Add BreakendParser and tests #37
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Thanks for the PR - I somehow didn't see this until now. Will merge in manually as there are conflicts. I think this is the final piece in the puzzle. |
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I should have mentioned you.. 🙂 I'll do that from now on |
| throw new IllegalArgumentException("Unknown mate contig `" + mateContigName + '`'); | ||
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| Position matePos = null; | ||
| try { |
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Looking at this now, we don't even need to be catching this. If the alt allele is matched by BND_ALT_PATTERN, then the content of the pos group should be able to be parsed into an integer. Unless it overflows the INT 😖
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True, true - see 58359c2
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@ielis I've merged these changes renaming the new class as util/BreakendResolver like you originally wanted to name it. I think we've addressed all the major issues, so can you try them out and then if we're looking good, lets do a 1.0.0 release! |
Adding
BreakendParserand extensive tests that exercise all possible breakend orientations as well as almost all lines of code.