Commits on May 1, 2020

1. Fix bug in the samblaster module …

   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.

   

   haizi-zh committed May 1, 2020
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