Fix CRAM container offset calculation #1167
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@cmnbroad, could you take a look when you get a chance please? I found the bug when I was testing large CRAM files with Disq. |
Codecov Report
@@ Coverage Diff @@
## master #1167 +/- ##
===============================================
+ Coverage 68.354% 68.372% +0.018%
- Complexity 8003 8005 +2
===============================================
Files 541 541
Lines 32674 32674
Branches 5531 5531
===============================================
+ Hits 22334 22340 +6
+ Misses 8115 8111 -4
+ Partials 2225 2223 -2
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cmnbroad
requested changes
Jul 18, 2018
| // try to read a container from the offset to check it's correct | ||
| try (SeekableFileStream seekableFileStream = new SeekableFileStream(cramFile)) { | ||
| seekableFileStream.seek(headerOnlyContainer.offset); | ||
| ContainerIO.readContainer(actualHeader.getVersion(), seekableFileStream); |
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Since you have the actual fullContainer that corresponds to the container you're reading from the stream, can you grab the return value from readContainer and add a couple of equality asserts, maybe for alignmentStart, alignmentSpan, nofRecords, checksum, to verify the container is intact.
tomwhite
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cmnbroad
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Jul 19, 2018
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I hope I'm not stepping on any toes as I merge this.... |
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Thanks @yfarjoun! |
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Description
Fixes a bug from #1129, and added a test to check for the error (which fails without the fix).
Checklist