File Changes for markd

v337_base to v338_preview (2016-08-15 to 2016-08-22) v338

• src/aladdin/aladdin/aladdin.c
  • lines changed 3, context: html, text, full: html, text
    90339aa1d74677c8180a416e9361280acfab9caa Tue Aug 16 19:23:22 2016 -0700
    fix compilation error with C99 style inline used by default by clang on OS/X
    
• src/hg/getRnaPred/getRnaPred.c
  • lines changed 9, context: html, text, full: html, text
    7edc888861d9fd7769d0a21ae55d5f3e75e61587 Fri Aug 19 17:06:17 2016 -0700
    Added genePredToProt that translates genePred files to protein.
    It handles cases where there the annotations has frameshifting
    indels described in the exonFrames column. Partial codons will be skipped.
    This differs from getRnaPred, which only handles initial, incomplete codons.
    
• src/hg/hgTablesTest/hgTablesTest.c
  • lines changed 5, context: html, text, full: html, text
    d371431b09ee29373cf24d57f387f8dd0bee4ab9 Wed Aug 17 17:10:30 2016 -0700
    changed to compile on OS/X
    
• src/hg/lib/genbank.c
  • lines changed 1, context: html, text, full: html, text
    d371431b09ee29373cf24d57f387f8dd0bee4ab9 Wed Aug 17 17:10:30 2016 -0700
    changed to compile on OS/X
    
• src/hg/utils/genePredToProt/genePredToProt.c
  • lines changed 167, context: html, text, full: html, text
    7edc888861d9fd7769d0a21ae55d5f3e75e61587 Fri Aug 19 17:06:17 2016 -0700
    Added genePredToProt that translates genePred files to protein.
    It handles cases where there the annotations has frameshifting
    indels described in the exonFrames column. Partial codons will be skipped.
    This differs from getRnaPred, which only handles initial, incomplete codons.
    
  • lines changed 142, context: html, text, full: html, text
    2b39df1c5734d12c598ee15f6fe27ecb5798ef68 Sun Aug 21 09:15:11 2016 -0700
    Added option to output PSL of CDS alignment and to add suffixes
    to the protin and cds ids.
    
  • lines changed 1, context: html, text, full: html, text
    3a90d3637f25ea59ea95bcbae8cf0dd63ff4fbfd Sun Aug 21 15:11:50 2016 -0700
    fixed bug where CDS is empty when last condon is incomplete
    
• src/hg/utils/genePredToProt/makefile
  • lines changed 10, context: html, text, full: html, text
    7edc888861d9fd7769d0a21ae55d5f3e75e61587 Fri Aug 19 17:06:17 2016 -0700
    Added genePredToProt that translates genePred files to protein.
    It handles cases where there the annotations has frameshifting
    indels described in the exonFrames column. Partial codons will be skipped.
    This differs from getRnaPred, which only handles initial, incomplete codons.
    
  • lines changed 6, context: html, text, full: html, text
    6fa9908b5a36a45fb2f951157395de0a9a953a17 Sat Aug 20 09:14:32 2016 -0700
    removed duplicate targets in makefile
    
• src/hg/utils/genePredToProt/tests/expected/refSeqSuffixTest.cds.fa
  • lines changed 377, context: html, text, full: html, text
    2b39df1c5734d12c598ee15f6fe27ecb5798ef68 Sun Aug 21 09:15:11 2016 -0700
    Added option to output PSL of CDS alignment and to add suffixes
    to the protin and cds ids.
    
• src/hg/utils/genePredToProt/tests/expected/refSeqSuffixTest.cds.psl
  • lines changed 24, context: html, text, full: html, text
    2b39df1c5734d12c598ee15f6fe27ecb5798ef68 Sun Aug 21 09:15:11 2016 -0700
    Added option to output PSL of CDS alignment and to add suffixes
    to the protin and cds ids.
    
• src/hg/utils/genePredToProt/tests/expected/refSeqSuffixTest.prot.fa
  • lines changed 147, context: html, text, full: html, text
    2b39df1c5734d12c598ee15f6fe27ecb5798ef68 Sun Aug 21 09:15:11 2016 -0700
    Added option to output PSL of CDS alignment and to add suffixes
    to the protin and cds ids.
    
• src/hg/utils/genePredToProt/tests/expected/refSeqTest.cds.fa
  • lines changed 377, context: html, text, full: html, text
    7edc888861d9fd7769d0a21ae55d5f3e75e61587 Fri Aug 19 17:06:17 2016 -0700
    Added genePredToProt that translates genePred files to protein.
    It handles cases where there the annotations has frameshifting
    indels described in the exonFrames column. Partial codons will be skipped.
    This differs from getRnaPred, which only handles initial, incomplete codons.
    
• src/hg/utils/genePredToProt/tests/expected/refSeqTest.cds.psl
  • lines changed 24, context: html, text, full: html, text
    2b39df1c5734d12c598ee15f6fe27ecb5798ef68 Sun Aug 21 09:15:11 2016 -0700
    Added option to output PSL of CDS alignment and to add suffixes
    to the protin and cds ids.
    
• src/hg/utils/genePredToProt/tests/expected/refSeqTest.prot.fa
  • lines changed 147, context: html, text, full: html, text
    7edc888861d9fd7769d0a21ae55d5f3e75e61587 Fri Aug 19 17:06:17 2016 -0700
    Added genePredToProt that translates genePred files to protein.
    It handles cases where there the annotations has frameshifting
    indels described in the exonFrames column. Partial codons will be skipped.
    This differs from getRnaPred, which only handles initial, incomplete codons.
    
• src/hg/utils/genePredToProt/tests/input/refseq.grch38.gp
  • lines changed 24, context: html, text, full: html, text
    7edc888861d9fd7769d0a21ae55d5f3e75e61587 Fri Aug 19 17:06:17 2016 -0700
    Added genePredToProt that translates genePred files to protein.
    It handles cases where there the annotations has frameshifting
    indels described in the exonFrames column. Partial codons will be skipped.
    This differs from getRnaPred, which only handles initial, incomplete codons.
    
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
  • lines changed 2, context: html, text, full: html, text
    fc5b9650f28c87f2757a97a44c0c1682538725c0 Fri Aug 19 17:42:53 2016 -0700
    fixed incorrect help message
    
• src/hg/utils/makefile
  • lines changed 2, context: html, text, full: html, text
    7edc888861d9fd7769d0a21ae55d5f3e75e61587 Fri Aug 19 17:06:17 2016 -0700
    Added genePredToProt that translates genePred files to protein.
    It handles cases where there the annotations has frameshifting
    indels described in the exonFrames column. Partial codons will be skipped.
    This differs from getRnaPred, which only handles initial, incomplete codons.
    
• src/inc/twoBit.h
  • lines changed 7, context: html, text, full: html, text
    017f1ebbfad81dd9a4759d391debdc44b227b595 Fri Aug 19 23:25:17 2016 -0700
    Cache twoBit sequence header information for the last sequence
    accessed to avoid rereading N and mask blocks when sequentially
    reader fragments of the genome. This resulted in a 20% speedup
    for pslRecalcMatch.
    
• src/lib/twoBit.c
  • lines changed 82, context: html, text, full: html, text
    017f1ebbfad81dd9a4759d391debdc44b227b595 Fri Aug 19 23:25:17 2016 -0700
    Cache twoBit sequence header information for the last sequence
    accessed to avoid rereading N and mask blocks when sequentially
    reader fragments of the genome. This resulted in a 20% speedup
    for pslRecalcMatch.