File Changes for angie

v283_preview to v283_preview2 (2013-04-23 to 2013-04-30) v283

• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 1, context: html, text, full: html, text
    Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
    
• src/hg/inc/annoGratorGpVar.h
  • lines changed 2, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
• src/hg/inc/gpFx.h
  • lines changed 40, context: html, text, full: html, text
    Added detection of many new SO terms to gpFx: {5,3} UTR, splice_{donor,acceptor},non_coding_exon, and very detailed coding change terms to match Ensembl e.g.
    stop_retained_variant, NMD_transcript_variant). Also tweaks to annoFormatVep to
    represent insertion positions the way they do.
    TODO: lots more testing! and convert gpFx to use localmem.
    refs #6152
    
  • lines changed 3, context: html, text, full: html, text
    Converted variant and gpFx to use localmem. Also got rid of a coupleunnecessary conversions from genePred to bed and psl in annoGratorGpVar
    and gpFx. refs #6152
    
• src/hg/inc/soTerm.h
  • lines changed 42, context: html, text, full: html, text
    Added detection of many new SO terms to gpFx: {5,3} UTR, splice_{donor,acceptor},non_coding_exon, and very detailed coding change terms to match Ensembl e.g.
    stop_retained_variant, NMD_transcript_variant). Also tweaks to annoFormatVep to
    represent insertion positions the way they do.
    TODO: lots more testing! and convert gpFx to use localmem.
    refs #6152
    
• src/hg/inc/variant.h
  • lines changed 6, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
  • lines changed 2, context: html, text, full: html, text
    typo fix in comment
  • lines changed 5, context: html, text, full: html, text
    Converted variant and gpFx to use localmem. Also got rid of a coupleunnecessary conversions from genePred to bed and psl in annoGratorGpVar
    and gpFx. refs #6152
    
• src/hg/lib/annoFormatVep.c
  • lines changed 32, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
  • lines changed 53, context: html, text, full: html, text
    Added detection of many new SO terms to gpFx: {5,3} UTR, splice_{donor,acceptor},non_coding_exon, and very detailed coding change terms to match Ensembl e.g.
    stop_retained_variant, NMD_transcript_variant). Also tweaks to annoFormatVep to
    represent insertion positions the way they do.
    TODO: lots more testing! and convert gpFx to use localmem.
    refs #6152
    
  • lines changed 2, context: html, text, full: html, text
    Code review feedback, thanks Tim. refs #10680
• src/hg/lib/annoGratorGpVar.c
  • lines changed 44, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
  • lines changed 116, context: html, text, full: html, text
    Added detection of many new SO terms to gpFx: {5,3} UTR, splice_{donor,acceptor},non_coding_exon, and very detailed coding change terms to match Ensembl e.g.
    stop_retained_variant, NMD_transcript_variant). Also tweaks to annoFormatVep to
    represent insertion positions the way they do.
    TODO: lots more testing! and convert gpFx to use localmem.
    refs #6152
    
  • lines changed 48, context: html, text, full: html, text
    Converted variant and gpFx to use localmem. Also got rid of a coupleunnecessary conversions from genePred to bed and psl in annoGratorGpVar
    and gpFx. refs #6152
    
• src/hg/lib/gpFx.c
  • lines changed 284, context: html, text, full: html, text
    Added detection of many new SO terms to gpFx: {5,3} UTR, splice_{donor,acceptor},non_coding_exon, and very detailed coding change terms to match Ensembl e.g.
    stop_retained_variant, NMD_transcript_variant). Also tweaks to annoFormatVep to
    represent insertion positions the way they do.
    TODO: lots more testing! and convert gpFx to use localmem.
    refs #6152
    
  • lines changed 197, context: html, text, full: html, text
    Converted variant and gpFx to use localmem. Also got rid of a coupleunnecessary conversions from genePred to bed and psl in annoGratorGpVar
    and gpFx. refs #6152
    
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 2, context: html, text, full: html, text
    Adding NULL check.
• src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
  • lines changed 49, context: html, text, full: html, text
    Added detection of many new SO terms to gpFx: {5,3} UTR, splice_{donor,acceptor},non_coding_exon, and very detailed coding change terms to match Ensembl e.g.
    stop_retained_variant, NMD_transcript_variant). Also tweaks to annoFormatVep to
    represent insertion positions the way they do.
    TODO: lots more testing! and convert gpFx to use localmem.
    refs #6152
    
• src/hg/lib/tests/expected/annoGrator/vepOut.txt
  • lines changed 12, context: html, text, full: html, text
    Added detection of many new SO terms to gpFx: {5,3} UTR, splice_{donor,acceptor},non_coding_exon, and very detailed coding change terms to match Ensembl e.g.
    stop_retained_variant, NMD_transcript_variant). Also tweaks to annoFormatVep to
    represent insertion positions the way they do.
    TODO: lots more testing! and convert gpFx to use localmem.
    refs #6152
    
• src/hg/lib/variant.c
  • lines changed 20, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
  • lines changed 12, context: html, text, full: html, text
    Converted variant and gpFx to use localmem. Also got rid of a coupleunnecessary conversions from genePred to bed and psl in annoGratorGpVar
    and gpFx. refs #6152
    
• src/inc/annoFormatter.h
  • lines changed 12, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
• src/inc/annoGrator.h
  • lines changed 2, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
• src/inc/annoStreamer.h
  • lines changed 14, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
  • lines changed 1, context: html, text, full: html, text
    Code review feedback, thanks Tim. refs #10680
• src/inc/localmem.h
  • lines changed 3, context: html, text, full: html, text
    Converted variant and gpFx to use localmem. Also got rid of a coupleunnecessary conversions from genePred to bed and psl in annoGratorGpVar
    and gpFx. refs #6152
    
• src/inc/vcf.h
  • lines changed 4, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
• src/lib/annoFormatter.c
  • lines changed 13, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
• src/lib/annoGrateWig.c
  • lines changed 3, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
• src/lib/annoGrator.c
  • lines changed 2, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
• src/lib/annoGratorQuery.c
  • lines changed 1, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
• src/lib/annoStreamer.c
  • lines changed 15, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
• src/lib/vcf.c
  • lines changed 23, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152