using a minimap sam file, the first three columns of the psl file will probably be wrong, since most aligners use M to indicate matches and mismatches without using X or = in their CIGAR strings. However, matches and mismatches can be calculated using the NM:i: and nn:i: tags that minimap produces.

• The strand is determined using the 0x10 bit, as per the SAM file format spec. If you have a spliced minimap alignment, it will check for the extra tag ts:A:, which overwrites what was calculated from the bit.

• Be sure to leave the header in the SAM file, as it's needed for the target sizes.