File Changes for angie

v245_preview to v245_preview2 (2010-12-14 to 2010-12-21) v245

• src/hg/dbTrash/dbTrash.c
  • lines changed 1, context: html, text, full: html, text
    Resolved compilation warnings from gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9),mostly by folding unnecessary safef's into hgHistoryComment which takes varargs (pragma recently added by MarkD meant newly detected lack of format strings).
• src/hg/hgc/hgc.c
  • lines changed 3, context: html, text, full: html, text
    Resolved compilation warnings from gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9),mostly by folding unnecessary safef's into hgHistoryComment which takes varargs (pragma recently added by MarkD meant newly detected lack of format strings).
• src/hg/inc/snp132Ext.h
  • lines changed 81, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added new columns to SNP table(snp132Ext.as) in doDbSnp.pl and snpNcbiToUcsc. It now runs successfully on hg19 snp132; I have verified that the first 17 columns match the old snp132.bed and that the pre-existing exceptions match the old snp132Exceptions.bed. The snp125 code in hgTracks/hgTrackUi/hgc works find on the new snp132 -- new columns are ignored. There is still some polishing to do before doDbSnp.pl is ready for general use -- more consistency checks, and much more info for the developer about what they need to follow through on. But next I plan to enhance the CGIs to make use of the new columns so we can get snp132 out the door.
• src/hg/lib/liftOver.c
  • lines changed 6, context: html, text, full: html, text
    bedOverSmall had a limit of 20 words per line, while other functionshad a limit of 64. The new snp132Ext has >20 columns and lines were truncated due to the 20-word limit. Changed limit to 64 everywhere.
  • lines changed 1, context: html, text, full: html, text
    follow-on to 4963dda: Fixed one more spot with a hardcoded lower wordcount limit.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added new columns to SNP table(snp132Ext.as) in doDbSnp.pl and snpNcbiToUcsc. It now runs successfully on hg19 snp132; I have verified that the first 17 columns match the old snp132.bed and that the pre-existing exceptions match the old snp132Exceptions.bed. The snp125 code in hgTracks/hgTrackUi/hgc works find on the new snp132 -- new columns are ignored. There is still some polishing to do before doDbSnp.pl is ready for general use -- more consistency checks, and much more info for the developer about what they need to follow through on. But next I plan to enhance the CGIs to make use of the new columns so we can get snp132 out the door.
• src/hg/lib/snp132Ext.as
  • lines changed 30, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added new columns to SNP table(snp132Ext.as) in doDbSnp.pl and snpNcbiToUcsc. It now runs successfully on hg19 snp132; I have verified that the first 17 columns match the old snp132.bed and that the pre-existing exceptions match the old snp132Exceptions.bed. The snp125 code in hgTracks/hgTrackUi/hgc works find on the new snp132 -- new columns are ignored. There is still some polishing to do before doDbSnp.pl is ready for general use -- more consistency checks, and much more info for the developer about what they need to follow through on. But next I plan to enhance the CGIs to make use of the new columns so we can get snp132 out the door.
• src/hg/lib/snp132Ext.c
  • lines changed 345, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added new columns to SNP table(snp132Ext.as) in doDbSnp.pl and snpNcbiToUcsc. It now runs successfully on hg19 snp132; I have verified that the first 17 columns match the old snp132.bed and that the pre-existing exceptions match the old snp132Exceptions.bed. The snp125 code in hgTracks/hgTrackUi/hgc works find on the new snp132 -- new columns are ignored. There is still some polishing to do before doDbSnp.pl is ready for general use -- more consistency checks, and much more info for the developer about what they need to follow through on. But next I plan to enhance the CGIs to make use of the new columns so we can get snp132 out the door.
• src/hg/makeDb/doc/equCab2.txt
  • lines changed 10, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): work-in-progress: getting the new doDbSnp.pl to work on hg19 snp132.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 45, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): work-in-progress: getting the new doDbSnp.pl to work on hg19 snp132.
  • lines changed 12, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): doDbSnp.pl now runs successfullyon hg19 snp132 and loads the additional tables into hg19snp132 (Allele, Batch, SNPAlleleFreq, SNPSubSNPLink, SNP_bitfield, SubSNP). Next, make use of that new info to add some columns to snp132...
  • lines changed 7, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added new columns to SNP table(snp132Ext.as) in doDbSnp.pl and snpNcbiToUcsc. It now runs successfully on hg19 snp132; I have verified that the first 17 columns match the old snp132.bed and that the pre-existing exceptions match the old snp132Exceptions.bed. The snp125 code in hgTracks/hgTrackUi/hgc works find on the new snp132 -- new columns are ignored. There is still some polishing to do before doDbSnp.pl is ready for general use -- more consistency checks, and much more info for the developer about what they need to follow through on. But next I plan to enhance the CGIs to make use of the new columns so we can get snp132 out the door.
• src/hg/makeDb/hgLoadBed/hgLoadBed.c
  • lines changed 7, context: html, text, full: html, text
    Resolved compilation warnings from gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9),mostly by folding unnecessary safef's into hgHistoryComment which takes varargs (pragma recently added by MarkD meant newly detected lack of format strings).
• src/hg/makeDb/hgLoadBlastTab/hgLoadBlastTab.c
  • lines changed 4, context: html, text, full: html, text
    Resolved compilation warnings from gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9),mostly by folding unnecessary safef's into hgHistoryComment which takes varargs (pragma recently added by MarkD meant newly detected lack of format strings).
• src/hg/makeDb/hgLoadChain/hgLoadChain.c
  • lines changed 4, context: html, text, full: html, text
    Resolved compilation warnings from gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9),mostly by folding unnecessary safef's into hgHistoryComment which takes varargs (pragma recently added by MarkD meant newly detected lack of format strings).
• src/hg/makeDb/hgLoadNet/hgLoadNet.c
  • lines changed 4, context: html, text, full: html, text
    Resolved compilation warnings from gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9),mostly by folding unnecessary safef's into hgHistoryComment which takes varargs (pragma recently added by MarkD meant newly detected lack of format strings).
• src/hg/makeDb/hgLoadPsl/hgLoadPsl.c
  • lines changed 5, context: html, text, full: html, text
    Resolved compilation warnings from gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9),mostly by folding unnecessary safef's into hgHistoryComment which takes varargs (pragma recently added by MarkD meant newly detected lack of format strings).
• src/hg/makeDb/hgLoadSqlTab/hgLoadSqlTab.c
  • lines changed 6, context: html, text, full: html, text
    Resolved compilation warnings from gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9),mostly by folding unnecessary safef's into hgHistoryComment which takes varargs (pragma recently added by MarkD meant newly detected lack of format strings).
• src/hg/makeDb/hgLoadWiggle/hgLoadWiggle.c
  • lines changed 1, context: html, text, full: html, text
    Resolved compilation warnings from gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9),mostly by folding unnecessary safef's into hgHistoryComment which takes varargs (pragma recently added by MarkD meant newly detected lack of format strings).
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
  • lines changed 2, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): tweaks to get doDbSnp.pl to runsuccessfully on hg19 snp132.
  • lines changed 473, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added new columns to SNP table(snp132Ext.as) in doDbSnp.pl and snpNcbiToUcsc. It now runs successfully on hg19 snp132; I have verified that the first 17 columns match the old snp132.bed and that the pre-existing exceptions match the old snp132Exceptions.bed. The snp125 code in hgTracks/hgTrackUi/hgc works find on the new snp132 -- new columns are ignored. There is still some polishing to do before doDbSnp.pl is ready for general use -- more consistency checks, and much more info for the developer about what they need to follow through on. But next I plan to enhance the CGIs to make use of the new columns so we can get snp132 out the door.
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 31, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): work-in-progress: getting the new doDbSnp.pl to work on hg19 snp132.
  • lines changed 204, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): tweaks to get doDbSnp.pl to runsuccessfully on hg19 snp132.
  • lines changed 152, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): doDbSnp.pl now runs successfullyon hg19 snp132 and loads the additional tables into hg19snp132 (Allele, Batch, SNPAlleleFreq, SNPSubSNPLink, SNP_bitfield, SubSNP). Next, make use of that new info to add some columns to snp132...
  • lines changed 117, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added new columns to SNP table(snp132Ext.as) in doDbSnp.pl and snpNcbiToUcsc. It now runs successfully on hg19 snp132; I have verified that the first 17 columns match the old snp132.bed and that the pre-existing exceptions match the old snp132Exceptions.bed. The snp125 code in hgTracks/hgTrackUi/hgc works find on the new snp132 -- new columns are ignored. There is still some polishing to do before doDbSnp.pl is ready for general use -- more consistency checks, and much more info for the developer about what they need to follow through on. But next I plan to enhance the CGIs to make use of the new columns so we can get snp132 out the door.