File Changes for angie

v242_base to v243_preview (2010-10-12 to 2010-10-19) v243

• src/hg/bedIntersect/bedIntersect.c
  • lines changed 8, context: html, text, full: html, text
    Code review suggestion from Larry: errAbort if input has start==end items, but -allowStartEqualEnd not specified (thanks!).
• src/hg/bedIntersect/tests/input/subBlocks.bed
  • lines changed 6, context: html, text, full: html, text
    Code review suggestion from Larry: errAbort if input has start==end items, but -allowStartEqualEnd not specified (thanks!).
• src/hg/bedIntersect/tests/input/subBlocksWInserts.bed
  • lines changed 21, context: html, text, full: html, text
    Code review suggestion from Larry: errAbort if input has start==end items, but -allowStartEqualEnd not specified (thanks!).
• src/hg/bedIntersect/tests/makefile
  • lines changed 6, context: html, text, full: html, text
    Code review suggestion from Larry: errAbort if input has start==end items, but -allowStartEqualEnd not specified (thanks!).
• src/hg/hgTables/gffOut.c
  • lines changed 234, context: html, text, full: html, text
    Redmine Bug #5 (Table Browser may return GTF lines with start > end): fixed, finally. GTF2's removal of stop_codons from CDS is a real pain when codons straddle introns -- we can't just work on each exon independently and use +3/-3 to get the codon end, we have to look forwards or backwards depending on strand, and even CDS exons that don't contain the stop codon have to watch out for their neighbors. Also, instead of wasting memory building up a list of GFF and using the list only for printing out, just print as we go.
• src/hg/hgTracks/cytoBandTrack.c
  • lines changed 1, context: html, text, full: html, text
    Fix for broken build -- Larry also checked in a fix. Checking in so I can git pull...
• src/hg/hgTracks/imageV2.c
  • lines changed 1, context: html, text, full: html, text
    Resolving compiler warnings from gcc (Ubuntu 4.4.1-4ubuntu9).
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    Redmine Bug #1304 (alignment numbering wrong when "viewing parts ofalignment"): fixed bug I introduced into fuzzyShow.c back in 2007. Also in hgc.c, trim the "Alignment of <query> to <chrN:s-e>" message at top of alignment display frame to query bounds (not just viewing window), to be more consistent with message in whole-alignment view.
• src/hg/makeDb/doc/hg18.txt
  • lines changed 45, context: html, text, full: html, text
    Redmine Track #1249 (hg19.snp131CodingDbSnp still has NCBI coords): Fixed coords in {hg18,hg19}.snp130CodingDbSnp and hg19.snp131CodingDbSnp.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 78, context: html, text, full: html, text
    Redmine Track #1249 (hg19.snp131CodingDbSnp still has NCBI coords): Fixed coords in {hg18,hg19}.snp130CodingDbSnp and hg19.snp131CodingDbSnp.
  • lines changed 9, context: html, text, full: html, text
    hg19.snp131CodingDbSnp was missing some items -- noticed while working on #1249.
• src/hg/utils/makeTrackIndex/makeTrackIndex.c
  • lines changed 1, context: html, text, full: html, text
    Resolving compiler warnings from gcc (Ubuntu 4.4.1-4ubuntu9).
• src/lib/fuzzyShow.c
  • lines changed 1, context: html, text, full: html, text
    Redmine Bug #1304 (alignment numbering wrong when "viewing parts ofalignment"): fixed bug I introduced into fuzzyShow.c back in 2007. Also in hgc.c, trim the "Alignment of <query> to <chrN:s-e>" message at top of alignment display frame to query bounds (not just viewing window), to be more consistent with message in whole-alignment view.