Always call next() on both tokenizers, to make sure both r1 and r2 files are read to the end #53
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…les are read to the end (#1) * Tokenizer.next() fix for Illumina#41 * Also fix alignDualFastq
This was referenced May 14, 2023
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edmundmiller
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…les are read to the end * Tokenizer.next() fix for Illumina#41 * Also fix alignDualFastq Illumina#53
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There's an edge case where the
r2Tokenizer's buffer hasn't read to the end of ther2file yet, but the conditionalr1Tokenizer.next() && r2Tokenizer.next()gets short-circuited, leading tor2Tokenizer.next()not being called. That will triggerassert(inputR2.eof()).Fixes #41.