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InterleavedFastqInFormatter should sort by readInFragment #1702

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fnothaft opened this Issue Aug 30, 2017 · 0 comments

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fnothaft commented Aug 30, 2017

Otherwise, you can get reads that are flipped in order. From WIP on bigdatagenomics/cannoli#65:

SNAP exited with exit code 1 from line 404 of file SNAPLib/FASTQ.cpp
PairedInterleavedFASTQReader: second read of batch doesn't have ID ending with /2: 'H06JUADXX130110:1:2112:13939:74406/1'
PairedInterleavedFASTQReader: second read of batch doesn't have ID ending with /2: 'H06HDADXX130110:2:1212:7495:26889/1'
SNAP exited with exit code 1 from line 404 of file SNAPLib/FASTQ.cpp
PairedInterleavedFASTQReader: first read of batch doesn't have ID ending with /1: 'H06HDADXX130110:1:2112:18137:64299/2'
SNAP exited with exit code 1 from line 404 of file SNAPLib/FASTQ.cpp
SNAP exited with exit code 1 from line 399 of file SNAPLib/FASTQ.cpp
PairedInterleavedFASTQReader: first read of batch doesn't have ID ending with /1: 'H06JUADXX130110:1:1115:17025:85774/2'
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