angie: changes by commit
switch to grouped by file view, user index
review to branch (2009-09-22 to 2009-09-29) v216
- Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
- src/cdnaAli/findCdna/findCdna.c 1.5 - lines changed: 1, context: html, text, full: html, text
- src/gfServer/gfServer.c 1.55 - lines changed: 10, context: html, text, full: html, text
- src/hg/borfBig/borfBig.c 1.6 - lines changed: 1, context: html, text, full: html, text
- src/hg/encode/hgEncodeVocab/hgEncodeVocab.c 1.26 - lines changed: 1, context: html, text, full: html, text
- src/hg/encode/validateFiles/validateFiles.c 1.27 - lines changed: 3, context: html, text, full: html, text
- src/hg/gsBig/gsBig.c 1.16 - lines changed: 1, context: html, text, full: html, text
- src/hg/hgGene/rnaStructure.c 1.11 - lines changed: 2, context: html, text, full: html, text
- src/hg/hgGene/wikiTrack.c 1.24 - lines changed: 2, context: html, text, full: html, text
- src/hg/hgGenome/mainPage.c 1.28 - lines changed: 1, context: html, text, full: html, text
- src/hg/hgKnownGeneList/hgKnownGeneList.c 1.7 - lines changed: 3, context: html, text, full: html, text
- src/hg/hgPcr/hgPcr.c 1.29 - lines changed: 1, context: html, text, full: html, text
- src/hg/hgSession/hgSession.c 1.52 - lines changed: 1, context: html, text, full: html, text
- src/hg/hgTables/identifiers.c 1.29 - lines changed: 1, context: html, text, full: html, text
- src/hg/hgTracks/config.c 1.84 - lines changed: 1, context: html, text, full: html, text
- src/hg/hgTracks/hgTracks.c 1.1600 - lines changed: 5, context: html, text, full: html, text
- src/hg/hgTracks/rnaPLFoldTrack.c 1.8 - lines changed: 1, context: html, text, full: html, text
- src/hg/hgTracks/simpleTracks.c 1.106 - lines changed: 2, context: html, text, full: html, text
- src/hg/hgc/hgc.c 1.1573 - lines changed: 39, context: html, text, full: html, text
- src/hg/hgc/hgdpClick.c 1.8 - lines changed: 9, context: html, text, full: html, text
- src/hg/lib/customFactory.c 1.104 - lines changed: 2, context: html, text, full: html, text
- src/hg/lib/hgFind.c 1.222 - lines changed: 2, context: html, text, full: html, text
- src/hg/lib/hui.c 1.238 - lines changed: 6, context: html, text, full: html, text
- src/hg/lib/jksql.c 1.136 - lines changed: 2, context: html, text, full: html, text
- src/hg/lib/web.c 1.171 - lines changed: 1, context: html, text, full: html, text
- src/hg/liftOver/liftOver.c 1.28 - lines changed: 1, context: html, text, full: html, text
- src/hg/makeDb/hgCountAlign/hgCountAlign.c 1.7 - lines changed: 1, context: html, text, full: html, text
- src/hg/makeDb/hgLoadMaf/hgLoadMaf.c 1.27 - lines changed: 14, context: html, text, full: html, text
- src/hg/makeDb/hgLoadMaf/hgLoadMafSummary.c 1.20 - lines changed: 3, context: html, text, full: html, text
- src/hg/makeDb/hgMrnaRefseq/hgMrnaRefseq.c 1.5 - lines changed: 2, context: html, text, full: html, text
- src/hg/makeDb/outside/hgBioCyc/hgBioCyc.c 1.4 - lines changed: 2, context: html, text, full: html, text
- src/hg/makeDb/outside/hgCGAP/hgCGAP.c 1.3 - lines changed: 3, context: html, text, full: html, text
- src/hg/makeDb/outside/hgKegg/hgKegg.c 1.4 - lines changed: 4, context: html, text, full: html, text
- src/hg/makeDb/outside/hgKegg2/hgKegg2.c 1.4 - lines changed: 4, context: html, text, full: html, text
- src/hg/makeDb/outside/hgKegg3/hgKegg3.c 1.7 - lines changed: 4, context: html, text, full: html, text
- src/hg/makeDb/outside/hgSuperfam/hgSuperfam.c 1.5 - lines changed: 4, context: html, text, full: html, text
- src/hg/makeDb/outside/samHit/samHit.c 1.3 - lines changed: 3, context: html, text, full: html, text
- src/hg/mouseStuff/chainSplit/chainSplit.c 1.10 - lines changed: 1, context: html, text, full: html, text
- src/hg/mouseStuff/netSplit/netSplit.c 1.6 - lines changed: 1, context: html, text, full: html, text
- src/hg/near/hgClusterGenes/hgClusterGenes.c 1.13 - lines changed: 1, context: html, text, full: html, text
- src/hg/phyloGif/phyloGif.c 1.23 - lines changed: 2, context: html, text, full: html, text
- src/hg/protein/kgAliasKgXref/kgAliasKgXref.c 1.5 - lines changed: 2, context: html, text, full: html, text
- src/hg/protein/kgAliasM/kgAliasM.c 1.9 - lines changed: 4, context: html, text, full: html, text
- src/hg/protein/kgAliasRefseq/kgAliasRefseq.c 1.5 - lines changed: 2, context: html, text, full: html, text
- src/hg/protein/kgPepMrna/kgPepMrna.c 1.5 - lines changed: 4, context: html, text, full: html, text
- src/hg/protein/kgPick/kgPick.c 1.9 - lines changed: 3, context: html, text, full: html, text
- src/hg/protein/kgProtAlias/kgProtAlias.c 1.7 - lines changed: 2, context: html, text, full: html, text
- src/hg/protein/kgProtAliasNCBI/kgProtAliasNCBI.c 1.7 - lines changed: 2, context: html, text, full: html, text
- src/hg/protein/kgXref/kgXref.c 1.8 - lines changed: 2, context: html, text, full: html, text
- src/hg/protein/kgXref2/kgXref2.c 1.7 - lines changed: 2, context: html, text, full: html, text
- src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c 1.8 - lines changed: 1, context: html, text, full: html, text
- src/hg/protein/pbCalResStd/pbCalResStd.c 1.11 - lines changed: 8, context: html, text, full: html, text
- src/hg/protein/pbHgnc/pbHgnc.c 1.6 - lines changed: 1, context: html, text, full: html, text
- src/hg/protein/pfamXref/pfamXref.c 1.9 - lines changed: 6, context: html, text, full: html, text
- src/hg/protein/rmKGPepMrna/rmKGPepMrna.c 1.8 - lines changed: 4, context: html, text, full: html, text
- src/hg/protein/spOrganism/spOrganism.c 1.4 - lines changed: 1, context: html, text, full: html, text
- src/hg/protein/spToProteins/spToProteins.c 1.6 - lines changed: 4, context: html, text, full: html, text
- src/hg/protein/spm3/spm3.c 1.5 - lines changed: 4, context: html, text, full: html, text
- src/hg/protein/spm6/spm6.c 1.7 - lines changed: 4, context: html, text, full: html, text
- src/hg/protein/spm7/spm7.c 1.11 - lines changed: 4, context: html, text, full: html, text
- src/hg/qa/apacheMonitor.c 1.17 - lines changed: 1, context: html, text, full: html, text
- src/hg/sim4big/sim4big.c 1.6 - lines changed: 3, context: html, text, full: html, text
- src/hg/trfBig/trfBig.c 1.17 - lines changed: 1, context: html, text, full: html, text
- src/inc/common.h 1.154 - lines changed: 12, context: html, text, full: html, text
- src/isPcr/webPcr/webPcr.c 1.6 - lines changed: 1, context: html, text, full: html, text
- src/jkOwnLib/gfBlatLib.c 1.28 - lines changed: 4, context: html, text, full: html, text
- src/jkOwnLib/gfPcrLib.c 1.11 - lines changed: 2, context: html, text, full: html, text
- src/lib/common.c 1.132 - lines changed: 32, context: html, text, full: html, text
- src/lib/fa.c 1.38 - lines changed: 2, context: html, text, full: html, text
- src/lib/htmlPage.c 1.38 - lines changed: 5, context: html, text, full: html, text
- src/lib/net.c 1.72 - lines changed: 7, context: html, text, full: html, text
- src/lib/obscure.c 1.48 - lines changed: 2, context: html, text, full: html, text
- src/lib/options.c 1.27 - lines changed: 5, context: html, text, full: html, text
- src/lib/snof.c 1.5 - lines changed: 2, context: html, text, full: html, text
- src/lib/twoBit.c 1.28 - lines changed: 6, context: html, text, full: html, text
- src/lib/wormdna.c 1.11 - lines changed: 3, context: html, text, full: html, text
- src/reformat/gbtofa/gbtofa.c 1.4 - lines changed: 1, context: html, text, full: html, text
- src/utils/ccCp/ccCp.c 1.7 - lines changed: 2, context: html, text, full: html, text
- src/weblet/counter/counter.c 1.6 - lines changed: 1, context: html, text, full: html, text
- src/weblet/hitreport/hitreport.c 1.6 - lines changed: 1, context: html, text, full: html, text
- Added bamShowFlagsEnglish to explain the flag bits.
- src/hg/hgc/bamClick.c 1.9 - lines changed: 10, context: html, text, full: html, text
- src/hg/inc/bamFile.h 1.9 - lines changed: 3, context: html, text, full: html, text
- src/hg/lib/bamFile.c 1.8 - lines changed: 35, context: html, text, full: html, text
- Added bamGetQueryQuals for displaying sequence quality scores.
- src/hg/hgc/bamClick.c 1.10 - lines changed: 10, context: html, text, full: html, text
- src/hg/inc/bamFile.h 1.10 - lines changed: 3, context: html, text, full: html, text
- src/hg/lib/bamFile.c 1.9 - lines changed: 17, context: html, text, full: html, text
- Initialize orgForm.clade to empty string instead of NULL (oops!) which causes segfault on solaris. orgForm.clade is overwritten w/selected value when mainForm select is changed, and ignored if genome or db is changed, so initializing to stub value is fine.
- src/hg/hgCustom/hgCustom.c 1.132 - lines changed: 2, context: html, text, full: html, text
- Adding refreshSessionCtFiles*csh which have been living in ~qateam/bin/scripts, and souped them up to use tmp file names based on hour, and to watch out for signs of multiple refresh jobs happening at once. makeExclusionList.pl now accepts doNotRmFile as an arg instead of hardcoding it.
- src/hg/utils/refreshNamedSessionCustomTracks/makeExclusionList.pl 1.8 - lines changed: 3, context: html, text, full: html, text
- src/hg/utils/refreshNamedSessionCustomTracks/makefile 1.5 - lines changed: 2, context: html, text, full: html, text
- src/hg/utils/refreshNamedSessionCustomTracks/refreshSessionCtFiles.csh 1.1 - lines changed: 22, context: html, text, full: html, text
- src/hg/utils/refreshNamedSessionCustomTracks/refreshSessionCtFilesInner.csh 1.1 - lines changed: 58, context: html, text, full: html, text
- Move aside tmp output after failure; keep a lastLog file with most recent successful log.
- src/hg/utils/refreshNamedSessionCustomTracks/refreshSessionCtFiles.csh 1.2 - lines changed: 8, context: html, text, full: html, text
- Adding uptime command after error/warning messages so we can see whether load is high.
- src/hg/utils/refreshNamedSessionCustomTracks/refreshSessionCtFilesInner.csh 1.2 - lines changed: 3, context: html, text, full: html, text
- snp125: Add a persistent shadow variable to the list of gene tracks, so we can distinguish between a 'clicked to deselect all' vs. 'hasn't made any selections'. Should cart.c make multshad variables persistent?
- src/hg/hgTrackUi/hgTrackUi.c 1.503 - lines changed: 1, context: html, text, full: html, text
- src/hg/hgc/hgc.c 1.1576 - lines changed: 11, context: html, text, full: html, text
- Added description of repetitive sequence highlighting in re-alignment of flanking sequences.
- src/hg/makeDb/trackDb/snp130.html 1.10 - lines changed: 7, context: html, text, full: html, text
- Genome Variants: added Korean (SJK). Added base counts to 1000 Genomes SNPs.
- src/hg/makeDb/doc/hg18.txt 1.384 - lines changed: 107, context: html, text, full: html, text
- pgSnp: added pgSjk, moved 1000 Genomes NA* from pgSnpHgwdev to pgSnp.
- src/hg/makeDb/trackDb/human/hg18/pgSnp.html 1.8 - lines changed: 79, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.420 - lines changed: 17, context: html, text, full: html, text
switch to grouped by file view, user index