Commits for angie
switch to files view, user index
v363_preview to v363_preview2 (2018-03-12 to 2018-03-19) v363
Show details
dfd0e37b8be3b2b516728de719e9a7d5345ec295 Fri Mar 9 10:23:05 2018 -0800
- Use Mark's awesome new -refseqHacks option for gff3ToGenePred; it automatically turns on -useName, -allowMinimalGenes and processAllGeneChildren, and handles genes whose children are CDS (no transcript-level record). refs #20215
- src/hg/utils/automation/doNcbiRefSeq.pl - lines changed 2, context: html, text, full: html, text
baed67b5aa7f67279b04e4cf2e33cafd2268f10d Mon Mar 12 15:46:09 2018 -0700
- Adding obscure util pslFixCdsJoinGap, to correct the output of genePredToFakePsl for transcripts with +1 ribosomal frameshift.
genePred exons skip over a base to maintain frame; genePredToFakePsl sees a 1-base gap on target, 0-base gap on query.
However, the query base is skipped as described in Genbank CDS strings such as "join(168..260,262..741)".
Use CDS strings to recognize these cases, and if the PSL has a 1-sided gap on target at the exact position of the skipped
base then make the gap 2-sided to avoid making the alignment off-by-1 after that point and becoming a swamp of mismatches.
The ideal solution would be to remove the gap and properly interpret join CDS in the rest of our software, but this will at
least prevent totally incorrect genePred-derived PSL for transcripts with +1 ribosomal frameshift for now.
refs #21048
- src/hg/utils/pslFixCdsJoinGap/makefile - lines changed 3, context: html, text, full: html, text
- src/hg/utils/pslFixCdsJoinGap/pslFixCdsJoinGap.c - lines changed 138, context: html, text, full: html, text
454e33bd121d0b0d5c8a714b793b6b1d060a1e56 Tue Mar 13 09:18:45 2018 -0700
- Oops, forgot to update qNumInsert and qBaseInsert columns when adding the q gap. Thanks Chris L! refs #20215 #21048
- src/hg/utils/pslFixCdsJoinGap/pslFixCdsJoinGap.c - lines changed 2, context: html, text, full: html, text
6546198dd3ce4f12b81225c5093163f3a176b5e3 Tue Mar 13 14:17:15 2018 -0700
- Adding twoBitSeqWindow{New,Free} for seqWindow on 2bit files.
- src/hg/lib/seqWindow.c - lines changed 72, context: html, text, full: html, text
a0d13c768fa16b3baf5f6c50babff087f13b1421 Wed Mar 14 17:06:27 2018 -0700
- Use wgEncodeGencodeCompV* for ENS* searches, not just the Basic subset. refs #21076
1ee99ce653ae839e4774120c3f3923dc129c8533 Fri Mar 16 14:41:14 2018 -0700
- Moved jsonStringEscape inside jsonWriteString because it's silly to have to remember to call it first every time.
tagStorm programs were doing their own limited escaping (double-quotes only); now they get the same escaping as everywhere else.
refs MLQ #21113
- src/hg/hgChooseDb/hgChooseDb.c - lines changed 2, context: html, text, full: html, text
- src/hg/hgGateway/hgGateway.c - lines changed 3, context: html, text, full: html, text
- src/hg/hgIntegrator/hgIntegrator.c - lines changed 18, context: html, text, full: html, text
- src/tagStorm/tagSchemaToJson/tagSchemaToJson.c - lines changed 1, context: html, text, full: html, text
- src/tagStorm/tagStormToJson/tagStormToJson.c - lines changed 1, context: html, text, full: html, text
4f80b3af4cb02e10216ba047ea8de0378c4abe3d Mon Mar 19 09:58:16 2018 -0700
- hListGencodeTables' version comparison didn't account for the 'VM' mouse version strings; if there's a letter following the V, skip it. Thanks Cath! refs #21076
switch to files view, user index