Commits for angie

bdf3d9eabb14427335916b677dbf2bb2f145af9a Mon Jul 23 16:43:14 2018 -0700

Adding settings gbdbLoc1 and forceTwoBit to suggested .hg.conf contents in mysql.html for utilities that need to access /gbdb and retrieve genomic sequence.
- src/hg/htdocs/goldenPath/help/mysql.html - lines changed 14, context: html, text, full: html, text

13dddf36dc0f43a27a792519213d87939b51d99c Wed Jul 25 16:23:50 2018 -0700

Revert "Use the new annoStreamDb params rightJoinDtf and rightJoinMainField to restrict ncbiRefSeqPsl rows to only those that appear in the selected genePred table (e.g. ncbiRefSeqCurated)." This reverts commit dd285f81141e45dabf1caf0f90723810f2c6f8a1.
- src/hg/lib/annoStreamDbPslPlus.c - lines changed 3, context: html, text, full: html, text

c60ed6e679740c931f15ad7c7f86fa542dcf9b2c Wed Jul 25 16:26:56 2018 -0700

Revert "Added new config parameters rightJoinDtf and rightJoinMainField to give the option of limiting rows to those that join with some other table. The motivation for this is wanting to get only the rows of ncbiRefSeqPsl that join with ncbiRefSeqCurated." This reverts commit 869708731727a455813ab88e67d46be978ab77b0.
- src/hg/lib/annoStreamDb.c - lines changed 25, context: html, text, full: html, text

61cf5e21f11e752e855b40094d72c0348687c27b Wed Jul 25 16:58:53 2018 -0700

Instead of a SQL join to restrict ncbiRefSeqPsl rows to ncbiRefSeqCurated or Predicted subset, use an ID hash because when a transcript has multiple placements on main and _alt chroms, the join was producing redundant results. refs #21770
- src/hg/lib/annoStreamDbPslPlus.c - lines changed 17, context: html, text, full: html, text