Commits for angie

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

• Redmine Track #1249 (hg19.snp131CodingDbSnp still has NCBI coords): Fixed coords in {hg18,hg19}.snp130CodingDbSnp and hg19.snp131CodingDbSnp.
  • src/hg/makeDb/doc/hg18.txt - lines changed 45, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 78, context: html, text, full: html, text
• hg19.snp131CodingDbSnp was missing some items -- noticed while working on #1249.
  • src/hg/makeDb/doc/hg19.txt - lines changed 9, 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/cytoBandTrack.c - lines changed 1, 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/hgTables/gffOut.c - lines changed 234, 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/bedIntersect.c - lines changed 8, context: html, text, full: html, text
  • src/hg/bedIntersect/tests/input/subBlocks.bed - lines changed 6, context: html, text, full: html, text
  • src/hg/bedIntersect/tests/input/subBlocksWInserts.bed - lines changed 21, context: html, text, full: html, text
  • src/hg/bedIntersect/tests/makefile - lines changed 6, context: html, text, full: html, text
• Resolving compiler warnings from gcc (Ubuntu 4.4.1-4ubuntu9).
  • src/hg/hgTracks/imageV2.c - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/makeTrackIndex/makeTrackIndex.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.
  • src/hg/hgc/hgc.c - lines changed 2, context: html, text, full: html, text
  • src/lib/fuzzyShow.c - lines changed 1, context: html, text, full: html, text