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Description
Describe the bug
Qprofiler Fastq mode is complaining about trying to convert a String to an Integer:
16:39:32.674 [pool-2-thread-6] SEVERE org.qcmg.qprofiler.fastq.FastqSummaryReport - Can't convert string to integer: H2TVWBBXY
java.lang.NumberFormatException: For input string: "H2TVWBBXY"
see following log files for more info:
/working/genomeinfo/data/20210128_BarbourOeso/ForQIMR_Jan2021/Deduped-MelR101_1.fastq.gz.qp.xml.log
/working/genomeinfo/data/20210128_BarbourOeso/ForQIMR_Jan2021/Deduped-MelR101_se.fastq.gz.qp.xml.log
/working/genomeinfo/data/20210128_BarbourOeso/ForQIMR_Jan2021/Deduped-MelR101_2.fastq.gz.qp.xml.log
To Reproduce
Steps to reproduce the behavior:
- Run qprofiler against the fastqs listed above
- See error
Expected behavior
qp fastq mode should be able to handle the case where a String contains text rather than numerals. At the very least, a more detailed error message should be displayed.
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