#263 correctPacBio paired filtering always fails due to commit r4443

correction
closed-fixed
nobody
None
5
2014-04-04
2013-11-08
Harm van Bakel
No

Commit [r4443] updated correctPacBio paired filtering to proceed if the new overlap store creation failed. As part of this update, the "assert(system(command)==0);" statements for the deletion of any previous overlapstore and the creation of the paired list needed for the new overlap store creation were removed. As a result, the overlap store building will always fail because the system command to create the paired.list file is never run. The fix would be to run the system commands without the asserts, i.e. change lines 444 and 445 to:

sprintf(command, "rm -rf %s.paired.ovlStore", thread_globals.prefix);
system(command);
sprintf(command, "find . \\( -name %s\\*ovb \\) -print > %s.paired.list", thread_globals.prefix, thread_globals.prefix);
system(command);

Related

Commit: [r4443]

Discussion

  • Sergey Koren
    Sergey Koren
    2014-04-04

    Has been fixed in CA 8.1

     
  • Sergey Koren
    Sergey Koren
    2014-04-04

    • status: open --> closed-fixed