Skip to content

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

@holmeso

Description

@holmeso

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.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type
    No fields configured for issues without a type.

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions