Commits for angie

v354_base to v355_preview (2017-08-28 to 2017-09-04) v355

814eddee14b8a282e9cdb1ca94e040b31cd37c12 Mon Aug 28 14:05:46 2017 -0700

• Function comment clarification.
  • src/hg/inc/variantProjector.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/variantProjector.c - lines changed 3, context: html, text, full: html, text

3d7b476fc7a80bb445107cf2f6cdfd10070f4321 Mon Aug 28 14:07:40 2017 -0700

• Use pointer subtraction instead of strlen, HT Braney in code review, refs #19992
  • src/lib/dnaseq.c - lines changed 1, context: html, text, full: html, text

b5b259b8314a0253ed8c26811bb8f9167f10829d Mon Aug 28 14:11:56 2017 -0700

• hgvs{C,N}FromVpTx: when variant spans exon/intron boundary, use genomic ref instead of transcript ref so that intron bases aren't omitted. Thanks ChrisL for example in #19968-note17. refs #19968
  • src/hg/lib/hgHgvs.c - lines changed 13, context: html, text, full: html, text
  • src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_agree.tab - lines changed 1, context: html, text, full: html, text

332a47e0d16a980c4d5c2edb30c0758f42949412 Wed Aug 30 12:04:17 2017 -0700

• Print out proper search description instead of table name for bigBed search result heading. Don't print out hgFindSpec search description to the right of each individual item from trix search.
  • src/hg/lib/bigBedFind.c - lines changed 24, context: html, text, full: html, text

7eb22dd81e518527427204a2c5b9474402b7889f Wed Aug 30 12:05:49 2017 -0700

• Use database-specific searchTrix file for ncbiRefSeqOther.
  • src/hg/makeDb/hgTrackDb/hgTrackDb.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/refSeqComposite.ra - lines changed 2, context: html, text, full: html, text

8fc04f0d2d4ff08ea7ba0f45ec21f440140cfac2 Wed Aug 30 12:15:29 2017 -0700

• When a searchTrix file doesn't exist, warn instead of aborting with an otherwise empty page.
  • src/hg/lib/bigBedFind.c - lines changed 8, context: html, text, full: html, text

556daa1b7d9c0fdf4a4ea184fd4b3dfcca00ccce Thu Aug 31 11:53:37 2017 -0700

• Added stable test data for vcfToHgvs's "Personalis Ground Truth" test set, to avoid nightly build test errors caused by regular RefSeq updates. Instead of trying to recreate a subset of refGene/genbank tables and files, I'm using the ncbiRefSeq* schema since it is much more self-contained. In order to reduce the test set size a bit, I excluded some alternate transcripts whose HGVS terms weren't very different from the primary transcripts. The tests/expected/Personalis* files changed instead of simply shrinking because now the transcript acc column includes version number because that's the ncbiRefSeq way. The hg38 stopLoss test might conceivably change someday in an ncbiRefSeq update -- but that should be rare enough that I don't think it's worth the effort and git bloat to make stable test data for it at this point.
  • src/hg/utils/vcfToHgvs/tests/PGTdb/chromAlias.tab - lines changed 25, context: html, text, full: html, text
  • src/hg/utils/vcfToHgvs/tests/PGTdb/chromInfo.tab - lines changed 25, context: html, text, full: html, text
  • src/hg/utils/vcfToHgvs/tests/PGTdb/ncbiRefSeq.gp.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/utils/vcfToHgvs/tests/PGTdb/ncbiRefSeqCds.tab.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/utils/vcfToHgvs/tests/PGTdb/ncbiRefSeqLink.tab.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/utils/vcfToHgvs/tests/PGTdb/ncbiRefSeqPepTable.tab.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/utils/vcfToHgvs/tests/PGTdb/ncbiRefSeqPsl.psl.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/utils/vcfToHgvs/tests/PGTdb/seqNcbiRefSeq.rna.fa.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_agree.tab - lines changed 474, context: html, text, full: html, text
  • src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_disagree.tab - lines changed 32, context: html, text, full: html, text
  • src/hg/utils/vcfToHgvs/tests/makefile - lines changed 25, context: html, text, full: html, text

4317d66f127eb7d193d9f464e3889279e5c58d9d Fri Sep 1 08:52:33 2017 -0700

• Doh, forgot to use -f in clean target rm... rm -f, rm -f, rm -f.
  • src/hg/utils/vcfToHgvs/tests/makefile - lines changed 1, context: html, text, full: html, text