Filter alignments in a single step about tigmint HOT 7 CLOSED

I've fixed 1. I will fix 2. Thanks for both suggestions, @abmudd!

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awk is quite slow. Do you know of a faster tool to filter a SAM or BAM file based on AS and NM?

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Did you get Tigmint running? Any trouble with installation?

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I don't know if pysam would be any faster than gawk. You can run the gawk command as a single line though:

gawk -v ascore=$ASCORE -v mismatch=$MISMATCH -F'\t' ' BEGIN { print "Flags\tRname\tPos\tMapq\tAS\tNM\tBX\tMI" } { as = bx = mi = nm = "NA" } match($$0, "AS:.:([^\t]*)", x) { as = x[1] } match($$0, "NM:.:([^\t]*)", x) { nm = x[1] } match($$0, "BX:Z:([^\t]*)", x) { bx = x[1] } match($$0, "MI:i:([^\t]*)", x) { mi = x[1] } { if (as >= ascore && nm <= mismatch) {print $2 "\t" $3 "\t" $4 "\t" $5 "\t" as "\t" nm "\t" bx "\t" mi }}'

Unfortunately, I have been unable to get tigmint running due to the large number of dependencies and conflicts within my system.

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I'll merge the gawk steps, hopefully next week. I'll experiment with finding faster options, and try out pysam.

Sorry to hear of your troubles installing Tigmint. It does have a lot of dependencies. Have you tried using Linuxbrew to install the dependencies? 🍺🐧 http://linuxbrew.sh
Tigmint has a Brewfile: https://github.com/bcgsc/tigmint/blob/master/Brewfile
I'll create a Docker image.

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I've created a Docker image bcgsc/tigmint with all the dependencies installed.
https://hub.docker.com/r/bcgsc/tigmint/
https://github.com/bcgsc/tigmint/blob/master/Dockerfile

docker run -it --name=tigmint bcgsc/tigmint
tigmint-make help

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Alignments are now filtered (in one step) by tigmint-molecule, which takes a SAM/BAM file of reads aligned to the reference (sorted by barcode with samtools -t BX) and outputs a BED file of molecules.

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