AdamaJava / adamajava

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fix(qprofiler2): add ordering of readgroups in BamSummaryReport #378

Closed newellf closed 1 month ago

newellf commented 1 month ago

To ensure same order in xml output each time, read groups in the BamSummaryReport needed to be sorted before writing to xml

Description

XML produced was not consistent due to read groups not being sorted. Read groups are now sorted before writing to XML

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?

Added unit tests and ran multiple time on a test BAM file.

Are WDL Updates Required?

WDL test file workflow/test/testSDFTM_GS_xmls.sh need to be updated with new MD5sum for new order

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