17:51:02.922 [pool-2-thread-5] SEVERE org.qcmg.qprofiler.bam.BamSummarizerMT - error caught parsing SAMRecord with readName: consensus_read_TTGCCAG+AGAGACG_0_854556_15_3779068_5
java.lang.NumberFormatException: For input string: "MantaBND:0:129003:129004:0:0:0:0|PR"
java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:67)
java.base/java.lang.Integer.parseInt(Integer.java:661)
java.base/java.lang.Integer.parseInt(Integer.java:777)
org.qcmg.qprofiler.bam.BamSummaryReport.parseTAGs(BamSummaryReport.java:591)
org.qcmg.qprofiler.bam.BamSummaryReport.parseRecord(BamSummaryReport.java:552)
org.qcmg.qprofiler.bam.BamSummarizerMT$Consumer.run(BamSummarizerMT.java:324)
To Reproduce
As above.
Expected behavior
qProfiler should run on any bam, including bams that use a different semantics for custom tags than we do internally. The root cause of the issue is that qProfiler is assuming that if ZM tag appears, that it is an integer and it has the meaning that we assign internally. At a minimum we should be using the tag type (in this case it's Z for string, not i for integer) of custom tags to determine if it's sensible to perform numeric operations on them.
Describe the bug Running qprofiler on a bam from the DRAGEN TSO500 workflow with records like this:
fails with
java.lang.NumberFormatException
:To Reproduce As above.
Expected behavior qProfiler should run on any bam, including bams that use a different semantics for custom tags than we do internally. The root cause of the issue is that qProfiler is assuming that if
ZM
tag appears, that it is an integer and it has the meaning that we assign internally. At a minimum we should be using the tag type (in this case it'sZ
for string, noti
for integer) of custom tags to determine if it's sensible to perform numeric operations on them.