…mitting the "WARNING: BAM index file ... is older than BAM " message.
Description
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.
Things to think about before submitting:
[x] Make sure your changes compile and new tests pass locally.
[ ] Add new tests or update existing ones:
A bug fix should include a test that previously would have failed and passes now.
New features should come with new tests that exercise and validate the new functionality.
[ ] Extended the README / documentation, if necessary
[x] Check your code style.
[x] Write a clear commit title and message
The commit message should describe what changed and is targeted at htsjdk developers
Breaking changes should be mentioned in the commit message.
…mitting the "WARNING: BAM index file ... is older than BAM " message.
Description
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.
Things to think about before submitting: