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  • ensembl-gh-mirror
  • Bio-DB-HTS
  • Issues
  • #6

Closed
Open
Created Mar 09, 2016 by Marek Szuba@mks

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

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