File Changes for galt

v335_preview2 to v335_base (2016-06-27 to 2016-07-04) v335

• src/blat/version.doc
  • lines changed 2, context: html, text, full: html, text
    cf293df150f4b256d195e90b5a20817d8479ece0 Sat Jul 2 13:17:59 2016 -0700
    fixes #17624. -maxIntron= was broken in blat whenever a non-default value was used causing it to run cutAtBigIntrons() which did not support protein. The fix was using trans3GenoPos() to get correct coordinates handling 3 frames, and also calling ffScoreProtein() instead of ffScore() when it is a protein query.
    
• src/hg/hgTablesTest/hgTablesTest.c
  • lines changed 127, context: html, text, full: html, text
    8ba435bdd1a1fda7d9f05e027477b6b9d8bdc7f4 Wed Jun 29 11:18:08 2016 -0700
    About to remove findExpectedIntersectingRows() because it seems less necessary now.
    
  • lines changed 70, context: html, text, full: html, text
    90048b6df4aec62edab4c7f49f7a5084776db6a8 Wed Jun 29 11:23:00 2016 -0700
    hgTablesTest, cleaned up. hgTablesTest now supports new options -seed=N and -noShuffle.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 33, context: html, text, full: html, text
    e3fb0aba1be876cee6d93465cc0e585dac75529a Thu Jun 30 17:40:34 2016 -0700
    fixes #17617. Just changed customUrl mode to act like em and gm. instead of trying to have the user switch to a full-virt-chrom view, it simply tries to find the nearest position, which is just what em and gm modes do.
    
• src/hg/makeDb/trackDb/augustusGene.html
  • lines changed 1, context: html, text, full: html, text
    cece6b7f7907dcf32f7af1dc62a1355e9fd43bc0 Mon Jun 27 17:23:07 2016 -0700
    track description .html errors found by hgTablesTest.
    
• src/hg/makeDb/trackDb/human/hg38/cons7way.html
  • lines changed 1, context: html, text, full: html, text
    cece6b7f7907dcf32f7af1dc62a1355e9fd43bc0 Mon Jun 27 17:23:07 2016 -0700
    track description .html errors found by hgTablesTest.
    
• src/inc/genoFind.h
  • lines changed 1, context: html, text, full: html, text
    cf293df150f4b256d195e90b5a20817d8479ece0 Sat Jul 2 13:17:59 2016 -0700
    fixes #17624. -maxIntron= was broken in blat whenever a non-default value was used causing it to run cutAtBigIntrons() which did not support protein. The fix was using trans3GenoPos() to get correct coordinates handling 3 frames, and also calling ffScoreProtein() instead of ffScore() when it is a protein query.
    
• src/jkOwnLib/supStitch.c
  • lines changed 17, context: html, text, full: html, text
    cf293df150f4b256d195e90b5a20817d8479ece0 Sat Jul 2 13:17:59 2016 -0700
    fixes #17624. -maxIntron= was broken in blat whenever a non-default value was used causing it to run cutAtBigIntrons() which did not support protein. The fix was using trans3GenoPos() to get correct coordinates handling 3 frames, and also calling ffScoreProtein() instead of ffScore() when it is a protein query.