Commits for markd

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

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/aladdin/aladdin/aladdin.c - lines changed 3, context: html, text, full: html, text

d371431b09ee29373cf24d57f387f8dd0bee4ab9 Wed Aug 17 17:10:30 2016 -0700

• changed to compile on OS/X
  
  • src/hg/hgTablesTest/hgTablesTest.c - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/genbank.c - lines changed 1, 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/getRnaPred/getRnaPred.c - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/genePredToProt.c - lines changed 167, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/makefile - lines changed 10, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/expected/refSeqTest.cds.fa - lines changed 377, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/expected/refSeqTest.prot.fa - lines changed 147, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/input/refseq.grch38.gp - lines changed 24, context: html, text, full: html, text
  • src/hg/utils/makefile - 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/gff3ToGenePred/gff3ToGenePred.c - lines changed 2, 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/inc/twoBit.h - lines changed 7, context: html, text, full: html, text
  • src/lib/twoBit.c - lines changed 82, context: html, text, full: html, text

6fa9908b5a36a45fb2f951157395de0a9a953a17 Sat Aug 20 09:14:32 2016 -0700

• removed duplicate targets in makefile
  
  • src/hg/utils/genePredToProt/makefile - lines changed 6, 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/genePredToProt.c - lines changed 142, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/expected/refSeqSuffixTest.cds.fa - lines changed 377, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/expected/refSeqSuffixTest.cds.psl - lines changed 24, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/expected/refSeqSuffixTest.prot.fa - lines changed 147, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/expected/refSeqTest.cds.psl - lines changed 24, 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/genePredToProt.c - lines changed 1, context: html, text, full: html, text