Commits for angie
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v363_preview2 to v363_base (2018-03-19 to 2018-03-26) v363
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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
- src/hg/lib/txAliMismatch.as - lines changed 14, context: html, text, full: html, text
- src/hg/lib/txAliQSkipped.as - lines changed 13, context: html, text, full: html, text
- src/hg/lib/txAliShiftyGap.as - lines changed 20, context: html, text, full: html, text
- src/hg/lib/txAliShortGap.as - lines changed 16, context: html, text, full: html, text
- src/hg/utils/pslMismatchGapToBed/makefile - lines changed 3, context: html, text, full: html, text
- src/hg/utils/pslMismatchGapToBed/pslMismatchGapToBed.c - lines changed 518, 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/bedToBigBed.c - lines changed 1, context: html, text, full: html, text
- src/utils/bedToBigBed/tests/input/multiInsAtEnd.bed - lines changed 2, context: html, text, full: html, text
- src/utils/bedToBigBed/tests/makefile - lines changed 6, 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/hg/utils/pslMismatchGapToBed/pslMismatchGapToBed.c - lines changed 5, context: html, text, full: html, text
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