Fix bug in the samblaster module #1176
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The samblaster module tries to capture samblaster log files, and retrieve the mark duplicates statistics via regex pattern matching. However, sometimes the regex fails to capture certain samblaster logs, such as the example below: samblaster: Version 0.1.25(3.2 KiB/s) with 1 file(s) remaining samblaster: Inputting from stdin samblaster: Outputting to stdout samblaster: Loaded 84 header sequence entries. samblaster: samblaster: Pair Type Type_ID_Count %Type/All_IDs Dup_ID_Count %Dups/Type_ID_Count %Dups/All_Dups %Dups/All_IDs samblaster: --------------------------------------------------------------------------------------------------------------- samblaster: Both Unmapped 2645 0.077 0 0.000 0.000 0.000 samblaster: Orphan/Singleton 24303 0.706 1952 8.032 0.212 0.057 samblaster: Both Mapped 3416627 99.217 920794 26.950 99.788 26.739 samblaster: Total 3443575 100.000 922746 26.796 100.000 26.796 samblaster: samblaster: Marked 922746 of 3443575 (26.796%) total read ids as duplicates using 49304k memory in 4.779S CPU seconds and 14S wall time. Previously the regex can't match the last line.
ewels
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Great stuff, thanks! 👍 |
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The samblaster module tries to capture samblaster log files, and retrieve the mark duplicates statistics via regex pattern matching. However, sometimes the regex fails to capture certain samblaster logs, such as the example below:
(generated by samblaster 0.1.25 processing bam files aligned by
bwa mem)Previously the regex is:
It can't match the last line.
Many thanks to contributing to MultiQC!
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