Fix edge case when haplotypes have leading insertion after trimming #6518
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takutosato
approved these changes
Mar 23, 2020
| @@ -141,6 +141,9 @@ public static GATKRead createReadAlignedToRef(final GATKRead originalRead, | |||
| * | |||
| * If refStart or refEnd would start or end the new bases within a deletion, this function will return null | |||
| * | |||
| * If the cigar starts with an insertion, the inserted bases are considered as coming before the start position and | |||
| * are therefore excluded from the result. That is getBasesCoveringRefInterval(0, 3, "ACTTGT", 0) should yield "TTGT". | |||
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I would add the cigar "2I4M" here: so
That is getBasesCoveringRefInterval(0, 3, "ACTTGT", 0) -> That is getBasesCoveringRefInterval(0, 3, "ACTTGT", 0, "2I4M")
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@takutosato Two quick edge cases and new unit tests. These were exposed when fixing other bugs.