Memory improvement when writing missing positions to pet #7098
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ahaessly
approved these changes
Feb 24, 2021
| @@ -168,7 +168,7 @@ task CreateImportTsvs { | |||
| --mode GENOMES \ | |||
| -SNM ~{sample_map} \ | |||
| --ref-version 38 | |||
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you can remove this class from the PR - only whitespace changes
kcibul
approved these changes
Feb 24, 2021
| public static List<List<String>> createMissingTSV(long start, long end, String sampleName) { | ||
| List<List<String>> rows = new ArrayList<>(); | ||
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| public void createMissingTSV(long start, long end, String sampleName) throws IOException { |
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rename to writeMissingEntry or something else with write?
| public static List<List<String>> createMissingTSV(long start, long end, String sampleName) { | ||
| List<List<String>> rows = new ArrayList<>(); | ||
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| public void createMissingTSV(long start, long end, String sampleName) throws IOException { | ||
| for (long position = start; position <= end; position ++){ |
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nit -- remove space on postincrement operator (ie position++)
kcibul
pushed a commit
that referenced
this pull request
Mar 9, 2021
* WIP memory improvements - only do one loop * move log to end of loop * reduce memory/cpus for ImportGenomes, re-enable non-TSV outputs * just kidding, let's not change the wdl yet * remove redundant outputType inputs * remove debugging log * rename createMissingTSV to writeMissingPositions, minor edits * revert whitespace-only changes
mmorgantaylor
added a commit
that referenced
this pull request
Apr 6, 2021
* WIP memory improvements - only do one loop * move log to end of loop * reduce memory/cpus for ImportGenomes, re-enable non-TSV outputs * just kidding, let's not change the wdl yet * remove redundant outputType inputs * remove debugging log * rename createMissingTSV to writeMissingPositions, minor edits * revert whitespace-only changes
This was referenced Mar 17, 2023
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related to issue #211 and #233 - in CreateVariantIngestFiles, when writing missing positions to the pet tsv, we were looping through blocks of missing intervals twice, once to construct the pet rows, holding them all in memory, and again to write the pet rows. in this PR, we merge those steps into one: for each missing block, we write the pet lines to file as we loop through, avoiding the need to hold large blocks in memory.
note that this does not resolve the memory issues that originally prompted issues #211 and #233, but it's nonetheless a minor improvement that helps immensely when there are large numbers of missing locations.