Commits for angie

07f19e67fafd6351ff6408c07c4e6b546f3cbb16 Mon Dec 19 11:03:05 2016 -0800

Make hgVai's back-end default for include_intergenic the same as the UI default. refs #12216 note-23
- src/hg/hgVai/hgVai.c - lines changed 1, context: html, text, full: html, text

a7c9586b9cdeefd418f099915bf06c51981297f8 Tue Dec 20 11:53:25 2016 -0800

Added command line options for filtering output by functional category. refs #12216 note-25
- src/hg/utils/vai.pl - lines changed 22, context: html, text, full: html, text

e47b56dbd11cb3936098df9694704fc8ea086a67 Wed Dec 21 15:11:55 2016 -0800

hgTables was missing support for "comma" or "separator" field in non-primary field lines of all.joiner. refs #18586
- src/hg/hgTables/joining.c - lines changed 22, context: html, text, full: html, text

e25ec5b271d3ba3073de307e3d80bc2503ad7207 Thu Dec 22 11:49:14 2016 -0800

tableExists was always opening a sql connection, but only rarely do we get a table with a sql wildcard that needs a sql query. So open a sql conn only when necessary -- speeds up all.joiner searches with many matches to tables in different databases like knownGene.
- src/hg/lib/joiner.c - lines changed 28, context: html, text, full: html, text

ad1cf0cc166a6d5b0a3e81a580e5144f37a4a016 Thu Dec 22 12:19:07 2016 -0800

Move knownToRefSeq way up in the field list for knownGeneId -- when connecting knownGene to omimId tables, keggPathway was taking precedence but has low coverage of knownGene, so most results were missed. refs #18586
- src/hg/makeDb/schema/all.joiner - lines changed 2, context: html, text, full: html, text

799b4fefa8e3e5e1453ff8d79e7d1f23f3812546 Thu Dec 22 13:12:00 2016 -0800

Piggyback on my last commit: get the real wordCount from chopString because the last separator might not have anything after it (null idWord -> SEGV). Trim spaces on the way into idHash as well as on the way out. refs #18586
- src/hg/hgTables/joining.c - lines changed 4, context: html, text, full: html, text