Commits for markd

v338_preview to v338_preview2 (2016-08-22 to 2016-08-29) v338

326c527afbeb869c709e48743e006ca276612c38 Sun Aug 21 15:46:27 2016 -0700

• fixed case where exon becomes zero length
  
  • src/hg/utils/genePredToProt/genePredToProt.c - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/expected/refSeqSuffixTest.cds.fa - lines changed 139, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/expected/refSeqSuffixTest.prot.fa - lines changed 49, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/expected/refSeqTest.cds.fa - lines changed 139, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/expected/refSeqTest.prot.fa - lines changed 49, context: html, text, full: html, text

20becadd2c1dda0ccf5f5596be47a93e192e46ae Mon Aug 22 20:43:19 2016 -0700

• added options to genePredToProt to handle stop codons in various different ways
  
  • src/hg/utils/genePredToProt/genePredToProt.c - lines changed 74, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/expected/combinedStopOptionsTest.prot.fa - lines changed 201, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/expected/includeStopTest.prot.fa - lines changed 201, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/expected/refSeqSuffixTest.cds.fa - lines changed 12, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/expected/refSeqSuffixTest.cds.psl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/expected/refSeqSuffixTest.prot.fa - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/expected/refSeqTest.cds.fa - lines changed 12, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/expected/refSeqTest.cds.psl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/expected/refSeqTest.prot.fa - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/expected/starForInframeStopsTest.prot.fa - lines changed 201, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/expected/translateSelnoTest.prot.fa - lines changed 201, context: html, text, full: html, text
  • src/hg/utils/genePredToProt/tests/input/refseq.grch38.gp - lines changed 3, context: html, text, full: html, text

370394fc362cce1b14f32e1a9d548fd5654063a0 Tue Aug 23 09:59:15 2016 -0700

• Account for bin column when loading estOrientInfo data.
  Add function to read selected PSLs from a table into memory.
  
  • src/hg/inc/pslReader.h - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/estOrientInfo.c - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/pslReader.c - lines changed 13, context: html, text, full: html, text