Commits for kent
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v293_preview2 to v293_base (2013-12-02 to 2013-12-09) v293
- Removing lineFileNextRealWithSize - it was buggy and hard to fix in general case, and only one module was using it. Replaced it with something local to fastqStatsAndSubsample.c.
- src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c - lines changed 30, context: html, text, full: html, text
- Adding paired_end and technical_replicate tag handling to edwValidFile table.
- src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c - lines changed 2, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h - lines changed 4, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 4, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 21, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 3, context: html, text, full: html, text
- Simplified to avoid a bug.
- src/hg/encode3/encodeDataWarehouse/edwFixGbb2/edwFixGbb2.c - lines changed 12, context: html, text, full: html, text
- Patch to pull paired_end and technical_replicate out of edwFile and into the appropriate columns of edwValidFile now applied.
- src/hg/encode3/encodeDataWarehouse/edwFixTechRep1/edwFixTechRep1.c - lines changed 72, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/edwFixTechRep1/makefile - lines changed 4, context: html, text, full: html, text
- Starting to work on program to check read pairing for fastqs. It is maybe 1/3 baked now.
- src/hg/encode3/encodeDataWarehouse/edwMakePairedEndQa/edwMakePairedEndQa.c - lines changed 120, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/edwMakePairedEndQa/makefile - lines changed 4, context: html, text, full: html, text
- Actually using seed.
- src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c - lines changed 1, context: html, text, full: html, text
- A change that will hopefully make the build utils work again.
- src/hg/encode3/encodeDataWarehouse/makefile - lines changed 1, context: html, text, full: html, text
- Simplifying initial step down to make it give consistent result across read pairs.
- src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c - lines changed 103, context: html, text, full: html, text
- Further work, maybe 2/3rds baked now.
- src/hg/encode3/encodeDataWarehouse/edwMakePairedEndQa/edwMakePairedEndQa.c - lines changed 70, context: html, text, full: html, text
- Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
- src/hg/encode3/encodeDataWarehouse/fix/README - lines changed 3, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixAddFastq/edwFixAddFastq.c - lines changed 47, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixAddFastq/makefile - lines changed 4, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixAddFastq/makk - lines changed 3, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixBzip/edwFixBzip.c - lines changed 73, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixBzip/makefile - lines changed 4, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixGtfBigBed/edwFixGtfBigBed.c - lines changed 134, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixGtfBigBed/makefile - lines changed 4, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixQualsAtPos/edwFixQualsAtPos.c - lines changed 73, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixQualsAtPos/makefile - lines changed 4, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixQualsAtPos/makk - lines changed 3, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixRevoked/edwFixRevoked.c - lines changed 90, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixRevoked/makefile - lines changed 4, context: html, text, full: html, text
- Moving rest of edwFix programs to subdirectory
- src/hg/encode3/encodeDataWarehouse/edwFixBasesInSample/edwFixBasesInSample.c - lines changed 62, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/edwFixBasesInSample/makefile - lines changed 4, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/edwFixCshlSpikeins/edwFixCshlSpikeins.c - lines changed 77, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/edwFixCshlSpikeins/makefile - lines changed 4, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/edwFixGbb2/edwFixGbb2.c - lines changed 49, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/edwFixGbb2/makefile - lines changed 4, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/edwFixRenamed/edwFixRenamed.c - lines changed 101, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/edwFixRenamed/makefile - lines changed 4, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/edwFixReplaced/edwFixReplaced.c - lines changed 284, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/edwFixReplaced/makefile - lines changed 4, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/edwFixTechRep1/edwFixTechRep1.c - lines changed 72, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/edwFixTechRep1/makefile - lines changed 4, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixBasesInSample/edwFixBasesInSample.c - lines changed 62, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixBasesInSample/makefile - lines changed 4, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixCshlSpikeins/edwFixCshlSpikeins.c - lines changed 77, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixCshlSpikeins/makefile - lines changed 4, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixGbb2/edwFixGbb2.c - lines changed 49, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixGbb2/makefile - lines changed 4, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixRenamed/edwFixRenamed.c - lines changed 101, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixRenamed/makefile - lines changed 4, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixReplaced/edwFixReplaced.c - lines changed 284, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixReplaced/makefile - lines changed 4, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixTechRep1/edwFixTechRep1.c - lines changed 72, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixTechRep1/makefile - lines changed 4, context: html, text, full: html, text
- Program to figure out how well pairs align together from sam file seems to work.
- src/hg/encode3/encodeDataWarehouse/utils/README - lines changed 3, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/utils/edwSamPairedEndStats/edwSamPairedEndStats.c - lines changed 136, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/utils/edwSamPairedEndStats/makefile - lines changed 3, context: html, text, full: html, text
- Script to copy exe to production added.
- src/hg/encode3/encodeDataWarehouse/edwMakePairedEndQa/makk - lines changed 3, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/utils/edwSamPairedEndStats/makk - lines changed 4, context: html, text, full: html, text
- Program to add pairedEnd qa seems to work.
- src/hg/encode3/encodeDataWarehouse/edwMakePairedEndQa/edwMakePairedEndQa.c - lines changed 168, context: html, text, full: html, text
- Adding script to copy into production.
- src/hg/encode3/encodeDataWarehouse/edwSubmit/makk - lines changed 3, context: html, text, full: html, text
- Adding script to copy into production.
- src/hg/encode3/encodeDataWarehouse/edwChangeFormat/makk - lines changed 3, context: html, text, full: html, text
- Adding technicalReplicate and pairedEnd to vf view.
- src/hg/encode3/encodeDataWarehouse/lib/resetEdw - lines changed 1, context: html, text, full: html, text
- Adding to tables that get records deleted when a file needs revalidation. Moving edwMakeTempfFastqSample here where it can be shared.
- src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 37, context: html, text, full: html, text
- Adding edwQaPairedEndFastq table.
- src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h - lines changed 74, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 15, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 178, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 17, context: html, text, full: html, text
- Moving edwMakeTempFastqSample to library where it can be shared.
- src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 3, context: html, text, full: html, text
- Updating makefile path to reflect new position in source tree.
- src/hg/encode3/encodeDataWarehouse/fix/edwFixBasesInSample/makefile - lines changed 2, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixCshlSpikeins/makefile - lines changed 2, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixGbb2/makefile - lines changed 2, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixGtfBigBed/makefile - lines changed 2, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixQualsAtPos/makefile - lines changed 2, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixRenamed/makefile - lines changed 2, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixReplaced/makefile - lines changed 2, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixRevoked/makefile - lines changed 2, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/fix/edwFixTechRep1/makefile - lines changed 2, context: html, text, full: html, text
- Moving edwMakeTempFastqSample to library where it can be shared.
- src/hg/encode3/encodeDataWarehouse/edwMakeContaminationQa/edwMakeContaminationQa.c - lines changed 26, context: html, text, full: html, text
- Somehow this stray got lost in directory move.
- src/hg/encode3/encodeDataWarehouse/edwFixRevoked/edwFixRevoked.c - lines changed 90, context: html, text, full: html, text
- Adding a bunch of functions to help work with output of jsParse.
- src/hg/lib/jsHelper.c - lines changed 270, context: html, text, full: html, text
- INcreasing buffer size for sql query in edwFileAllIntactBetween.
- src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 1, context: html, text, full: html, text
- Program to build a table based on ENCODED experiments seems to work.
- src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/makefile - lines changed 3, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/rsyncEdwExpDataType.c - lines changed 99, context: html, text, full: html, text
- Separating out generic portable JSON parser from Genome Browser specific stuff in jsHelper module, creating jsonParse module.
- src/hg/inc/jsHelper.h - lines changed 124, context: html, text, full: html, text
- src/hg/lib/jsHelper.c - lines changed 682, context: html, text, full: html, text
- Splitting jsonParse out of jsHelper.
- Removing jsonGlabalsHash from library routines. Now it is restricted to hgTrackUi.
- src/hg/hgTrackUi/hgTrackUi.c - lines changed 25, context: html, text, full: html, text
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