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Allow the BAM index to be up to 5 seconds older than the BAM before e… #1634

Merged
merged 1 commit into from
Nov 16, 2022
Merged

Allow the BAM index to be up to 5 seconds older than the BAM before e… #1634

merged 1 commit into from
Nov 16, 2022

Commits on Nov 16, 2022

  1. Allow the BAM index to be up to 5 seconds older than the BAM before e… 

    …mitting the "WARNING: BAM index file ... is older than BAM " message.

HTSJDK itself when writing a BAM and indexing it will frequently leave an mtime on the index that is slightly older than the BAM itself, and this causes a lot of spurious warnings.  This is a simple attempt to fix those.
    @tfenne
    tfenne committed Nov 16, 2022
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