broadinstitute/oncotator — pull request #278 by lbergelson (2014-12-13 04:28:28+00:00)
Title: Fixing OnpCombiner for indels only files

fix for #276 in release-1.4
fixing an additional indel ordering issue
added tests to check for cases where there are only indels and ending indels
added a warning for out of order files when running with ``--infer-onps``
running out of order may fail to combine some onps
it may also lead to storing large numbers of mutations in memory while waiting to combine them