File Changes for angie

v288_base to v289_preview (2013-08-19 to 2013-08-26) v289

• src/hg/makeDb/doc/hg19.txt
  • lines changed 96, context: html, text, full: html, text
    MLQs #11474 and #11504 alerted us to strand errors for some SNPs thatcaused incorrect allele frequencies, sometimes making a rare SNP seem
    common e.g. when the alleles are C/G and dbSNP's SNPAlleleFreq contains
    - strand data while dbSNP's SNPAlleleFreq_TGP (1000 Genomes) always has
    + strand data. I was using an insufficient kludge to detect strand-swapping.
    Now strand is taken from bNNN_SNPContigLoc so we know exactly when to
    complement alleles before adding counts.
    fixes #11544
    
• src/hg/phyloGif/makefile
  • lines changed 1, context: html, text, full: html, text
    Tweaked phyloGif/makefile's installation to tolerate the use of the samedirectory for CGI binaries and utils.
    
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 1, context: html, text, full: html, text
    MLQs #11474 and #11504 alerted us to strand errors for some SNPs thatcaused incorrect allele frequencies, sometimes making a rare SNP seem
    common e.g. when the alleles are C/G and dbSNP's SNPAlleleFreq contains
    - strand data while dbSNP's SNPAlleleFreq_TGP (1000 Genomes) always has
    + strand data. I was using an insufficient kludge to detect strand-swapping.
    Now strand is taken from bNNN_SNPContigLoc so we know exactly when to
    complement alleles before adding counts.
    fixes #11544
    
• src/hg/utils/automation/snpAddTGPAlleleFreq.pl
  • lines changed 95, context: html, text, full: html, text
    MLQs #11474 and #11504 alerted us to strand errors for some SNPs thatcaused incorrect allele frequencies, sometimes making a rare SNP seem
    common e.g. when the alleles are C/G and dbSNP's SNPAlleleFreq contains
    - strand data while dbSNP's SNPAlleleFreq_TGP (1000 Genomes) always has
    + strand data. I was using an insufficient kludge to detect strand-swapping.
    Now strand is taken from bNNN_SNPContigLoc so we know exactly when to
    complement alleles before adding counts.
    fixes #11544
    
• src/inc/common.mk
  • lines changed 4, context: html, text, full: html, text
    If a non-standard $SSL_DIR has been specified, add the necessary lib and inc settings.