Commits for cline
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v258_base to v259_preview (2011-10-10 to 2011-10-25) v259
- Aded some exception cases for Rfam and tRNA genes, which don't have accessions of the expected format
- src/hg/txCds/txInfoAssemble/txInfoAssemble.c - lines changed 43, context: html, text, full: html, text
- Adjusted the pipeline for adding Rfam and tRNA content after txWalk, rather than as part of txWalk
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh - lines changed 28, context: html, text, full: html, text
- Addressing Redmine bug #5592: rewording the error message 'Couldn't find NM_214677 in refLink table - database inconsistency.' as 'Couldn't find NM_214677 in refLink table - this accession may no longer be available.'. I'd previously fixed this in one place, but there were still two more places to fix
- UCSC Genes pipeline changes: changed txGeneXref to control for the possibility that a gene has not come through the txWalk pipeline. Checked in final revisions of the proteins build script. Tweaked a debugging script by adding back in a missing flag, that somehow hadn't been an issue before
- src/hg/makeDb/doc/proteins/111004.txt - lines changed 12, context: html, text, full: html, text
- src/hg/txGene/txGeneValidation/compareModifiedFileSizes.csh - lines changed 1, context: html, text, full: html, text
- src/hg/txGene/txGeneXref/txGeneXref.c - lines changed 2, context: html, text, full: html, text
- After taking another look at the code, moved some special case code for antibodies under the code for general mRNAs
- src/hg/txGene/txGeneXref/txGeneXref.c - lines changed 28, context: html, text, full: html, text
- Updated some of the cluster timing information in the UCSC Genes build script
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh - lines changed 20, context: html, text, full: html, text
- Updated the list of symbolic database links to be updated after this script is run
- src/hg/makeDb/doc/proteins/111004.txt - lines changed 2, context: html, text, full: html, text
- Clarified the instructions for updating the symbolic database links
- src/hg/makeDb/doc/proteins/111004.txt - lines changed 3, context: html, text, full: html, text
- Setting up the script to run the segment that copies data from the temporary database to hg19
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh - lines changed 14, context: html, text, full: html, text
- Updated the Parasol timing results for various batches of jobs that ran on swarm
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh - lines changed 40, context: html, text, full: html, text
- Added a temporary track to help Brooke in her work of QAing UCSC Genes. This track shows the Rfam transcripts that contributed to the UCSC Genes input data. Note that this is a subset of Rfam, the transcripts in regions syntenic to mm9 and not duplicated, so the track has a funny name (RfamSyn) to guard against misuse
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 14, context: html, text, full: html, text
- Cleaned up the statement linking hg19.kgXref.tRnaName to tRNAs.name. Added new links between knownGene.name and hg19.knownGeneTxMrna plus hg19.knownGneTxPep
- src/hg/makeDb/schema/all.joiner - lines changed 3, context: html, text, full: html, text
- Removing the commands to make web pages for Google searches, as the instructions (from Ann) are clear that we're not doing that anymore
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh - lines changed 11, context: html, text, full: html, text
- Addressing git code review # 5474: Ensuring that the newly-expanded kgXref schema doesn't break anything. The kgXref functions are called in three places: txGeneAlias, hgKgGetText, and spKgMap. txGeneAlias is not likely to be run on old data, as it's part of the UCSC Genes build, and will errAbort gracefully (albeit with a nonspecific error message) if it finds that the kgXref table has the wrong number of fields. Added code to the other two functions to check that the number of fields in the database table is the number expected, and errAbort if not
- src/hg/makeDb/hgKgGetText/hgKgGetText.c - lines changed 10, context: html, text, full: html, text
- src/hg/protein/lib/spKgMap.c - lines changed 11, context: html, text, full: html, text
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