Memory leak in Faidx.pm/xs
Created by: keiranmraine
Hi,
It looks like there is a mem leak in the Faidx.pm/xs module:
$ /usr/bin/time perl snpPanelGcCorrections.pl genome.fa SnpPositions.tsv
Chr Position ...
AUTO_1 1 3023783 ...
0.19user 0.02system 0:00.22elapsed 97%CPU (0avgtext+0avgdata 129104maxresident)k
0inputs+0outputs (0major+10915minor)pagefaults 0swaps
$ /usr/bin/time perl snpPanelGcCorrections.pl genome.fa SnpPositions.tsv
Chr Position ...
AUTO_1 1 3023783 ...
AUTO_2 1 3036178 ...
0.36user 0.03system 0:00.40elapsed 97%CPU (0avgtext+0avgdata 237648maxresident)k
0inputs+0outputs (0major+18918minor)pagefaults 0swaps
$ /usr/bin/time perl snpPanelGcCorrections.pl genome.fa SnpPositions.tsv
Chr Position ...
AUTO_1 1 3023783 ...
AUTO_2 1 3036178 ...
AUTO_3 1 3050521 ...
0.52user 0.06system 0:00.60elapsed 95%CPU (0avgtext+0avgdata 308112maxresident)k
0inputs+0outputs (0major+25291minor)pagefaults 0swaps
Each line is the result of 16 requests against faidx around a position increasing up to 10mb