Fix decoding of long CIGAR ops in BAM #173
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@@ Coverage Diff @@
## master #173 +/- ##
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Coverage 86.9% 86.9%
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Files 73 73
Lines 5683 5683
Branches 482 482
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Hits 4939 4939
Misses 262 262
Partials 482 482
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Problem
cljam.io.bamfails to decode alignments with CIGAR operations longer than 134217728Cause
A CIGAR is stored as an array of
op_len<<4|opinuint32_t[n_cigar_op].Thus
op_lencan be as long as 28bit0x0FFFFFFFbut it is not handled properly due to type promotion from int to long.Changes
Use
Integer/toUnsignedLongto get a positive long value.Tests
lein check🆗lein test :all🆗lein cloverage🆗lein eastwood🆗