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norm: left-align <DUP> with INFO/END but no INFO/SVLEN - #2602
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A <DUP> took its length only from INFO/SVLEN, so one described by INFO/END alone was returned unchanged rather than realigned. The <DEL> branch uses line->rlen, which htslib already derives from INFO/END or INFO/SVLEN for both types, so do the same for <DUP>. Assisted-by: Claude:claude-fable-5-1 Signed-off-by: Dave Lawrence <davmlaw@gmail.com>
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With some modification, this is now merged. Thank you |
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Human Summary
Fixes #2601 - this makes
<DUP>behave the same as<DEL>. Added new tests, old tests still passAI Summary
realign()read a<DUP>'s length only fromINFO/SVLEN, so a<DUP>withINFO/ENDbut noSVLENcame back asERR_SYMBOLICand was not left-aligned. A<DEL>with onlyENDalready was, because the<DEL>branch takes its length fromline->rlen, and htslib'sget_rlen()derivesrlenfromINFO/ENDorINFO/SVLENfor both<DEL>and<DUP>. This makes the<DUP>branch userlenthe same way and drops the separateSVLENlookup.Test
norm.symbolic.4(reusing thenorm.symbolic.3reference) has the explicit dup, theEND-only<DUP>and theSVLEN+END<DUP>; all three now normalize to position 11 withEND=18. Output is unchanged for<DUP>withSVLEN,<DEL>, and the other symbolic types (<INV>,<INS>,<CNV>,<*>, breakends), which are still passed through.test/test.plpasses.Assisted-by: Claude:claude-fable-5-1