Creating omopolymeric positions (span=4) from reference file ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa
Loading chromosome names from index file ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa.fai
1 chromosome names found
Opening reference file ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa.
Reference file ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa opened.
Loading reference sequence for chromosome AL123456.3
Reference sequence for chromosome AL123456.3 loaded (len: 4411532)
Reference file ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa closed.
35368 total omopolymeric positions found.
Time to produce all the omopolymeric positions: 0:00:00.550978
Writing omopolymeric positions to file: ../mtuberculosis2/4-snvCalling/homopol/mycobacteriumTuberculosis/SRR25787975.homopol.txt.
Omopolymeric positions written into file: ../mtuberculosis2/4-snvCalling/homopol/mycobacteriumTuberculosis/SRR25787975.homopol.txt.
Loading omopolymeric positions from file ../mtuberculosis2/4-snvCalling/homopol/mycobacteriumTuberculosis/SRR25787975.homopol.txt
[None] 149358 total omopolymeric positions found.