AdamaJava / adamajava

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fix(qprofiler): don't assume type of SAM attribute #354

Closed holmeso closed 4 months ago

holmeso commented 4 months ago

Description

Updated qprofiler so that it will only attempt to cast/parse SAM attribute into a particular type if it is an instanceof that type.

Fixes # 353

Type of change

Please delete options that are not relevant.

[X] Bug fix (non-breaking change which fixes an issue)

How Has This Been Tested?

Unit test has been added and code has been run against BAM file that produced the error originally (successfully)

Are WDL Updates Required?

no

Checklist:

[X] My code follows the style guidelines of this project
[X] I have performed a self-review of my own code
[X] I have commented my code, particularly in hard-to-understand areas
[X] I have made corresponding changes to the documentation
[X] My changes generate no new warnings
[X] I have added tests that prove my fix is effective or that my feature works
[X] New and existing unit tests pass locally with my changes

holmeso commented 4 months ago

Apologies - this is hard to review because of the whole file formatting that I did. Key lines of BamSummaryReport file are 579-588, and 629-645.