Commits for galt

v329_base to v330_preview (2016-02-29 to 2016-03-07) v330

• Fixes #16872. bigBedToBed on HTTPS URL was terminating with exitcode 141 and being killed by default SIGPIPE behavior. This now has a fairly elegant solution that should work on most OSes.
  
  • src/lib/https.c - lines changed 35, context: html, text, full: html, text
• Oops, preserving errno better in messages
  
  • src/lib/https.c - lines changed 3, context: html, text, full: html, text
• Adding description requested by Angie.
  
  • src/hg/hgTracks/hgTracks.c - lines changed 15, context: html, text, full: html, text
• Replacing simple literal NOSQLINJ in string with the #define NOSQLINJ. This is slightly better because the compiler can catch a mis-spelling of the NOSQLINJ keyword. This was suggested by Angie.
  
  • src/hg/bedItemOverlapCount/bedItemOverlapCount.c - lines changed 1, context: html, text, full: html, text
  • src/hg/bioImage/bioImageLoad/bioImageLoad.c - lines changed 1, context: html, text, full: html, text
  • src/hg/bioImage/knownToBioImage/knownToBioImage.c - lines changed 2, context: html, text, full: html, text
  • src/hg/checkTableCoords/checkTableCoords.c - lines changed 1, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c - lines changed 1, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 1, context: html, text, full: html, text
  • src/hg/das/das.c - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/hgEncodeScheduler/hgEncodeScheduler.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/importEncode2/encode2Meta/encode2Meta.c - lines changed 1, context: html, text, full: html, text
  • src/hg/estOrient/estOrient.c - lines changed 1, context: html, text, full: html, text
  • src/hg/featureBits/featureBits.c - lines changed 2, context: html, text, full: html, text
  • src/hg/geneBounds/clusterRna/clusterRna.c - lines changed 2, context: html, text, full: html, text
  • src/hg/geneBounds/eisenInput/eisenInput.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/estLibStats/estLibStats.c - lines changed 2, context: html, text, full: html, text
  • src/hg/getRnaPred/getRnaPred.c - lines changed 1, context: html, text, full: html, text
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  • src/hg/hgcentralTidy/hgcentralTidy.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/cartTrackDb.c - lines changed 1, context: html, text, full: html, text
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  • src/hg/makeDb/genbank/src/ccds/ccdsCommon.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/ccds/ccdsImport.c - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/dbload/gbMetaData.c - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/gbSanity/chkAlignTbls.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/gbSanity/chkMetaDataTbls.c - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/gbSanity/gbSanity.c - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/extFileTbl.c - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbLoadedTbl.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbStatusTbl.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/imageCloneTbl.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/seqTbl.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/sqlDeleter.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/repair/refPepRepair.c - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/hgClonePos/hgClonePos.c - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/hgCtgPos/hgCtgPos.c - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/hgDeleteChrom/hgDeleteChrom.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgGcPercent/hgGcPercent.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgGeneBands/hgGeneBands.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgKgGetText/hgKgGetText.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgKgMrna/hgKgMrna.c - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/hgKnownMore.oo21/hgKnownMore.c - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/hgKnownMore/hgKnownMore.c - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadChromGraph/hgLoadChromGraph.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadWiggle/hgLoadWiggle.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgStsAlias/hgStsAlias.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgTomRough/hgTomRough.c - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/hgTpf/hgTpf.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgFiberglass/hgFiberglass.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgFlyBase/hgFlyBase.c - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgLsSnpPdbLoad/hgLsSnpPdbLoad.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgSoftPromoter/hgSoftPromoter.c - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgSoftberryHom/hgSoftberryHom.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/yeast/hgSgdGfp/hgSgdGfp.c - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/schema/dbFindFieldsWith/dbFindFieldsWith.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/schema/dbSnoop/dbSnoop.c - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/schema/makeTableDescriptions/makeTableDescriptions.c - lines changed 1, context: html, text, full: html, text
  • src/hg/mouseStuff/bedCoverage/bedCoverage.c - lines changed 1, context: html, text, full: html, text
  • src/hg/mouseStuff/knownVsBlat/knownVsBlat.c - lines changed 1, context: html, text, full: html, text
  • src/hg/mouseStuff/libScan/libScan.c - lines changed 2, context: html, text, full: html, text
  • src/hg/mouseStuff/mafCoverage/mafCoverage.c - lines changed 1, context: html, text, full: html, text
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  • src/hg/mouseStuff/regionPicker/regionPicker.c - lines changed 1, context: html, text, full: html, text
  • src/hg/mouseStuff/rikenBestInCluster/rikenBestInCluster.c - lines changed 3, context: html, text, full: html, text
  • src/hg/near/hgKnownToSuper/hgKnownToSuper.c - lines changed 2, context: html, text, full: html, text
  • src/hg/near/knownToHprd/knownToHprd.c - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/cacheMergedRanges/cacheMergedRanges.c - lines changed 3, context: html, text, full: html, text
  • src/hg/oneShot/cartSim/cartSim.c - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/cartSimNoInsert/cartSimNoInsert.c - lines changed 2, context: html, text, full: html, text
  • src/hg/oneShot/fakeHomozygousity/fakeHomozygousity.c - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/getHumanBrainRna/getHumanBrainRna.c - lines changed 4, context: html, text, full: html, text
  • src/hg/oneShot/randomEst/randomEst.c - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/rcvs/rcvs.c - lines changed 2, context: html, text, full: html, text
  • src/hg/perf/hgTracksRandom.c - lines changed 1, context: html, text, full: html, text
  • src/hg/poster/finPoster/finPoster.c - lines changed 1, context: html, text, full: html, text
  • src/hg/poster/foldDb/foldDb.c - lines changed 1, context: html, text, full: html, text
  • src/hg/protein/gadPos/gadPos.c - lines changed 1, context: html, text, full: html, text
  • src/hg/protein/kgAttachKegg/kgAttachKegg.c - lines changed 3, context: html, text, full: html, text
  • src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c - lines changed 1, context: html, text, full: html, text
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  • src/hg/protein/pfamXref/pfamXref.c - lines changed 1, context: html, text, full: html, text
  • src/hg/pslCheck/pslCheck.c - lines changed 1, context: html, text, full: html, text
  • src/hg/qa/timePosTable.c - lines changed 1, context: html, text, full: html, text
  • src/hg/recycleDb/bedUp/bedUp.c - lines changed 1, context: html, text, full: html, text
  • src/hg/snp/details/dbSnp.c - lines changed 1, context: html, text, full: html, text
  • src/hg/snp/snpLoad/snpContigLocFilter.c - lines changed 1, context: html, text, full: html, text
  • src/hg/snp/snpLoad/snpContigLocFilter125.c - lines changed 1, context: html, text, full: html, text
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  • src/hg/snp/snpLoad/snpLoadFromTmp.c - lines changed 1, context: html, text, full: html, text
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  • src/hg/tutorial/affyVsIlluminaCommon/affyVsIlluminaCommon.c - lines changed 2, context: html, text, full: html, text
  • src/hg/txCds/txCdsGoodBed/txCdsGoodBed.c - lines changed 1, context: html, text, full: html, text
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  • src/hg/utils/mysqlSecurityCheck/mysqlSecurityCheck.c - lines changed 7, context: html, text, full: html, text
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  • src/hg/visiGene/vgLoadMahoney/vgLoadMahoney.c - lines changed 2, context: html, text, full: html, text
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