Code

Intel GKL-PDHMM update#9123

Code

Open

chirayuharyan wants to merge 29 commits intobroadinstitute:masterbroadinstitute/gatk:masterfrom

chirayuharyan:pdhmm-updatechirayuharyan/gatk:pdhmm-updateCopy head branch name to clipboard

Commits

Commits on Mar 19, 2025

• Add in the preview GKL build as a dependency

  Show description for da0c2a7
  

  droazen

  authored and

  lbergelson

  committed
  da0c2a7

  Copy full SHA for da0c2a7

• Added the java code to wrap the IntelPDPairHMM implementation for DRAGEN-GATK testing

  

  jamesemery

  authored and

  lbergelson

  committed
  59f4e20

  Copy full SHA for 59f4e20

• Switch to gkl-0.8.11-3-g26de538-SNAPSHOT.jar

  

  droazen

  authored and

  lbergelson

  committed
  84ccbe6

  Copy full SHA for 84ccbe6

• Switch to gkl-2024_05_31, incorporate Intel patch to VectorLoglessPairPDHMM

  

  droazen

  authored and

  lbergelson

  committed
  440cbdb

  Copy full SHA for 440cbdb

• Temporarily revert Intel patch to VectorLoglessPairPDHMM.java, for testing purposes

  

  droazen

  authored and

  lbergelson

  committed
  ec7ae75

  Copy full SHA for ec7ae75

• Restore one-line Intel patch to VectorLoglessPairPDHMM

  

  droazen

  authored and

  lbergelson

  committed
  9a278bb

  Copy full SHA for 9a278bb

• added some debugging for figuring out what is going on with the gkl memory usage

  

  jamesemery

  authored and

  lbergelson

  committed
  ea5bf2a

  Copy full SHA for ea5bf2a

• error

  

  jamesemery

  authored and

  lbergelson

  committed
  4b670ee

  Copy full SHA for 4b670ee

• adding quick remote test

  

  jamesemery

  authored and

  lbergelson

  committed
  4ddd54d

  Copy full SHA for 4ddd54d

• ;

  

  jamesemery

  authored and

  lbergelson

  committed
  dc2ba8d

  Copy full SHA for dc2ba8d

• of course i can't run this anywhere

  

  jamesemery

  authored and

  lbergelson

  committed
  cbfe20f

  Copy full SHA for cbfe20f

• piggybacking off of one that may have worked past?

  

  jamesemery

  authored and

  lbergelson

  committed
  96e3960

  Copy full SHA for 96e3960

• more permissions

  

  jamesemery

  authored and

  lbergelson

  committed
  70be2b2

  Copy full SHA for 70be2b2

• why didn't that last one work?

  

  jamesemery

  authored and

  lbergelson

  committed
  970d239

  Copy full SHA for 970d239

• group

  

  jamesemery

  authored and

  lbergelson

  committed
  0d82c8d

  Copy full SHA for 0d82c8d

• restart? hopefully transient

  

  jamesemery

  authored and

  lbergelson

  committed
  6816d48

  Copy full SHA for 6816d48

• Refactored the interface to the new GKL JNI to batch submissions to avoid overflows or memory issues in oversaturated assembly regions

  

  jamesemery

  authored and

  lbergelson

  committed
  0376756

  Copy full SHA for 0376756

• two tweeks and one bug

  

  jamesemery

  authored and

  lbergelson

  committed
  61dbe95

  Copy full SHA for 61dbe95

• yet more guardrails

  

  jamesemery

  authored and

  lbergelson

  committed
  543d542

  Copy full SHA for 543d542

• assert failure

  

  jamesemery

  authored and

  lbergelson

  committed
  05de4ff

  Copy full SHA for 05de4ff

• testing limits for batches

  

  jamesemery

  authored and

  lbergelson

  committed
  f345645

  Copy full SHA for f345645

• Switch to latest GKL build (2024-08-08)

  

  droazen

  authored and

  lbergelson

  committed
  7c1340a

  Copy full SHA for 7c1340a

• update to test new jar

  lbergelson

  committed
  5f467d8

  Copy full SHA for 5f467d8

• update with new gkl version

  Show description for 81ecece
  lbergelson

  committed
  81ecece

  Copy full SHA for 81ecece

• adding new jars

  lbergelson

  committed
  68ebc55

  Copy full SHA for 68ebc55

Commits on Mar 24, 2025

• Updated Native Bindings and VCF missing entries bugfix

  chirayuharyan

  committed
  5c9bf29

  Copy full SHA for 5c9bf29

• Removed old JARs

  chirayuharyan

  committed
  1a1446e

  Copy full SHA for 1a1446e

• Added write to file function

  chirayuharyan

  committed
  d89b5c7

  Copy full SHA for d89b5c7

Commits on Mar 25, 2025

• Updated the repo with latest GKL JAR(Removed unnecessary memset from GKL PDHMM). Added seperate timer for post processing in VectorLoglessPairPDHMM.

  chirayuharyan

  committed
  1bf6a5c

  Copy full SHA for 1bf6a5c