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cancerit / PCAP-core

NGS reference implementations and helper code for mapping (originally part of ICGC-TCGA-PanCancer)
GNU General Public License v2.0
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Changes required to provide a merging script which is aware of mmQc #50

Closed keiranmraine closed 4 years ago

keiranmraine commented 4 years ago

Still setting up additional flow in internal large-scale CI for new elements

keiranmraine commented 4 years ago

Internal CI report: https://casm.pages.internal.sanger.ac.uk/cit-github/pcap-core/results/feature-mergeOrMark/summary/

keiranmraine commented 4 years ago

@AndyMenzies there is a review pending from 20th December

AndyMenzies commented 4 years ago

Code looks good. WGS results are good. Do we know why the results for Amplicon and WXS differed from previous?

keiranmraine commented 4 years ago

Do we know why the results for Amplicon and WXS differed from previous?

Those are physical remaps where we expect a small variance in result (as described in the report).

MARK/MERGE is the change to the code, they are exact as mapping is precalculated, only merging or duplicate marking (with inline merging) occur. These are via completely new routines and script.

keiranmraine commented 4 years ago

@AndyMenzies also, if you compare to previous reports for other tags, they are the same differences so actually stable against the new container.

AndyMenzies commented 4 years ago

Agreed, all looks good to me.

keiranmraine commented 4 years ago

This has been pulled into the bwamem2 branch as already approved.