File Changes for kent
switch to commits view, user indexv330_preview2.1 to v330_base (2016-03-14 to 2016-03-21) v330
- src/hg/cirm/cdw/README
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A file that attempts to give an overview of the CIRM Data Warehouse system.
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Updating to reflect how things work now.
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Adding some program descriptions to README
- src/hg/cirm/cdw/cdwAddAssembly/cdwAddAssembly.c
- lines changed 1, context: html, text, full: html, text
Adding submitId column to job table.
- src/hg/cirm/cdw/cdwAddQaEnrichTarget/cdwAddQaEnrichTarget.c
- lines changed 1, context: html, text, full: html, text
Adding submitId column to job table.
- src/hg/cirm/cdw/cdwChangeFormat/cdwChangeFormat.c
- lines changed 1, context: html, text, full: html, text
Adding submitId column to job table.
- src/hg/cirm/cdw/cdwCorrectFileTags/cdwCorrectFileTags.c
- lines changed 1, context: html, text, full: html, text
Adding submitId column to job table.
- src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c
- lines changed 15, context: html, text, full: html, text
Slightly more robust error reporting if tags in database are messed up. Fixing up so that sqlDyStringPrintf is only used at start of command, since it is a bit overaggressive about flagging errors on partially built queries if you use it throughout a query build.
- src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
- lines changed 5, context: html, text, full: html, text
Adding minimal support for Tabix validation on vcf indices.
- src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
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Adding verbose status message about copying a file.
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Adding -test option so it can look at meta and manifest files without updating database. In test mode it will currently also start checking controlled vocabs.
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Removing some unused code. Making a sql command go through sql injection checking that was bypassing it.
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Adding submitId column to job table. Checking to make sure they don't put full path name in manifest file, which went from being a necessary hassle to being an error a few versions back.
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Adding submitId column to job table. Checking to make sure they don't put full path name in manifest file, which went from being a necessary hassle to being an error a few versions back.
- src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
- lines changed 5, context: html, text, full: html, text
Removing a set but not used symbol to get code to compile again with stricter warnings.
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Fixing bug where browse tracks errored out when there were no chromosome tags.
- src/hg/cirm/cdw/fix/cdwFixDoubleHivePath/cdwFixDoubleHivePath.c
- lines changed 65, context: html, text, full: html, text
Another little database fix utility. No longer need to include directory name in path, but forgot that.
- src/hg/cirm/cdw/fix/cdwFixDoubleHivePath/makefile
- lines changed 3, context: html, text, full: html, text
Another little database fix utility. No longer need to include directory name in path, but forgot that.
- src/hg/cirm/cdw/inc/cdw.h
- lines changed 4, context: html, text, full: html, text
Adding submitId column to job table.
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Removing no longer used cdwSubmitJob table.
- src/hg/cirm/cdw/inc/cdwLib.h
- lines changed 3, context: html, text, full: html, text
Adding submitId column to job table.
- src/hg/cirm/cdw/inc/cdwValid.h
- lines changed 2, context: html, text, full: html, text
Starting to implement checking of tag values for controlled vocabularies.
- lines changed 3, context: html, text, full: html, text
Adding minimal support for Tabix validation. Making it avoid GEO_SAMPLE and GEO_SERIES tags, which should be lower case since they are ones we get even if the set is not wrangled out of GEO.
- src/hg/cirm/cdw/lib/cdw.as
- lines changed 2, context: html, text, full: html, text
Adding submitId column to job table.
- lines changed 13, context: html, text, full: html, text
Removing no longer used cdwSubmitJob table.
- src/hg/cirm/cdw/lib/cdw.c
- lines changed 20, context: html, text, full: html, text
Adding submitId column to job table.
- lines changed 179, context: html, text, full: html, text
Removing no longer used cdwSubmitJob table.
- src/hg/cirm/cdw/lib/cdw.sql
- lines changed 2, context: html, text, full: html, text
Adding submitId column to job table.
- lines changed 14, context: html, text, full: html, text
Removing no longer used cdwSubmitJob table.
- src/hg/cirm/cdw/lib/cdwLib.c
- lines changed 7, context: html, text, full: html, text
Adding submitId column to job table.
- src/hg/cirm/cdw/lib/cdwValid.c
- lines changed 153, context: html, text, full: html, text
Starting to implement checking of tag values for controlled vocabularies.
- lines changed 32, context: html, text, full: html, text
Adding minimal support for Tabix validation. Making it avoid GEO_SAMPLE and GEO_SERIES tags, which should be lower case since they are ones we get even if the set is not wrangled out of GEO.
- src/hg/cirm/cdw/wrangle/addToStepTables/makefile
- lines changed 2, context: html, text, full: html, text
Changing paths in makefile so they work on cirm-01 as well as hgwdev.
- src/inc/common.h
- lines changed 3, context: html, text, full: html, text
Adding isSymbolString function to common string library.
- src/lib/common.c
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Adding isSymbolString function to common string library.
- src/tagStorm/tagStormReformat/tagStormReformat.c
- lines changed 5, context: html, text, full: html, text
Changing order of command line interpretation so that -flatten doesn't exclude -tab.
- src/utils/stringify/stringify.c
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