File Changes for angie

v363_preview2 to v363_base (2018-03-19 to 2018-03-26) v363

• src/hg/inc/hgHgvs.h
  • lines changed 3, context: html, text, full: html, text
    b91a917e39c8d58d0de5e6325606f098ef0fb60b Wed Mar 21 09:22:21 2018 -0700
    New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts. Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed. This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track. refs #21079
• src/hg/lib/hgHgvs.c
  • lines changed 1, context: html, text, full: html, text
    b91a917e39c8d58d0de5e6325606f098ef0fb60b Wed Mar 21 09:22:21 2018 -0700
    New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts. Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed. This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track. refs #21079
• src/hg/lib/txAliDoubleGap.as
  • lines changed 15, context: html, text, full: html, text
    b91a917e39c8d58d0de5e6325606f098ef0fb60b Wed Mar 21 09:22:21 2018 -0700
    New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts. Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed. This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track. refs #21079
• src/hg/lib/txAliMismatch.as
  • lines changed 14, context: html, text, full: html, text
    b91a917e39c8d58d0de5e6325606f098ef0fb60b Wed Mar 21 09:22:21 2018 -0700
    New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts. Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed. This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track. refs #21079
• src/hg/lib/txAliQSkipped.as
  • lines changed 13, context: html, text, full: html, text
    b91a917e39c8d58d0de5e6325606f098ef0fb60b Wed Mar 21 09:22:21 2018 -0700
    New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts. Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed. This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track. refs #21079
• src/hg/lib/txAliShiftyGap.as
  • lines changed 20, context: html, text, full: html, text
    b91a917e39c8d58d0de5e6325606f098ef0fb60b Wed Mar 21 09:22:21 2018 -0700
    New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts. Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed. This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track. refs #21079
• src/hg/lib/txAliShortGap.as
  • lines changed 16, context: html, text, full: html, text
    b91a917e39c8d58d0de5e6325606f098ef0fb60b Wed Mar 21 09:22:21 2018 -0700
    New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts. Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed. This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track. refs #21079
• src/hg/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    b91a917e39c8d58d0de5e6325606f098ef0fb60b Wed Mar 21 09:22:21 2018 -0700
    New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts. Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed. This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track. refs #21079
• src/hg/utils/pslMismatchGapToBed/makefile
  • lines changed 3, context: html, text, full: html, text
    b91a917e39c8d58d0de5e6325606f098ef0fb60b Wed Mar 21 09:22:21 2018 -0700
    New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts. Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed. This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track. refs #21079
• src/hg/utils/pslMismatchGapToBed/pslMismatchGapToBed.c
  • lines changed 518, context: html, text, full: html, text
    b91a917e39c8d58d0de5e6325606f098ef0fb60b Wed Mar 21 09:22:21 2018 -0700
    New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts. Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed. This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track. refs #21079
  • lines changed 5, context: html, text, full: html, text
    65a5a83fd4a3921e2a725241e24be49054c1ae40 Wed Mar 21 15:25:56 2018 -0700
    Oops, ignoreQNamePrefix needs to be applied before we call checkTranscript. refs #21079
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 1, context: html, text, full: html, text
    2b9e72f7cb3c431864f468e03d5ff5910ee165bc Wed Mar 21 15:21:30 2018 -0700
    Fixing an odd corner case in bedToBigBed: multiple insertions at the end of a sequence. Tangentially refs #21079
• src/utils/bedToBigBed/tests/input/multiInsAtEnd.bed
  • lines changed 2, context: html, text, full: html, text
    2b9e72f7cb3c431864f468e03d5ff5910ee165bc Wed Mar 21 15:21:30 2018 -0700
    Fixing an odd corner case in bedToBigBed: multiple insertions at the end of a sequence. Tangentially refs #21079
• src/utils/bedToBigBed/tests/makefile
  • lines changed 6, context: html, text, full: html, text
    2b9e72f7cb3c431864f468e03d5ff5910ee165bc Wed Mar 21 15:21:30 2018 -0700
    Fixing an odd corner case in bedToBigBed: multiple insertions at the end of a sequence. Tangentially refs #21079