Commits for braney

v339_preview2 to v339_base (2016-09-19 to 2016-09-26) v339

f964b14dff2b59b626586c2a6e89c18006669f90 Mon Sep 19 10:05:56 2016 -0700

• get default species maf onto hg38
  
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 29, context: html, text, full: html, text

58457bc18da6a8c2868b375b4265ae40fba2cad4 Mon Sep 19 10:35:26 2016 -0700

• add detail page for refGenePfam track
  
  • src/hg/makeDb/trackDb/refGenePfam.html - lines changed 47, context: html, text, full: html, text

29c8bf71cef86b2444f7de78d213d527b78081be Tue Sep 20 09:44:08 2016 -0700

• make makeDoc entry for Pfam track follow undocumented standards. ;-)
  
  • src/hg/makeDb/doc/dm6.txt - lines changed 2, context: html, text, full: html, text

b41fc14e54398ab40c4141e6931df0693cb4b019 Wed Sep 21 11:08:40 2016 -0700

• recognize refSeqAli as a genbank table when grabbing sequence
  
  • src/hg/hgTracks/cds.c - lines changed 1, context: html, text, full: html, text

00c3b2c9fdcd83c851db8f9c12fc47551dabdcd1 Wed Sep 21 12:20:58 2016 -0700

• fix the order of items in bigGenePred driven knownGene display
  
  • src/hg/hgTracks/simpleTracks.c - lines changed 1, context: html, text, full: html, text

0ca843e479b32307898a24a0538e9478834e7cab Wed Sep 21 16:48:03 2016 -0700

• more thinks I have to pay attention to in order for them to be ignored
  
  • src/hg/makeDb/genbank/etc/ignore.idx - lines changed 24, context: html, text, full: html, text

86987338868c089ac07378d440a5c245d6ef654a Wed Sep 21 19:36:10 2016 -0700

• remove test 100way default species track
  
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 29, context: html, text, full: html, text

1490b71d8c02bdcc0690fc472bdcaada4496471f Thu Sep 22 12:14:45 2016 -0700

• modify how bigGenePreds are made from knownGene
  
  • src/hg/utils/genePredToBigGenePred/makeBigKnown - lines changed 2, context: html, text, full: html, text