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new find-locations module

Thomas Krannich requested to merge new-find-locations-module into main

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
...

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