Commits for braney

v337_preview to v337_preview2 (2016-08-01 to 2016-08-08) v337

f5ba6de31304850e1650c1a785f717971cbfa4a8 Tue Aug 2 12:28:30 2016 -0700

• fix problem with bigBed code calling SQL code during parallel load.
  This causes a crash because SQL code is not thread safe.
  
  • src/hg/hgTracks/bigBedTrack.c - lines changed 27, context: html, text, full: html, text
  • src/inc/bigBed.h - lines changed 3, context: html, text, full: html, text
  • src/lib/bigBed.c - lines changed 18, context: html, text, full: html, text

d63b7e753345e199748030d83e1d3aa497b350f9 Tue Aug 2 22:24:07 2016 -0700

• fix problem in bigPsl with '-' as strand for target sequence #17829
  
  • src/hg/hgc/hgc.c - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/bigPsl.c - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/pslToBigPsl/pslToBigPsl.c - lines changed 9, context: html, text, full: html, text

7bd3ab2b92d48520bf463fd43eeda13318dbe7cb Wed Aug 3 12:13:27 2016 -0700

• make the doc and AS file for bigPsl a little more explicit about the
  file contents
  
  • src/hg/htdocs/goldenPath/help/bigPsl.html - lines changed 8, context: html, text, full: html, text
  • src/hg/inc/bigPsl.h - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/bigPsl.as - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/bigPsl.c - lines changed 3, context: html, text, full: html, text

2d3f6f2a0d9e053167123d2c9ac89568413c51fd Wed Aug 3 15:03:53 2016 -0700

• add some tests for pslToBigPsl
  
  • src/hg/utils/bigPslToPsl/bigPslToPsl.c - lines changed 11, context: html, text, full: html, text
  • src/hg/utils/pslToBigPsl/tests/input/bigPsl.as - lines changed 33, context: html, text, full: html, text
  • src/hg/utils/pslToBigPsl/tests/input/chrom.sizes - lines changed 455, context: html, text, full: html, text
  • src/hg/utils/pslToBigPsl/tests/input/doubleStrand.psl - lines changed 415, context: html, text, full: html, text
  • src/hg/utils/pslToBigPsl/tests/input/singleStrand.psl - lines changed 2000, context: html, text, full: html, text
  • src/hg/utils/pslToBigPsl/tests/makefile - lines changed 33, context: html, text, full: html, text

2357b15831ef8daa3be1473145e293ee5cbf29c7 Wed Aug 3 15:17:57 2016 -0700

• add pslToBigPsl to the utilities with tests
  
  • src/hg/utils/makefile - lines changed 1, context: html, text, full: html, text

4be6f829c6ac805aa57007baa541f71faaebd82f Thu Aug 4 07:44:52 2016 -0700

• remove bigPsl.as from tests
  
  • src/hg/utils/pslToBigPsl/tests/input/bigPsl.as - lines changed 33, context: html, text, full: html, text
  • src/hg/utils/pslToBigPsl/tests/makefile - lines changed 2, context: html, text, full: html, text

295eb007699561de66fa5d813692168b6a4ce84c Thu Aug 4 07:51:55 2016 -0700

• redirect bedToBigBed's silly output
  
  • src/hg/utils/pslToBigPsl/tests/makefile - lines changed 2, context: html, text, full: html, text

00ea644ada0eb396a9a763e078062121b2a0bf3a Fri Aug 5 11:20:25 2016 -0700

• don't remove top level work directory in gbDbLoadStep since it
  interferes with more than one load working at a time
  
  • src/hg/makeDb/genbank/src/dbload/gbDbLoadStep - lines changed 3, context: html, text, full: html, text

7d49a2cb857d1cad62c92eecc6b05b51ac39df52 Sat Aug 6 13:46:48 2016 -0700

• align genbank dbs in the order they're given.
  
  • src/hg/makeDb/genbank/src/align/gbAlignStep - lines changed 1, context: html, text, full: html, text