All File Changes

v326_preview to v326_preview2 (2015-11-23 to 2015-11-30) v326

• src/cdnaAli/patCount/patCount.c
  • lines changed 2, context: html, text, full: html, text
    Correcting spelling mistakes in usage and error messages, refs #14062
    
• src/hg/altSplice/altSplice/altAnalysis.c
  • lines changed 2, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/altSplice/altSplice/altPaths.c
  • lines changed 9, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/altSplice/altSplice/altSplice.c
  • lines changed 3, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/cirm/cdw/cdwWebBrowse/tagDescriptions.h
  • lines changed 1, context: html, text, full: html, text
    Correcting spelling mistakes in usage and error messages, refs #14062
    
• src/hg/cirm/cdw/wrangle/kallistoToMatrix/kallistoToMatrix
  • lines changed 39, context: html, text, full: html, text
    adding meta data parsing to kallisto matrix builder, refs #16300
    
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
  • lines changed 3, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 8, context: html, text, full: html, text
    support htslib for sam/bam/cram/tabix support #14717
    
• src/hg/encode3/encodeDataWarehouse/utils/edwBamFilter/edwBamFilter.c
  • lines changed 12, context: html, text, full: html, text
    support htslib for sam/bam/cram/tabix support #14717
    
• src/hg/encode3/encodeDataWarehouse/utils/edwBamRemoveChrom/edwBamRemoveChrom.c
  • lines changed 12, context: html, text, full: html, text
    support htslib for sam/bam/cram/tabix support #14717
    
• src/hg/encode3/encodeDataWarehouse/utils/edwBamStats/edwBamStats.c
  • lines changed 28, context: html, text, full: html, text
    support htslib for sam/bam/cram/tabix support #14717
    
• src/hg/encode3/encodeDataWarehouse/utils/edwSamRepeatAnalysis/edwSamRepeatAnalysis.c
  • lines changed 8, context: html, text, full: html, text
    support htslib for sam/bam/cram/tabix support #14717
    
• src/hg/encode3/validateFiles/validateFiles.c
  • lines changed 17, context: html, text, full: html, text
    support htslib for sam/bam/cram/tabix support #14717
    
• src/hg/fishClones/fishClones.c
  • lines changed 4, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/fqToQac/fqToQac.c
  • lines changed 2, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/gbToFaRa/gbToFaRa.c
  • lines changed 2, context: html, text, full: html, text
    fixed unused variable warnings
    
• src/hg/geneBounds/twinOrf2/twinOrf2.c
  • lines changed 10, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/geneBounds/twinOrf3/twinOrf3.c
  • lines changed 3, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
  • lines changed 7, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/genePredToGtf/genePredToGtf.c
  • lines changed 5, context: html, text, full: html, text
    added missing transcript records in genePredToGtf conversion
    
• src/hg/genePredToGtf/tests/expected/basicSimpleTest.gtf
  • lines changed 12, context: html, text, full: html, text
    added missing transcript records in genePredToGtf conversion
    
• src/hg/genePredToGtf/tests/expected/basicTest.gtf
  • lines changed 15, context: html, text, full: html, text
    added missing transcript records in genePredToGtf conversion
    
• src/hg/genePredToGtf/tests/expected/honorTest.gtf
  • lines changed 15, context: html, text, full: html, text
    added missing transcript records in genePredToGtf conversion
    
• src/hg/genePredToGtf/tests/expected/utrSimpleTest.gtf
  • lines changed 12, context: html, text, full: html, text
    added missing transcript records in genePredToGtf conversion
    
• src/hg/genePredToGtf/tests/expected/utrTest.gtf
  • lines changed 15, context: html, text, full: html, text
    added missing transcript records in genePredToGtf conversion
    
• src/hg/genePredToGtf/tests/makefile
  • lines changed 5, context: html, text, full: html, text
    added missing transcript records in genePredToGtf conversion
    
• src/hg/hgCustom/hgCustom.c
  • lines changed 4, context: html, text, full: html, text
    hgCustom was removing its hgct_navDest var from the cart because it removes
    every "hgct_" cart var when it's done! Tweak the prefix to make navDest
    persist in the cart.
    
• src/hg/hgGene/hgGeneData/Human/links.ra
  • lines changed 1, context: html, text, full: html, text
    fixing malacards link, refs #14417
    
• src/hg/hgKnownGeneList/hgKnownGeneList.c
  • lines changed 6, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgTables/bam.c
  • lines changed 10, context: html, text, full: html, text
    support htslib for sam/bam/cram/tabix support #14717
    
• src/hg/hgTablesTest/hgTablesTest.c
  • lines changed 6, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgTracks/bamTrack.c
  • lines changed 12, context: html, text, full: html, text
    support htslib for sam/bam/cram/tabix support #14717
    
• src/hg/hgTracks/gtexTracks.c
  • lines changed 59, context: html, text, full: html, text
    Add map boxes with mouseover showing gene description to labe and gene model. Still needs some work on extent. refs #15645
    
  • lines changed 61, context: html, text, full: html, text
    Add tissue filter to GTEX gene track. refs #15645
    
  • lines changed 105, context: html, text, full: html, text
    Fix merge conflict
    
  • lines changed 153, context: html, text, full: html, text
    Remove ifdefs for multi-region.
    
  • lines changed 3, context: html, text, full: html, text
    Fix crash when searching for a SNP (0 items in track). refs #15645
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    changes to new keyboard shortcut, refs #16397
    
  • lines changed 11, context: html, text, full: html, text
    curMap is actually unused and unnecessary fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgTracks/imageV2.c
  • lines changed 4, context: html, text, full: html, text
    curMap is actually unused and unnecessary fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgc/bamClick.c
  • lines changed 4, context: html, text, full: html, text
    support htslib for sam/bam/cram/tabix support #14717
    
• src/hg/hgc/gtexClick.c
  • lines changed 8, context: html, text, full: html, text
    Add gene description to details page. refs #15645
    
• src/hg/hgc/retroClick.c
  • lines changed 10, context: html, text, full: html, text
    fixed unused variable warnings
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 29, context: html, text, full: html, text
    Adding news announcement about external tools refs #16308
    
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 6, context: html, text, full: html, text
    adding new reference
    
  • lines changed 2, context: html, text, full: html, text
    adjust formatting
    
• src/hg/htdocs/indexNews.html
  • lines changed 82, context: html, text, full: html, text
    Adding news announcement about external tools refs #16308
    
• src/hg/htdocs/training/index.html
  • lines changed 15, context: html, text, full: html, text
    dropped mention of workshops completed
    
• src/hg/inc/gtexUi.h
  • lines changed 1, context: html, text, full: html, text
    Change default comparison to difference graph. refs #15645
    
  • lines changed 3, context: html, text, full: html, text
    Add tissue filter to GTEX gene track. refs #15645
    
  • lines changed 4, context: html, text, full: html, text
    Fix merge conflict
    
• src/hg/inc/hgBam.h
  • lines changed 4, context: html, text, full: html, text
    support htslib for sam/bam/cram/tabix support #14717
    
• src/hg/lfsOverlap/lfsOverlap.c
  • lines changed 6, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/lib/cart.c
  • lines changed 3, context: html, text, full: html, text
    adding hg.conf option to suppress error output for very early errors
    refs #16439
    
• src/hg/lib/encode/encodePeak.c
  • lines changed 5, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/lib/gtexUi.c
  • lines changed 4, context: html, text, full: html, text
    Change default comparison to difference graph. refs #15645
    
  • lines changed 167, context: html, text, full: html, text
    Add tissue filter to GTEX gene track. refs #15645
    
  • lines changed 162, context: html, text, full: html, text
    Fix merge conflict
    
  • lines changed 6, context: html, text, full: html, text
    If not tissues are selected, select all. refs #15645
    
• src/hg/lib/hAnno.c
  • lines changed 4, context: html, text, full: html, text
    Now that annoStreamDb's asObj isn't externally imposed using trackDb,
    hAnnoGetAutoSqlForDbTable needs to watch out for the special case of
    pgSnp custom tracks -- no tableDescriptions, no trackDb when called
    by annoStreamDb, and pgSnp's quirk of including bin in its autoSql.
    
• src/hg/lib/hgBam.c
  • lines changed 22, context: html, text, full: html, text
    support htslib for sam/bam/cram/tabix support #14717
    
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added gorGor4 - gorilla refs #16220
    
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    Added gorGor4 - gorilla refs #16220
    
• src/hg/makeDb/genbank/src/align/gbAlignGet.c
  • lines changed 3, context: html, text, full: html, text
    fixed unused variable warnings
    
• src/hg/makeDb/genbank/src/lib/gbStatusTbl.c
  • lines changed 11, context: html, text, full: html, text
    Fixing issue with loadQuery using sqlSafefFrag improperly. Now maybe I can load genbank. refs #16220
    
• src/hg/makeDb/genbank/src/process/gbProcess.c
  • lines changed 2, context: html, text, full: html, text
    fixed unused variable warnings
    
• src/hg/makeDb/genbank/src/selectWithPsl/selectWithPsl.c
  • lines changed 1, context: html, text, full: html, text
    Correcting spelling mistakes in usage and error messages, refs #14062
    
• src/hg/makeDb/hgKgMrna/hgKgMrna.c
  • lines changed 2, context: html, text, full: html, text
    fixed unused variable warnings
    
• src/hg/makeDb/hgMrnaRefseq/hgMrnaRefseq.c
  • lines changed 21, context: html, text, full: html, text
    fixed unused variable warnings
    
• src/hg/makeDb/outside/hgBioCyc/hgBioCyc.c
  • lines changed 4, context: html, text, full: html, text
    fixed unused variable warnings
    
• src/hg/makeDb/outside/hgCGAP/hgCGAP.c
  • lines changed 2, context: html, text, full: html, text
    fixed unused variable warnings
    
• src/hg/makeDb/outside/hgJaxQtl/hgJaxQtl.c
  • lines changed 6, context: html, text, full: html, text
    fixed unused variable warnings
    
• src/hg/makeDb/outside/hgSuperfam/hgSuperfam.c
  • lines changed 13, context: html, text, full: html, text
    fixed unused variable warnings
    
• src/hg/makeDb/outside/yeast/hgYeastRegCode/hgYeastRegCode.c
  • lines changed 2, context: html, text, full: html, text
    fixed unused variable warnings
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    Fixing typo in all.joiner tablesIgnored and broken link on desc pages
    
  • lines changed 1, context: html, text, full: html, text
    Adding tgpPhase3 to tablesIgnored. refs #14325
    
• src/hg/makeDb/tfbsConsLoc/tfbsConsLoc.c
  • lines changed 2, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 1, context: html, text, full: html, text
    updating old links in trackDb. Note: Some html pages only on dev.
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.html
  • lines changed 1, context: html, text, full: html, text
    updating old links in trackDb. Note: Some html pages only on dev.
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV12.html
  • lines changed 1, context: html, text, full: html, text
    updating old links in trackDb. Note: Some html pages only on dev.
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV13.html
  • lines changed 1, context: html, text, full: html, text
    updating old links in trackDb. Note: Some html pages only on dev.
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV14.html
  • lines changed 1, context: html, text, full: html, text
    updating old links in trackDb. Note: Some html pages only on dev.
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV15.html
  • lines changed 1, context: html, text, full: html, text
    updating old links in trackDb. Note: Some html pages only on dev.
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV16.html
  • lines changed 1, context: html, text, full: html, text
    updating old links in trackDb. Note: Some html pages only on dev.
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV17.html
  • lines changed 1, context: html, text, full: html, text
    updating old links in trackDb. Note: Some html pages only on dev.
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV18.html
  • lines changed 1, context: html, text, full: html, text
    updating old links in trackDb. Note: Some html pages only on dev.
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV19.html
  • lines changed 1, context: html, text, full: html, text
    updating old links in trackDb. Note: Some html pages only on dev.
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV19.ra
  • lines changed 9, context: html, text, full: html, text
    added filter by tag and highlightBy method and tag to GENCODE V19 to match what is in hg38 GENCODE (no RM)
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.html
  • lines changed 1, context: html, text, full: html, text
    updating old links in trackDb. Note: Some html pages only on dev.
    
• src/hg/makeDb/trackDb/human/hg38/lincRNAs.html
  • lines changed 61, context: html, text, full: html, text
    Adding a missing .html page for the non-coding RNA super track, refs #11694
    
• src/hg/makeDb/trackDb/human/hg38/nonCodingRNAs.html
  • lines changed 1, context: html, text, full: html, text
    Updating ftp link on nonCodingRNAs super track desc page, refs #11694
    
  • lines changed 1, context: html, text, full: html, text
    Updating ftp link because of odd redirect error, link now points to mirbases sequence download page, refs #11694
    
  • lines changed 1, context: html, text, full: html, text
    Fixing typo in all.joiner tablesIgnored and broken link on desc pages
    
• src/hg/makeDb/trackDb/human/hg38/nonCodingRNAs.ra
  • lines changed 1, context: html, text, full: html, text
    Moving nonCodingRnas to genes group
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV19.html
  • lines changed 1, context: html, text, full: html, text
    updating old links in trackDb. Note: Some html pages only on dev.
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV20.html
  • lines changed 1, context: html, text, full: html, text
    updating old links in trackDb. Note: Some html pages only on dev.
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV21.html
  • lines changed 1, context: html, text, full: html, text
    updating old links in trackDb. Note: Some html pages only on dev.
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV22.html
  • lines changed 1, context: html, text, full: html, text
    updating old links in trackDb. Note: Some html pages only on dev.
    
• src/hg/makeDb/trackDb/human/wgRna.html
  • lines changed 1, context: html, text, full: html, text
    Fixing typo in all.joiner tablesIgnored and broken link on desc pages
    
  • lines changed 1, context: html, text, full: html, text
    updating mirbase link, refs #11694
    
• src/hg/makeDb/trackDb/mouse/mm10/defaultPriority.ra
  • lines changed 12, context: html, text, full: html, text
    Adding GENCODE as a default track, removing Ensembl as a default, and removing old retroposed genes from hgwdev default set, refs #16370
    
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    Adding GENCODE as a default track, removing Ensembl as a default, and removing old retroposed genes from hgwdev default set, refs #16370
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM2.html
  • lines changed 1, context: html, text, full: html, text
    updating old links in trackDb. Note: Some html pages only on dev.
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM2.ra
  • lines changed 1, context: html, text, full: html, text
    Adding GENCODE as a default track, removing Ensembl as a default, and removing old retroposed genes from hgwdev default set, refs #16370
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM3.html
  • lines changed 1, context: html, text, full: html, text
    updating old links in trackDb. Note: Some html pages only on dev.
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM3.ra
  • lines changed 1, context: html, text, full: html, text
    Adding GENCODE as a default track, removing Ensembl as a default, and removing old retroposed genes from hgwdev default set, refs #16370
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM4.html
  • lines changed 1, context: html, text, full: html, text
    updating old links in trackDb. Note: Some html pages only on dev.
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM4.ra
  • lines changed 1, context: html, text, full: html, text
    Adding GENCODE as a default track, removing Ensembl as a default, and removing old retroposed genes from hgwdev default set, refs #16370
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM7.ra
  • lines changed 2, context: html, text, full: html, text
    Adding GENCODE as a default track, removing Ensembl as a default, and removing old retroposed genes from hgwdev default set, refs #16370
    
• src/hg/makeDb/trackDb/mouse/snp142.html
  • lines changed 5, context: html, text, full: html, text
    tweak mm10 snp142 HTML files #15934
    
• src/hg/makeDb/trackDb/mouse/snp142.shared.html
  • lines changed 42, context: html, text, full: html, text
    tweak mm10 snp142 HTML files #15934
    
• src/hg/makeDb/trackDb/mouse/snp142Common.html
  • lines changed 1, context: html, text, full: html, text
    tweak mm10 snp142 HTML files #15934
    
• src/hg/makeDb/trackDb/mouse/snp142Mult.html
  • lines changed 1, context: html, text, full: html, text
    tweak mm10 snp142 HTML files #15934
    
• src/hg/makeDb/trackDb/tRNAs.html
  • lines changed 3, context: html, text, full: html, text
    Escaping quote and greater than chars to their html names for tRNA genes description page, refs #11694
    
• src/hg/makeDb/trackDb/zebrafish/danRer5/vegaGene.html
  • lines changed 1, context: html, text, full: html, text
    updating old links in trackDb. Note: Some html pages only on dev.
    
• src/hg/makeDb/trackDb/zebrafish/danRer5/vegaPseudoGene.html
  • lines changed 1, context: html, text, full: html, text
    updating old links in trackDb. Note: Some html pages only on dev.
    
• src/hg/makeDb/trackDb/zebrafish/vegaGeneZfish.html
  • lines changed 1, context: html, text, full: html, text
    updating old links in trackDb. Note: Some html pages only on dev.
    
• src/hg/mouseStuff/chainStats/chainStats.c
  • lines changed 215, context: html, text, full: html, text
    remove mouseStuff/chainStats... program never useful (no redmine)
    
• src/hg/mouseStuff/chainStats/makefile
  • lines changed 3, context: html, text, full: html, text
    remove mouseStuff/chainStats... program never useful (no redmine)
    
• src/hg/mouseStuff/makefile
  • lines changed 1, context: html, text, full: html, text
    remove chainStats from makefile
    
• src/hg/mouseStuff/orthologBySynteny/orthologBySynteny.c
  • lines changed 24, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
  • lines changed 2, context: html, text, full: html, text
    Fixing new warnings/errors caught by -Wunused-but-set-variable .
    
    The change to refreshNamedSessionCustomTracks.c is required by the
    newer-gcc warning -Wunused-result -- that's not a warning on clang (yet),
    but triggers warnings on Ubuntu builds from the past few years.
    Thanks Jonathan for rounding these up.
    
    Note: while merging, it turned out that Hiram had made similar changes.
    I kept my own, i.e. removing vs. commenting out and checking the result
    of the system call in refreshNamedSessionCustomTracks.c.
    
• src/hg/mouseStuff/simpleChain/simpleChain.c
  • lines changed 3, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/near/hgNearTest/hgNearTest.c
  • lines changed 3, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/oneShot/sangPairs/sangPairs.c
  • lines changed 1, context: html, text, full: html, text
    Correcting spelling mistakes in usage and error messages, refs #14062
    
• src/hg/oneShot/trimFosmids/trimFosmids.c
  • lines changed 1, context: html, text, full: html, text
    Correcting spelling mistakes in usage and error messages, refs #14062
    
• src/hg/patCount/patCount.c
  • lines changed 2, context: html, text, full: html, text
    Correcting spelling mistakes in usage and error messages, refs #14062
    
• src/hg/pslCrudeCmp/pslCrudeCmp.c
  • lines changed 2, context: html, text, full: html, text
    Correcting spelling mistakes in usage and error messages, refs #14062
    
• src/hg/ratStuff/mafAddIRows/mafAddIRows.c
  • lines changed 5, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/recycleDb/bedUp/bedUp.c
  • lines changed 4, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/sim4big/sim4big.c
  • lines changed 2, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/snp/snpValid/snpValid.c
  • lines changed 5, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/updateStsInfo/updateStsInfo.c
  • lines changed 9, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
  • lines changed 2, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
  • lines changed 2, context: html, text, full: html, text
    Fixing new warnings/errors caught by -Wunused-but-set-variable .
    
    The change to refreshNamedSessionCustomTracks.c is required by the
    newer-gcc warning -Wunused-result -- that's not a warning on clang (yet),
    but triggers warnings on Ubuntu builds from the past few years.
    Thanks Jonathan for rounding these up.
    
    Note: while merging, it turned out that Hiram had made similar changes.
    I kept my own, i.e. removing vs. commenting out and checking the result
    of the system call in refreshNamedSessionCustomTracks.c.
    
• src/hg/visiGene/hgVisiGene/printCaption.c
  • lines changed 2, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
  • lines changed 1, context: html, text, full: html, text
    Fixing new warnings/errors caught by -Wunused-but-set-variable .
    
    The change to refreshNamedSessionCustomTracks.c is required by the
    newer-gcc warning -Wunused-result -- that's not a warning on clang (yet),
    but triggers warnings on Ubuntu builds from the past few years.
    Thanks Jonathan for rounding these up.
    
    Note: while merging, it turned out that Hiram had made similar changes.
    I kept my own, i.e. removing vs. commenting out and checking the result
    of the system call in refreshNamedSessionCustomTracks.c.
    
• src/inc/bamFile.h
  • lines changed 22, context: html, text, full: html, text
    support htslib for sam/bam/cram/tabix support #14717
    
• src/inc/common.mk
  • lines changed 16, context: html, text, full: html, text
    support htslib for sam/bam/cram/tabix support #14717
    
  • lines changed 1, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/inc/htmshell.h
  • lines changed 4, context: html, text, full: html, text
    adding hg.conf option to suppress error output for very early errors
    refs #16439
    
• src/inc/linefile.h
  • lines changed 18, context: html, text, full: html, text
    support htslib for sam/bam/cram/tabix support #14717
    
• src/lib/bamFile.c
  • lines changed 58, context: html, text, full: html, text
    support htslib for sam/bam/cram/tabix support #14717
    
• src/lib/basicBed.c
  • lines changed 6, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/lib/htmshell.c
  • lines changed 10, context: html, text, full: html, text
    adding hg.conf option to suppress error output for very early errors
    refs #16439
    
• src/lib/knetUdc.c
  • lines changed 9, context: html, text, full: html, text
    support htslib for sam/bam/cram/tabix support #14717
    
• src/lib/linefile.c
  • lines changed 50, context: html, text, full: html, text
    support htslib for sam/bam/cram/tabix support #14717
    
• src/lib/tests/pipelineTester.c
  • lines changed 1, context: html, text, full: html, text
    pipelineTester needs INT_MAX from limits.h thqt is normally included by
    tabix.h
    
• src/product/ex.hg.conf
  • lines changed 5, context: html, text, full: html, text
    adding hg.conf option to suppress error output for very early errors
    refs #16439
    
  • lines changed 1, context: html, text, full: html, text
    Correcting spelling mistakes in usage and error messages, refs #14062
    
• src/utils/countChars/countChars.c
  • lines changed 1, context: html, text, full: html, text
    Correcting spelling mistakes in usage and error messages, refs #14062
    
• src/utils/gffPeek/gffPeek.c
  • lines changed 5, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/utils/linesInAllFiles/linesInAllFiles.c
  • lines changed 1, context: html, text, full: html, text
    Correcting spelling mistakes in usage and error messages, refs #14062
    
• src/utils/methylateGenome/methylateGenome.c
  • lines changed 1, context: html, text, full: html, text
    Correcting spelling mistakes in usage and error messages, refs #14062
    
• src/utils/newPythonProg/newPythonProg.c
  • lines changed 18, context: html, text, full: html, text
    Fixing a bug Jonathan caught with compiler warnings, refs #16156
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v326 preview2 refs #16419
    
• src/utils/uniprotLift
  • lines changed 1, context: html, text, full: html, text
    Correcting spelling mistakes in usage and error messages, refs #14062
    

• lines changed: 2001
• files changed: 157