File Changes for angie

v347_preview to v347_preview2 (2017-03-20 to 2017-03-27) v347

• src/hg/lib/hAnno.c
  • lines changed 10, context: html, text, full: html, text
    e52b9728905070e9979662928bccd604db61d8f4 Thu Mar 23 00:16:08 2017 +0000
    Commit 6072cb04b (#18445) introduced a bug: when hReplaceGbdb changes a path into a URL, fileExists() is no longer a sufficient test. Using hDbDbNibPath was unnecessarily complicated -- we have standardized on /gbdb/$db/$db.2bit for 2bit files. fixes #19113
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    861e6f43bdfd6fd801c12200f44631a204655064 Tue Mar 21 14:47:29 2017 -0700
    Yet another place where we need the all_ prefix for the table. fixes #19111
  • lines changed 3, context: html, text, full: html, text
    4c9e841fc4f0b1c8664e8b44ed889e38b5a3ad97 Thu Mar 23 11:40:36 2017 -0700
    Yet another place where we need the all_ prefix for the table (again, thanks Jairo!). fixes #19111
• src/hg/makeDb/doc/hg19.txt
  • lines changed 86, context: html, text, full: html, text
    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.
• src/hg/makeDb/doc/hg38/variation.txt
  • lines changed 79, context: html, text, full: html, text
    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.
• src/hg/makeDb/schema/all.joiner
  • lines changed 19, context: html, text, full: html, text
    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.
• src/hg/makeDb/trackDb/human/snp149.html
  • lines changed 36, context: html, text, full: html, text
    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.
• src/hg/makeDb/trackDb/human/snp149.shared.html
  • lines changed 484, context: html, text, full: html, text
    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.
• src/hg/makeDb/trackDb/human/snp149Common.html
  • lines changed 28, context: html, text, full: html, text
    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.
• src/hg/makeDb/trackDb/human/snp149Flagged.html
  • lines changed 29, context: html, text, full: html, text
    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.
• src/hg/makeDb/trackDb/human/snp149Mult.html
  • lines changed 25, context: html, text, full: html, text
    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 111, context: html, text, full: html, text
    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.
• src/hg/makeDb/trackDb/rhesus/rheMac8/description.html
  • lines changed 19, context: html, text, full: html, text
    65be6694c8e19b34d837f0668ea112444666ecdb Fri Mar 24 13:24:24 2017 -0700
    Clarifying that while Zimin et al. is the source of the very useful table, it is not a reference for rheMac8 itself.
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
  • lines changed 17, context: html, text, full: html, text
    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 62, context: html, text, full: html, text
    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.