File Changes for angie

v390_preview to v390_preview2 (2019-10-21 to 2019-10-28) v390

• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 49, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 12, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
• src/hg/hgTracks/hgTracks.c
  • lines changed 30, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
• src/hg/hgTracks/hgTracks.h
  • lines changed 6, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 9, context: html, text, full: html, text
    71b592154f2821cc5148993588e93e773915e084 Tue Apr 23 12:00:05 2019 -0700
    Fix the way that scaledBoxToPixelCoords treats 0-length insertion items. refs #23283 This didn't affect the snp tracks because they have their own drawItemAt, nor bigBed because bedDrawSimpleAt uses hvGfxBox and linkedFeaturesDrawAt has a special case for start==end. But now the bigDbSnp drawing code will use scaledBoxToPixelCoords.
  • lines changed 6, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
• src/hg/hgTracks/variation.c
  • lines changed 476, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
• src/hg/hgTracks/variation.h
  • lines changed 10, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
• src/hg/hgc/bigBedClick.c
  • lines changed 25, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
• src/hg/hgc/bigDbSnpClick.c
  • lines changed 451, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
• src/hg/hgc/hgc.c
  • lines changed 7, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
• src/hg/hgc/hgc.h
  • lines changed 6, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
• src/hg/hgc/makefile
  • lines changed 2, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
• src/hg/htdocs/style/HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
• src/hg/inc/bigDbSnp.h
  • lines changed 13, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
• src/hg/inc/hui.h
  • lines changed 6, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
• src/hg/inc/trackDb.h
  • lines changed 10, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
• src/hg/lib/bigDbSnp.c
  • lines changed 178, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
• src/hg/lib/customFactory.c
  • lines changed 17, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
• src/hg/lib/hAnno.c
  • lines changed 4, context: html, text, full: html, text
    171a5b44a2fa8be1dc747bbd8d620c713edd7027 Wed Oct 23 11:02:22 2019 -0700
    Now that saved session custom track table names can have a customData db prefix (like db=customTrash and table=customDataNN.t1_...), asObjectFromFields needs to skip past the dot to avoid autoSql parse error. refs #24358.
• src/hg/lib/hui.c
  • lines changed 147, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
  • lines changed 3, context: html, text, full: html, text
    b5e62153da4e34f2bd670a088adfd1e77afb9760 Tue Oct 15 10:14:57 2019 -0700
    hui: added link to ucscNotes description, thx Lou refs #23283
• src/hg/lib/trackDbCustom.c
  • lines changed 39, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
• src/hg/makeDb/doc/bigDbSnp.txt
  • lines changed 132, context: html, text, full: html, text
    aa6795a2461f1356b09ce782be1f979f7edbab9b Thu Oct 10 14:15:07 2019 -0700
    dbSnp152, dbSnp153: Count up how many distinct rsIDs got frequency counts from each source; also how many times each ucscNote was added. refs #23283
  • lines changed 12, context: html, text, full: html, text
    ca3f7e9e7bebb3ea6f35844fc03c90a988eb1330 Fri Oct 18 15:02:51 2019 -0700
    bigDbSnp: add Common, ClinVar, Mult subset tracks to bigBed and install steps. refs #23283
• src/hg/makeDb/doc/hg19.txt
  • lines changed 1, context: html, text, full: html, text
    435fbceebeaddec93ebca4eaa50b20123967a285 Fri Oct 25 11:40:25 2019 -0700
    LRG: if source URL is missing a protocol, prepend http:// . Thx Jairo. refs #24285
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 1, context: html, text, full: html, text
    435fbceebeaddec93ebca4eaa50b20123967a285 Fri Oct 25 11:40:25 2019 -0700
    LRG: if source URL is missing a protocol, prepend http:// . Thx Jairo. refs #24285
• src/hg/makeDb/trackDb/human/dbSnp152.html
  • lines changed 23, context: html, text, full: html, text
    895644af226dd57285d4b0469da87dc34df76e5e Thu Oct 24 13:55:25 2019 -0700
    trackDb and descriptions for new tracks dbSnp152* and dbSnp153*. tagTypes changes for bigDbSnp type (and subsequent big* types). refs #23283
• src/hg/makeDb/trackDb/human/dbSnp152.shared.html
  • lines changed 324, context: html, text, full: html, text
    895644af226dd57285d4b0469da87dc34df76e5e Thu Oct 24 13:55:25 2019 -0700
    trackDb and descriptions for new tracks dbSnp152* and dbSnp153*. tagTypes changes for bigDbSnp type (and subsequent big* types). refs #23283
• src/hg/makeDb/trackDb/human/dbSnp153Composite.html
  • lines changed 392, context: html, text, full: html, text
    895644af226dd57285d4b0469da87dc34df76e5e Thu Oct 24 13:55:25 2019 -0700
    trackDb and descriptions for new tracks dbSnp152* and dbSnp153*. tagTypes changes for bigDbSnp type (and subsequent big* types). refs #23283
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 86, context: html, text, full: html, text
    895644af226dd57285d4b0469da87dc34df76e5e Thu Oct 24 13:55:25 2019 -0700
    trackDb and descriptions for new tracks dbSnp152* and dbSnp153*. tagTypes changes for bigDbSnp type (and subsequent big* types). refs #23283
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 6, context: html, text, full: html, text
    895644af226dd57285d4b0469da87dc34df76e5e Thu Oct 24 13:55:25 2019 -0700
    trackDb and descriptions for new tracks dbSnp152* and dbSnp153*. tagTypes changes for bigDbSnp type (and subsequent big* types). refs #23283
• src/hg/utils/automation/doBigDbSnp.pl
  • lines changed 36, context: html, text, full: html, text
    ca3f7e9e7bebb3ea6f35844fc03c90a988eb1330 Fri Oct 18 15:02:51 2019 -0700
    bigDbSnp: add Common, ClinVar, Mult subset tracks to bigBed and install steps. refs #23283
• src/hg/utils/automation/parseLrgXml.pl
  • lines changed 4, context: html, text, full: html, text
    435fbceebeaddec93ebca4eaa50b20123967a285 Fri Oct 25 11:40:25 2019 -0700
    LRG: if source URL is missing a protocol, prepend http:// . Thx Jairo. refs #24285
• src/inc/dnautil.h
  • lines changed 4, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.
• src/lib/dnautil.c
  • lines changed 39, context: html, text, full: html, text
    d3752edc12da1bf08427946150f564dbdd5d2254 Thu Oct 24 13:55:51 2019 -0700
    bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*.