File Changes for markd

v297_preview to v297_preview2 (2014-03-03 to 2014-03-10) v297

• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    RM 12824 fix display of names in GENCODE 2-way pseudogenes
• src/hg/lib/genePred.c
  • lines changed 2, context: html, text, full: html, text
    Fixed bug in GTF to genePred conversion where an assertion was triggered when theGTF had a spliced stop codon where the exon containing the first part of the
    stop codon only consisted of the stop codon bases. For example, a two-base exon where
    with two bases are the first two bases of the stop codon.
    
  • lines changed 2, context: html, text, full: html, text
    commit 5a7542dced0497f6d08a503a95eba87619b23a8aAuthor: Mark Diekhans <markd@soe.ucsc.edu>
    Date: Wed Mar 5 19:35:34 2014 -0800
    
    Fixed bug in GTF to genePred conversion where an assertion was triggered when the
    GTF had a spliced stop codon where the exon containing the first part of the
    stop codon only consisted of the stop codon bases. For example, a two-base exon where
    with two bases are the first two bases of the stop codon. This commit handle negative
    strand case.
    
• src/hg/utils/gtfToGenePred/tests/expected/ensemblSplicedStop.gp
  • lines changed 1, context: html, text, full: html, text
    Fixed bug in GTF to genePred conversion where an assertion was triggered when theGTF had a spliced stop codon where the exon containing the first part of the
    stop codon only consisted of the stop codon bases. For example, a two-base exon where
    with two bases are the first two bases of the stop codon.
    
  • lines changed 1, context: html, text, full: html, text
    commit 5a7542dced0497f6d08a503a95eba87619b23a8aAuthor: Mark Diekhans <markd@soe.ucsc.edu>
    Date: Wed Mar 5 19:35:34 2014 -0800
    
    Fixed bug in GTF to genePred conversion where an assertion was triggered when the
    GTF had a spliced stop codon where the exon containing the first part of the
    stop codon only consisted of the stop codon bases. For example, a two-base exon where
    with two bases are the first two bases of the stop codon. This commit handle negative
    strand case.
    
• src/hg/utils/gtfToGenePred/tests/input/ensemblSplicedStop.gp
  • lines changed 71, context: html, text, full: html, text
    Fixed bug in GTF to genePred conversion where an assertion was triggered when theGTF had a spliced stop codon where the exon containing the first part of the
    stop codon only consisted of the stop codon bases. For example, a two-base exon where
    with two bases are the first two bases of the stop codon.
    
  • lines changed 31, context: html, text, full: html, text
    commit 5a7542dced0497f6d08a503a95eba87619b23a8aAuthor: Mark Diekhans <markd@soe.ucsc.edu>
    Date: Wed Mar 5 19:35:34 2014 -0800
    
    Fixed bug in GTF to genePred conversion where an assertion was triggered when the
    GTF had a spliced stop codon where the exon containing the first part of the
    stop codon only consisted of the stop codon bases. For example, a two-base exon where
    with two bases are the first two bases of the stop codon. This commit handle negative
    strand case.
    
• src/hg/utils/gtfToGenePred/tests/makefile
  • lines changed 7, context: html, text, full: html, text
    Fixed bug in GTF to genePred conversion where an assertion was triggered when theGTF had a spliced stop codon where the exon containing the first part of the
    stop codon only consisted of the stop codon bases. For example, a two-base exon where
    with two bases are the first two bases of the stop codon.
    
• src/lib/gff3.c
  • lines changed 1, context: html, text, full: html, text
    fixed check for include escape in GFF3 files