Public method for CRAMIntervalIterator for overlapping intervals #1120
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@@ Coverage Diff @@
## master #1120 +/- ##
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+ Coverage 66.052% 66.063% +0.011%
- Complexity 7685 7690 +5
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Files 538 538
Lines 32582 32584 +2
Branches 5529 5529
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+ Hits 21521 21526 +5
+ Misses 8909 8907 -2
+ Partials 2152 2151 -1
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| @@ -466,6 +466,32 @@ void enableFileSource(final SamReader reader, final boolean enabled) { | |||
| iterator.setFileSource(enabled ? reader : null); | |||
| } | |||
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| /** | |||
| * Prepare to iterate through SAMRecords that match the given intervals. | |||
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I think we should slightly narrow the description of what this method does. Since there is no validation that the provided chunks actually match (fully span) the territory covered by the intervals, it possible that the iterator doesn't return the full set of records matching the query. The records are constrained first by the chunks, then further constrained by the intervals.
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Good point. I've revised the wording to say "Prepare to iterate through SAMRecords that match the intersection of the given intervals and chunk boundaries."
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@tomwhite This looks good to me, it just needs a test for the new method.
…ping intervals, much like BAMFileReader#createIndexIterator.
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Added a new test. |
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@tomwhite Thank you. |
Description
Expose a method to create a CRAMIntervalIterator to get reads overlapping intervals, much like BAMFileReader#createIndexIterator. See #1112
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