File Changes for angie

v285_preview2 to v285_base (2013-06-11 to 2013-06-18) v285

• src/hg/hgCustom/hgCustom.c
  • lines changed 11, context: html, text, full: html, text
    Bugfixes and improvements suggested by Brooke in #6152 notes 36, 38, 42. refs #6152
• src/hg/hgVai/hgVai.c
  • lines changed 3, context: html, text, full: html, text
    Bugfixes and improvements suggested by Brooke in #6152 notes 36, 38, 42. refs #6152
  • lines changed 1, context: html, text, full: html, text
    Bugfix: forgot to pass through an argument, so all sections started up closed by default. refs #6152
  • lines changed 2, context: html, text, full: html, text
    Libifying a javascript trick to detect that the back button has been pressed, and reload the page to redraw with the latest cart vars. refs #6152
  • lines changed 2, context: html, text, full: html, text
    Added cgiExitTime to main.
  • lines changed 27, context: html, text, full: html, text
    Adding HTML version of VEP output format. refs #6152
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 15, context: html, text, full: html, text
    Libifying a javascript trick to detect that the back button has been pressed, and reload the page to redraw with the latest cart vars. refs #6152
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    Bugfixes and improvements suggested by Brooke in #6152 notes 36, 38, 42. refs #6152
• src/hg/inc/annoFormatVep.h
  • lines changed 2, context: html, text, full: html, text
    Adding HTML version of VEP output format. refs #6152
• src/hg/inc/gpFx.h
  • lines changed 1, context: html, text, full: html, text
    As Jonathan pointed out in note 46, Ensembl VEP always shows a/the alternate allele,even when the allele isn't used to make the functional prediction -- follow suit.
    refs #6152
    
• src/hg/inc/hCommon.h
  • lines changed 3, context: html, text, full: html, text
    Bugfixes and improvements suggested by Brooke in #6152 notes 36, 38, 42. refs #6152
• src/hg/inc/jsHelper.h
  • lines changed 4, context: html, text, full: html, text
    Libifying a javascript trick to detect that the back button has been pressed, and reload the page to redraw with the latest cart vars. refs #6152
• src/hg/lib/annoFormatVep.c
  • lines changed 23, context: html, text, full: html, text
    Addressing a couple VEP output issues that Jonathan found in #6152 note 46(DISTANCE sometimes off-by-1 vs Ensembl VEP; crazy long sequences reported
    for frameshifts) refs #6152
    
  • lines changed 251, context: html, text, full: html, text
    Adding HTML version of VEP output format. refs #6152
  • lines changed 22, context: html, text, full: html, text
    As Jonathan pointed out, to be consistent with VEP we should uppercase only the varying bases in the codon change column. refs #6152
• src/hg/lib/annoGratorGpVar.c
  • lines changed 8, context: html, text, full: html, text
    As Jonathan pointed out in note 46, Ensembl VEP always shows a/the alternate allele,even when the allele isn't used to make the functional prediction -- follow suit.
    refs #6152
    
• src/hg/lib/annoStreamDb.c
  • lines changed 17, context: html, text, full: html, text
    Bugfixes and improvements suggested by Brooke in #6152 notes 36, 38, 42. refs #6152
  • lines changed 9, context: html, text, full: html, text
    Fixing code review bugs -- Tim noticed I was not using lm when I meant to, and pointed out a contradiction in the way I was using nextChunkStart. refs #11034
  • lines changed 1, context: html, text, full: html, text
    oops, one more thing that Tim caught. refs #11034
  • lines changed 17, context: html, text, full: html, text
    More bugfixing after testing with artificially low ASD_CHUNK_SIZE.
  • lines changed 7, context: html, text, full: html, text
    Fixing bug w/interaction of merge state and chrom-skipping queries.
• src/hg/lib/gpFx.c
  • lines changed 238, context: html, text, full: html, text
    Changing how gpFx determines indel changes. Instead of padding the non-reference allele with hyphens, and using string comparison of CDS containing
    hyphens to determine effects on genes, use the genePred information directly
    to determine the variant's offset in CDS, and how many CDS bases are
    added/deleted. This solves two problems: 1) the reference was never padded,
    so the method didn't work for insertions because string comparison could not
    pick up the trail of identical bases again; 2) the hyphens were messing up
    protein translation.
    
  • lines changed 58, context: html, text, full: html, text
    As Jonathan pointed out in note 46, Ensembl VEP always shows a/the alternate allele,even when the allele isn't used to make the functional prediction -- follow suit.
    refs #6152
    
• src/hg/lib/hCommon.c
  • lines changed 7, context: html, text, full: html, text
    Bugfixes and improvements suggested by Brooke in #6152 notes 36, 38, 42. refs #6152
• src/hg/lib/hgFind.c
  • lines changed 3, context: html, text, full: html, text
    Bugfixes and improvements suggested by Brooke in #6152 notes 36, 38, 42. refs #6152
• src/hg/lib/jsHelper.c
  • lines changed 23, context: html, text, full: html, text
    Libifying a javascript trick to detect that the back button has been pressed, and reload the page to redraw with the latest cart vars. refs #6152
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 2, context: html, text, full: html, text
    Adding HTML version of VEP output format. refs #6152
• src/hg/lib/tests/expected/annoGrator/gpFx.txt
  • lines changed 1, context: html, text, full: html, text
    Addressing a couple VEP output issues that Jonathan found in #6152 note 46(DISTANCE sometimes off-by-1 vs Ensembl VEP; crazy long sequences reported
    for frameshifts) refs #6152
    
  • lines changed 6, context: html, text, full: html, text
    Oops, catching up VEP output test cases with that last commit.
  • lines changed 13, context: html, text, full: html, text
    As Jonathan pointed out in note 46, Ensembl VEP always shows a/the alternate allele,even when the allele isn't used to make the functional prediction -- follow suit.
    refs #6152
    
• src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
  • lines changed 13, context: html, text, full: html, text
    Changing how gpFx determines indel changes. Instead of padding the non-reference allele with hyphens, and using string comparison of CDS containing
    hyphens to determine effects on genes, use the genePred information directly
    to determine the variant's offset in CDS, and how many CDS bases are
    added/deleted. This solves two problems: 1) the reference was never padded,
    so the method didn't work for insertions because string comparison could not
    pick up the trail of identical bases again; 2) the hyphens were messing up
    protein translation.
    
  • lines changed 13, context: html, text, full: html, text
    As Jonathan pointed out in note 46, Ensembl VEP always shows a/the alternate allele,even when the allele isn't used to make the functional prediction -- follow suit.
    refs #6152
    
• src/hg/lib/tests/expected/annoGrator/vepOut.txt
  • lines changed 1, context: html, text, full: html, text
    Changing how gpFx determines indel changes. Instead of padding the non-reference allele with hyphens, and using string comparison of CDS containing
    hyphens to determine effects on genes, use the genePred information directly
    to determine the variant's offset in CDS, and how many CDS bases are
    added/deleted. This solves two problems: 1) the reference was never padded,
    so the method didn't work for insertions because string comparison could not
    pick up the trail of identical bases again; 2) the hyphens were messing up
    protein translation.
    
  • lines changed 2, context: html, text, full: html, text
    Addressing a couple VEP output issues that Jonathan found in #6152 note 46(DISTANCE sometimes off-by-1 vs Ensembl VEP; crazy long sequences reported
    for frameshifts) refs #6152
    
  • lines changed 2, context: html, text, full: html, text
    Oops, catching up VEP output test cases with that last commit.
  • lines changed 13, context: html, text, full: html, text
    As Jonathan pointed out in note 46, Ensembl VEP always shows a/the alternate allele,even when the allele isn't used to make the functional prediction -- follow suit.
    refs #6152
    
• src/hg/lib/variant.c
  • lines changed 28, context: html, text, full: html, text
    Changing how gpFx determines indel changes. Instead of padding the non-reference allele with hyphens, and using string comparison of CDS containing
    hyphens to determine effects on genes, use the genePred information directly
    to determine the variant's offset in CDS, and how many CDS bases are
    added/deleted. This solves two problems: 1) the reference was never padded,
    so the method didn't work for insertions because string comparison could not
    pick up the trail of identical bases again; 2) the hyphens were messing up
    protein translation.
    
  • lines changed 7, context: html, text, full: html, text
    Fix corner case (deletion falls across exon boundary; normally we wantto trim the part of the allele that falls outside, but for the deletion
    the allele is "").