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qprofiler - Fastq mode can't convert String to Integer #248

Open holmeso opened 3 years ago

holmeso commented 3 years ago

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:

  1. Run qprofiler against the fastqs listed above
  2. 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.

ChristinaXu2017 commented 3 years ago

read id "@K00171:1:1:1029:H2TVWBBXY:4:2106:18954:16753:GAGATGAG" can't be recognized by qprofiler but it should be able to accept by qprofiler2. There is the detailed error message on the log file: 

Error caught parsing FastqRecord with readHeader: K00171:5:2:1029:H2TVWBBXY:4:2205:11403:43726:GAGATGAG
...
record: @K00171:1:1:1029:H2TVWBBXY:4:1211:9008:43831:GAGATGAG
CTGCGCTTGCCTTCGCTGACGTGCCCACAGCTGGAATGGCAGAAACTGGGCCTGCTGACATCAGACAGCCCCGACTCCTTACTTTTACTGGTTACT
+
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