The goal of the new PR is to add a new module to popins4snake that generates a locations file per individual.
The new module works in the fashion of the other modules like popins2 find-locations sampleID [OPTIONS].
The new module was successfully tested on the simulated data (https://zenodo.org/record/4890793) sample S0001:
/<path>/popins4snake/popins2 find-locations S0001 --prefix /<path>/unmapped/ --reference chr21_ins.fa
[popins2 2022-01-19 17:09:09] Reading contig names from /<path>/unmapped/S0001/non_ref.bam
[popins2 2022-01-19 17:09:09] Reading chromosomes from chr21_ins.fa
[popins2 2022-01-19 17:09:09] Computing contig locations from anchoring reads in /<path>/unmapped/S0001/non_ref_new.bam
nonContigSeqs=1
[popins2 2022-01-19 17:09:09] [popins4snake find-locations] finished in 0 seconds.Resulting in a file locations.txt file like:
chr21:29383581-29383789 - contig_1 + 4 1
chr21:30721622-30721828 + contig_10 + 2 1
OTHER + contig_100 - 2 1
chr21:44072503-44072680 - contig_101 + 2 1
chr21:37573547-37573737 + contig_102 - 9 1
OTHER + contig_103 - 1 1
chr21:27904616-27904792 + contig_103 + 2 1
chr21:16637588-16637738 + contig_104 + 3 1
chr21:31262275-31262381 - contig_105 - 1 1
...