[med-svn] [seqtools] branch master updated (e246ec8 -> 660decb)
Andreas Tille
tille at debian.org
Wed Oct 25 14:32:39 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository seqtools.
from e246ec8 Initial packaging
new 3af5805 Add copyright entry (more to come)
new 1391326 Create dynamic library
new 3ad71ef Dynamic linking test; avoid blatSrc
new 49aba32 Force adding -lcurl which was somehow missing
new d17d95b Remove blatSrc and jsoncpp from upstream source
new 75cf31d New upstream version 4.44.1+dfsg
new 85c6bff Updated version 4.44.1+dfsg from 'upstream/4.44.1+dfsg'
new 1a71256 Use Debian packaged jsoncpp as well as get completely rid of blatSrc in automake configuration
new 660decb Fix include statement
The 9 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
debian/changelog | 2 +-
debian/control | 3 +-
debian/copyright | 32 +-
debian/patches/dynamic-lib.patch | 35 +
debian/patches/fix_missing_includes.patch | 15 +
debian/patches/prevent_usage_of_blatsrc.patch | 16 +
debian/patches/series | 4 +
debian/patches/use_debian_packaged_jsoncpp.patch | 292 ++
debian/rules | 7 +-
debian/watch | 2 +-
gbtools/src/blatSrc/Makefile.am | 277 --
gbtools/src/blatSrc/Makefile.in | 2688 -----------
gbtools/src/blatSrc/lib/aliType.c | 33 -
gbtools/src/blatSrc/lib/annoAssembly.c | 77 -
gbtools/src/blatSrc/lib/annoFilter.c | 357 --
gbtools/src/blatSrc/lib/annoFormatTab.c | 230 -
gbtools/src/blatSrc/lib/annoFormatter.c | 29 -
gbtools/src/blatSrc/lib/annoGrateWig.c | 112 -
gbtools/src/blatSrc/lib/annoGrator.c | 291 --
gbtools/src/blatSrc/lib/annoGratorQuery.c | 150 -
gbtools/src/blatSrc/lib/annoOption.c | 100 -
gbtools/src/blatSrc/lib/annoRow.c | 73 -
gbtools/src/blatSrc/lib/annoStreamBigBed.c | 251 --
gbtools/src/blatSrc/lib/annoStreamBigWig.c | 185 -
gbtools/src/blatSrc/lib/annoStreamTab.c | 236 -
gbtools/src/blatSrc/lib/annoStreamVcf.c | 368 --
gbtools/src/blatSrc/lib/annoStreamer.c | 154 -
gbtools/src/blatSrc/lib/apacheLog.c | 211 -
gbtools/src/blatSrc/lib/asParse.c | 664 ---
gbtools/src/blatSrc/lib/axt.c | 1106 -----
gbtools/src/blatSrc/lib/axtAffine.c | 781 ----
gbtools/src/blatSrc/lib/bPlusTree.c | 600 ---
gbtools/src/blatSrc/lib/bamFile.c | 797 ----
gbtools/src/blatSrc/lib/base64.c | 132 -
gbtools/src/blatSrc/lib/basicBed.c | 1752 --------
gbtools/src/blatSrc/lib/bbiRead.c | 797 ----
gbtools/src/blatSrc/lib/bbiWrite.c | 736 ---
gbtools/src/blatSrc/lib/bigBed.c | 651 ---
gbtools/src/blatSrc/lib/binRange.c | 392 --
gbtools/src/blatSrc/lib/bits.c | 418 --
gbtools/src/blatSrc/lib/blastOut.c | 833 ----
gbtools/src/blatSrc/lib/blastParse.c | 900 ----
gbtools/src/blatSrc/lib/boxClump.c | 315 --
gbtools/src/blatSrc/lib/boxLump.c | 162 -
gbtools/src/blatSrc/lib/bwgCreate.c | 1238 -----
gbtools/src/blatSrc/lib/bwgQuery.c | 402 --
gbtools/src/blatSrc/lib/bwgValsOnChrom.c | 216 -
gbtools/src/blatSrc/lib/cda.c | 477 --
gbtools/src/blatSrc/lib/chain.c | 647 ---
gbtools/src/blatSrc/lib/chainBlock.c | 453 --
gbtools/src/blatSrc/lib/chainConnect.c | 369 --
gbtools/src/blatSrc/lib/chainToAxt.c | 124 -
gbtools/src/blatSrc/lib/chainToPsl.c | 125 -
gbtools/src/blatSrc/lib/cheapcgi.c | 2306 ----------
gbtools/src/blatSrc/lib/cirTree.c | 635 ---
gbtools/src/blatSrc/lib/codebias.c | 147 -
gbtools/src/blatSrc/lib/colHash.c | 51 -
gbtools/src/blatSrc/lib/colHash.h | 41 -
gbtools/src/blatSrc/lib/common.c | 3537 ---------------
gbtools/src/blatSrc/lib/common.ps | 97 -
gbtools/src/blatSrc/lib/common.pss | 96 -
gbtools/src/blatSrc/lib/correlate.c | 80 -
gbtools/src/blatSrc/lib/crTree.c | 401 --
gbtools/src/blatSrc/lib/dgRange.c | 222 -
gbtools/src/blatSrc/lib/diGraph.c | 741 ---
gbtools/src/blatSrc/lib/diGraph.c.97 | 764 ----
gbtools/src/blatSrc/lib/diff | 0
gbtools/src/blatSrc/lib/diffs | 599 ---
gbtools/src/blatSrc/lib/dlist.c | 300 --
gbtools/src/blatSrc/lib/dnaLoad.c | 303 --
gbtools/src/blatSrc/lib/dnaMarkov.c | 242 -
gbtools/src/blatSrc/lib/dnaMotif.c | 631 ---
gbtools/src/blatSrc/lib/dnaMotif.pss | 61 -
gbtools/src/blatSrc/lib/dnaseq.c | 181 -
gbtools/src/blatSrc/lib/dnautil.c | 1186 -----
gbtools/src/blatSrc/lib/dtdParse.c | 469 --
gbtools/src/blatSrc/lib/dyOut.c | 379 --
gbtools/src/blatSrc/lib/dystring.c | 250 --
gbtools/src/blatSrc/lib/elmTree.c | 277 --
gbtools/src/blatSrc/lib/emblParse.c | 159 -
gbtools/src/blatSrc/lib/errAbort.c | 377 --
gbtools/src/blatSrc/lib/errCatch.c | 139 -
gbtools/src/blatSrc/lib/fa.c | 648 ---
gbtools/src/blatSrc/lib/ffAli.c | 185 -
gbtools/src/blatSrc/lib/ffScore.c | 215 -
gbtools/src/blatSrc/lib/fieldedTable.c | 124 -
gbtools/src/blatSrc/lib/filePath.c | 134 -
gbtools/src/blatSrc/lib/fixColor.c | 23 -
gbtools/src/blatSrc/lib/flydna.c | 112 -
gbtools/src/blatSrc/lib/fof.c | 581 ---
gbtools/src/blatSrc/lib/foo | 781 ----
gbtools/src/blatSrc/lib/fq.c | 65 -
gbtools/src/blatSrc/lib/fuzzyShow.c | 406 --
gbtools/src/blatSrc/lib/gapCalc.c | 354 --
gbtools/src/blatSrc/lib/gdf.c | 153 -
gbtools/src/blatSrc/lib/gemfont.c | 200 -
gbtools/src/blatSrc/lib/gemfont.h | 69 -
gbtools/src/blatSrc/lib/genomeRangeTree.c | 201 -
gbtools/src/blatSrc/lib/gfNet.c | 24 -
gbtools/src/blatSrc/lib/gff.c | 474 --
gbtools/src/blatSrc/lib/gff3.c | 1109 -----
gbtools/src/blatSrc/lib/gfxPoly.c | 50 -
gbtools/src/blatSrc/lib/gifLabel.c | 101 -
gbtools/src/blatSrc/lib/gifcodes.h | 48 -
gbtools/src/blatSrc/lib/gifcomp.c | 304 --
gbtools/src/blatSrc/lib/gifdecomp.c | 391 --
gbtools/src/blatSrc/lib/gifread.c | 186 -
gbtools/src/blatSrc/lib/gifwrite.c | 98 -
gbtools/src/blatSrc/lib/hacTree.c | 510 ---
gbtools/src/blatSrc/lib/hash.c | 749 ---
gbtools/src/blatSrc/lib/hex.c | 69 -
gbtools/src/blatSrc/lib/histogram.c | 270 --
gbtools/src/blatSrc/lib/hmac.c | 65 -
gbtools/src/blatSrc/lib/hmmPfamParse.c | 194 -
gbtools/src/blatSrc/lib/hmmstats.c | 48 -
gbtools/src/blatSrc/lib/htmlPage.c | 1851 --------
gbtools/src/blatSrc/lib/htmshell.c | 670 ---
gbtools/src/blatSrc/lib/https.c | 391 --
gbtools/src/blatSrc/lib/intExp.c | 153 -
gbtools/src/blatSrc/lib/intValTree.c | 105 -
gbtools/src/blatSrc/lib/internet.c | 162 -
gbtools/src/blatSrc/lib/itsa.c | 187 -
gbtools/src/blatSrc/lib/iupac.c | 216 -
gbtools/src/blatSrc/lib/jointalign.c | 74 -
gbtools/src/blatSrc/lib/jpegSize.c | 139 -
gbtools/src/blatSrc/lib/jsonParse.c | 687 ---
gbtools/src/blatSrc/lib/jsonWrite.c | 142 -
gbtools/src/blatSrc/lib/keys.c | 558 ---
gbtools/src/blatSrc/lib/knetUdc.c | 97 -
gbtools/src/blatSrc/lib/kxTok.c | 239 -
gbtools/src/blatSrc/lib/lineFileOnBigBed.c | 111 -
gbtools/src/blatSrc/lib/linefile.c | 1450 ------
gbtools/src/blatSrc/lib/localmem.c | 200 -
gbtools/src/blatSrc/lib/log.c | 354 --
gbtools/src/blatSrc/lib/longToList.c | 103 -
gbtools/src/blatSrc/lib/maf.c | 898 ----
gbtools/src/blatSrc/lib/maf.doc | 222 -
gbtools/src/blatSrc/lib/mafFromAxt.c | 81 -
gbtools/src/blatSrc/lib/mafScore.c | 186 -
gbtools/src/blatSrc/lib/mailViaPipe.c | 30 -
gbtools/src/blatSrc/lib/makefile | 65 -
gbtools/src/blatSrc/lib/md5.c | 86 -
gbtools/src/blatSrc/lib/memalloc.c | 519 ---
gbtools/src/blatSrc/lib/memgfx.c | 1325 ------
gbtools/src/blatSrc/lib/meta.c | 405 --
gbtools/src/blatSrc/lib/metaWig.c | 188 -
gbtools/src/blatSrc/lib/mgCircle.c | 81 -
gbtools/src/blatSrc/lib/mgPolygon.c | 438 --
gbtools/src/blatSrc/lib/mime.c | 687 ---
gbtools/src/blatSrc/lib/net.c | 2076 ---------
gbtools/src/blatSrc/lib/nib.c | 516 ---
gbtools/src/blatSrc/lib/nibTwo.c | 125 -
gbtools/src/blatSrc/lib/nt4.c | 260 --
gbtools/src/blatSrc/lib/numObscure.c | 106 -
gbtools/src/blatSrc/lib/obscure.c | 823 ----
gbtools/src/blatSrc/lib/oldGff.c | 643 ---
gbtools/src/blatSrc/lib/oligoTm.c | 333 --
gbtools/src/blatSrc/lib/options.c | 450 --
gbtools/src/blatSrc/lib/osunix.c | 711 ---
gbtools/src/blatSrc/lib/oswin9x.c | 98 -
gbtools/src/blatSrc/lib/pairDistance.c | 80 -
gbtools/src/blatSrc/lib/pairHmm.c | 346 --
gbtools/src/blatSrc/lib/paraFetch.c | 703 ---
gbtools/src/blatSrc/lib/peakCluster.c | 247 -
gbtools/src/blatSrc/lib/phyloTree.c | 421 --
gbtools/src/blatSrc/lib/pipeline.c | 735 ---
gbtools/src/blatSrc/lib/pngwrite.c | 115 -
gbtools/src/blatSrc/lib/portimpl.c | 136 -
gbtools/src/blatSrc/lib/portimpl.h | 39 -
gbtools/src/blatSrc/lib/psGfx.c | 413 --
gbtools/src/blatSrc/lib/psPoly.c | 53 -
gbtools/src/blatSrc/lib/pscmGfx.c | 816 ----
gbtools/src/blatSrc/lib/psl.as | 25 -
gbtools/src/blatSrc/lib/psl.c | 1961 --------
gbtools/src/blatSrc/lib/psl.sql | 33 -
gbtools/src/blatSrc/lib/pslGenoShow.c | 349 --
gbtools/src/blatSrc/lib/pslShow.c | 317 --
gbtools/src/blatSrc/lib/pslTbl.c | 90 -
gbtools/src/blatSrc/lib/pslTransMap.c | 328 --
gbtools/src/blatSrc/lib/pslWScore.as | 26 -
gbtools/src/blatSrc/lib/pslWScore.sql | 31 -
gbtools/src/blatSrc/lib/pthreadDoList.c | 82 -
gbtools/src/blatSrc/lib/pthreadWrap.c | 105 -
gbtools/src/blatSrc/lib/qa.c | 222 -
gbtools/src/blatSrc/lib/quickHeap.c | 196 -
gbtools/src/blatSrc/lib/quotedP.c | 117 -
gbtools/src/blatSrc/lib/ra.c | 400 --
gbtools/src/blatSrc/lib/raToStruct.c | 178 -
gbtools/src/blatSrc/lib/rainbow.c | 153 -
gbtools/src/blatSrc/lib/rangeTree.c | 354 --
gbtools/src/blatSrc/lib/rbTree.c | 740 ---
gbtools/src/blatSrc/lib/regexHelper.c | 93 -
gbtools/src/blatSrc/lib/repMask.c | 173 -
gbtools/src/blatSrc/lib/rle.c | 102 -
gbtools/src/blatSrc/lib/rnautil.c | 223 -
gbtools/src/blatSrc/lib/rqlEval.c | 335 --
gbtools/src/blatSrc/lib/rqlParse.c | 767 ----
gbtools/src/blatSrc/lib/rudp.c | 563 ---
gbtools/src/blatSrc/lib/scoreWindow.c | 51 -
gbtools/src/blatSrc/lib/seg.c | 476 --
gbtools/src/blatSrc/lib/seqOut.c | 330 --
gbtools/src/blatSrc/lib/seqStats.c | 39 -
gbtools/src/blatSrc/lib/servBrcMcw.c | 47 -
gbtools/src/blatSrc/lib/servCrunx.c | 51 -
gbtools/src/blatSrc/lib/servcis.c | 48 -
gbtools/src/blatSrc/lib/servcl.c | 49 -
gbtools/src/blatSrc/lib/servmsII.c | 45 -
gbtools/src/blatSrc/lib/servpws.c | 44 -
gbtools/src/blatSrc/lib/shaRes.c | 80 -
gbtools/src/blatSrc/lib/slog.c | 32 -
gbtools/src/blatSrc/lib/snof.c | 293 --
gbtools/src/blatSrc/lib/snofmake.c | 228 -
gbtools/src/blatSrc/lib/snofsig.c | 24 -
gbtools/src/blatSrc/lib/spaceSaver.c | 144 -
gbtools/src/blatSrc/lib/spacedColumn.c | 137 -
gbtools/src/blatSrc/lib/spacedSeed.c | 68 -
gbtools/src/blatSrc/lib/splatAli.as | 12 -
gbtools/src/blatSrc/lib/splatAli.c | 234 -
gbtools/src/blatSrc/lib/sqlList.c | 1273 ------
gbtools/src/blatSrc/lib/sqlNum.c | 301 --
gbtools/src/blatSrc/lib/status | 1638 -------
gbtools/src/blatSrc/lib/subText.c | 153 -
gbtools/src/blatSrc/lib/sufa.c | 142 -
gbtools/src/blatSrc/lib/sufx.c | 146 -
gbtools/src/blatSrc/lib/synQueue.c | 117 -
gbtools/src/blatSrc/lib/tabRow.c | 232 -
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gbtools/src/blatSrc/lib/trix.c | 760 ----
gbtools/src/blatSrc/lib/twoBit.c | 1235 -----
gbtools/src/blatSrc/lib/udc.c | 1686 -------
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gbtools/src/blatSrc/lib/vGif.c | 66 -
gbtools/src/blatSrc/lib/vPng.c | 68 -
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gbtools/src/blatSrc/lib/vcf.c | 1285 ------
gbtools/src/blatSrc/lib/vcfBits.c | 696 ---
gbtools/src/blatSrc/lib/verbose.c | 131 -
gbtools/src/blatSrc/lib/wildcmp.c | 116 -
gbtools/src/blatSrc/lib/wormdna.c | 1212 -----
gbtools/src/blatSrc/lib/xAli.as | 27 -
gbtools/src/blatSrc/lib/xAli.c | 282 --
gbtools/src/blatSrc/lib/xAli.sql | 33 -
gbtools/src/blatSrc/lib/xa.c | 230 -
gbtools/src/blatSrc/lib/xap.c | 182 -
gbtools/src/blatSrc/lib/xenshow.c | 65 -
gbtools/src/blatSrc/lib/xmlEscape.c | 82 -
gbtools/src/blatSrc/lib/xp.c | 553 ---
gbtools/src/blatSrc/lib/zlibFace.c | 94 -
gbtools/src/include/blatSrc/ace.h | 79 -
gbtools/src/include/blatSrc/aliType.h | 32 -
gbtools/src/include/blatSrc/annoAssembly.h | 35 -
gbtools/src/include/blatSrc/annoFilter.h | 83 -
gbtools/src/include/blatSrc/annoFormatTab.h | 11 -
gbtools/src/include/blatSrc/annoFormatter.h | 57 -
gbtools/src/include/blatSrc/annoGrateWig.h | 14 -
gbtools/src/include/blatSrc/annoGrator.h | 73 -
gbtools/src/include/blatSrc/annoGratorQuery.h | 30 -
gbtools/src/include/blatSrc/annoOption.h | 22 -
gbtools/src/include/blatSrc/annoRow.h | 43 -
gbtools/src/include/blatSrc/annoStreamBigBed.h | 13 -
gbtools/src/include/blatSrc/annoStreamBigWig.h | 11 -
gbtools/src/include/blatSrc/annoStreamTab.h | 13 -
gbtools/src/include/blatSrc/annoStreamVcf.h | 13 -
gbtools/src/include/blatSrc/annoStreamer.h | 114 -
gbtools/src/include/blatSrc/apacheLog.h | 43 -
gbtools/src/include/blatSrc/asParse.h | 151 -
gbtools/src/include/blatSrc/axt.h | 272 --
gbtools/src/include/blatSrc/bPlusTree.h | 127 -
gbtools/src/include/blatSrc/bamFile.h | 169 -
gbtools/src/include/blatSrc/bandExt.h | 42 -
gbtools/src/include/blatSrc/base64.h | 30 -
gbtools/src/include/blatSrc/basicBed.h | 312 --
gbtools/src/include/blatSrc/bbiFile.h | 454 --
gbtools/src/include/blatSrc/bigBed.h | 144 -
gbtools/src/include/blatSrc/bigWig.h | 124 -
gbtools/src/include/blatSrc/binRange.h | 120 -
gbtools/src/include/blatSrc/bits.h | 108 -
gbtools/src/include/blatSrc/blastParse.h | 116 -
gbtools/src/include/blatSrc/boxClump.h | 41 -
gbtools/src/include/blatSrc/boxLump.h | 25 -
gbtools/src/include/blatSrc/bwgInternal.h | 119 -
gbtools/src/include/blatSrc/cda.h | 104 -
gbtools/src/include/blatSrc/cgi_build_rules.mk | 48 -
gbtools/src/include/blatSrc/chain.h | 163 -
gbtools/src/include/blatSrc/chainBlock.h | 42 -
gbtools/src/include/blatSrc/chainConnect.h | 60 -
gbtools/src/include/blatSrc/chainToAxt.h | 15 -
gbtools/src/include/blatSrc/chainToPsl.h | 28 -
gbtools/src/include/blatSrc/cheapcgi.h | 564 ---
gbtools/src/include/blatSrc/cirTree.h | 85 -
gbtools/src/include/blatSrc/codebias.h | 33 -
gbtools/src/include/blatSrc/common.h | 1483 ------
gbtools/src/include/blatSrc/common.mk | 411 --
gbtools/src/include/blatSrc/correlate.h | 39 -
gbtools/src/include/blatSrc/crTree.h | 90 -
gbtools/src/include/blatSrc/crudeali.h | 26 -
gbtools/src/include/blatSrc/diGraph.h | 202 -
gbtools/src/include/blatSrc/diGraph.h.97 | 210 -
gbtools/src/include/blatSrc/dlist.h | 138 -
gbtools/src/include/blatSrc/dnaLoad.h | 40 -
gbtools/src/include/blatSrc/dnaMarkov.h | 43 -
gbtools/src/include/blatSrc/dnaMotif.h | 126 -
gbtools/src/include/blatSrc/dnaseq.h | 73 -
gbtools/src/include/blatSrc/dnautil.h | 270 --
gbtools/src/include/blatSrc/dtdParse.h | 57 -
gbtools/src/include/blatSrc/dyOut.h | 141 -
gbtools/src/include/blatSrc/dystring.h | 98 -
gbtools/src/include/blatSrc/elmTree.h | 122 -
gbtools/src/include/blatSrc/emblParse.h | 75 -
gbtools/src/include/blatSrc/ens.h | 168 -
gbtools/src/include/blatSrc/errAbort.h | 93 -
gbtools/src/include/blatSrc/errCatch.h | 61 -
gbtools/src/include/blatSrc/fa.h | 129 -
gbtools/src/include/blatSrc/fieldedTable.h | 44 -
gbtools/src/include/blatSrc/filePath.h | 31 -
gbtools/src/include/blatSrc/flydna.h | 32 -
gbtools/src/include/blatSrc/fof.h | 82 -
gbtools/src/include/blatSrc/fq.h | 26 -
gbtools/src/include/blatSrc/fuzzyFind.h | 260 --
gbtools/src/include/blatSrc/gapCalc.h | 44 -
gbtools/src/include/blatSrc/gdf.h | 61 -
gbtools/src/include/blatSrc/genoFind.h | 385 --
gbtools/src/include/blatSrc/genomeRangeTree.h | 113 -
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gbtools/src/include/blatSrc/gfPcrLib.h | 100 -
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gbtools/src/include/blatSrc/gff3.h | 268 --
gbtools/src/include/blatSrc/gfxPoly.h | 31 -
gbtools/src/include/blatSrc/gifLabel.h | 10 -
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gbtools/src/include/blatSrc/hash.h | 285 --
gbtools/src/include/blatSrc/hex.h | 27 -
gbtools/src/include/blatSrc/hgGene.h | 129 -
gbtools/src/include/blatSrc/hgap.h | 233 -
gbtools/src/include/blatSrc/hgdb.h | 46 -
gbtools/src/include/blatSrc/histogram.h | 26 -
gbtools/src/include/blatSrc/hmac.h | 12 -
gbtools/src/include/blatSrc/hmmPfamParse.h | 55 -
gbtools/src/include/blatSrc/hmmstats.h | 30 -
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gbtools/src/include/blatSrc/itsa.h | 90 -
gbtools/src/include/blatSrc/iupac.h | 42 -
gbtools/src/include/blatSrc/jointalign.h | 30 -
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gbtools/src/include/blatSrc/keys.h | 66 -
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gbtools/src/include/blatSrc/linefile.h | 296 --
gbtools/src/include/blatSrc/localEnvironment.mk | 0
gbtools/src/include/blatSrc/localmem.h | 66 -
gbtools/src/include/blatSrc/log.h | 74 -
gbtools/src/include/blatSrc/longToList.h | 52 -
gbtools/src/include/blatSrc/maDbRep.h | 62 -
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gbtools/src/include/blatSrc/mailViaPipe.h | 8 -
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gbtools/src/include/blatSrc/memgfx.h | 398 --
gbtools/src/include/blatSrc/meta.h | 93 -
gbtools/src/include/blatSrc/metaWig.h | 44 -
gbtools/src/include/blatSrc/mime.h | 62 -
gbtools/src/include/blatSrc/net.h | 267 --
gbtools/src/include/blatSrc/nib.h | 113 -
gbtools/src/include/blatSrc/nibTwo.h | 55 -
gbtools/src/include/blatSrc/nt4.h | 45 -
gbtools/src/include/blatSrc/obscure.h | 185 -
gbtools/src/include/blatSrc/oldGff.h | 103 -
gbtools/src/include/blatSrc/oligoTm.h | 98 -
gbtools/src/include/blatSrc/ooc.h | 16 -
gbtools/src/include/blatSrc/options.h | 100 -
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gbtools/src/include/blatSrc/pairHmm.h | 94 -
gbtools/src/include/blatSrc/paraFetch.h | 41 -
gbtools/src/include/blatSrc/patSpace.h | 48 -
gbtools/src/include/blatSrc/peakCluster.h | 98 -
gbtools/src/include/blatSrc/phyloTree.h | 77 -
gbtools/src/include/blatSrc/pipeline.h | 157 -
gbtools/src/include/blatSrc/portable.h | 168 -
gbtools/src/include/blatSrc/psGfx.h | 118 -
gbtools/src/include/blatSrc/psPoly.h | 31 -
gbtools/src/include/blatSrc/pscmGfx.h | 71 -
gbtools/src/include/blatSrc/psl.h | 316 --
gbtools/src/include/blatSrc/pslTbl.h | 42 -
gbtools/src/include/blatSrc/pslTransMap.h | 17 -
gbtools/src/include/blatSrc/pthreadDoList.h | 67 -
gbtools/src/include/blatSrc/pthreadWrap.h | 45 -
gbtools/src/include/blatSrc/qa.h | 65 -
gbtools/src/include/blatSrc/quickHeap.h | 53 -
gbtools/src/include/blatSrc/quotedP.h | 21 -
gbtools/src/include/blatSrc/ra.h | 81 -
gbtools/src/include/blatSrc/raToStruct.h | 64 -
gbtools/src/include/blatSrc/rainbow.h | 22 -
gbtools/src/include/blatSrc/rangeTree.h | 105 -
gbtools/src/include/blatSrc/rbTree.h | 102 -
gbtools/src/include/blatSrc/regexHelper.h | 29 -
gbtools/src/include/blatSrc/repMask.h | 56 -
gbtools/src/include/blatSrc/rle.h | 16 -
gbtools/src/include/blatSrc/rnautil.h | 55 -
gbtools/src/include/blatSrc/rql.h | 130 -
gbtools/src/include/blatSrc/rudp.h | 175 -
gbtools/src/include/blatSrc/scoreWindow.h | 7 -
gbtools/src/include/blatSrc/seg.h | 109 -
gbtools/src/include/blatSrc/seqOut.h | 91 -
gbtools/src/include/blatSrc/seqStats.h | 11 -
gbtools/src/include/blatSrc/shaRes.h | 45 -
gbtools/src/include/blatSrc/sig.h | 101 -
gbtools/src/include/blatSrc/slog.h | 18 -
gbtools/src/include/blatSrc/snof.h | 60 -
gbtools/src/include/blatSrc/snofmake.h | 35 -
gbtools/src/include/blatSrc/spaceSaver.h | 65 -
gbtools/src/include/blatSrc/spacedColumn.h | 46 -
gbtools/src/include/blatSrc/spacedSeed.h | 19 -
gbtools/src/include/blatSrc/splatAli.h | 80 -
gbtools/src/include/blatSrc/splix.h | 80 -
gbtools/src/include/blatSrc/sqlList.h | 142 -
gbtools/src/include/blatSrc/sqlNum.h | 83 -
gbtools/src/include/blatSrc/subText.h | 41 -
gbtools/src/include/blatSrc/sufa.h | 60 -
gbtools/src/include/blatSrc/sufx.h | 64 -
gbtools/src/include/blatSrc/supStitch.h | 73 -
gbtools/src/include/blatSrc/synQueue.h | 38 -
gbtools/src/include/blatSrc/tabRow.h | 45 -
gbtools/src/include/blatSrc/textOut.h | 48 -
gbtools/src/include/blatSrc/tokenizer.h | 66 -
gbtools/src/include/blatSrc/trans3.h | 59 -
gbtools/src/include/blatSrc/trix.h | 48 -
gbtools/src/include/blatSrc/twoBit.h | 209 -
gbtools/src/include/blatSrc/udc.h | 165 -
gbtools/src/include/blatSrc/unfin.h | 31 -
gbtools/src/include/blatSrc/userApp.mk | 49 -
gbtools/src/include/blatSrc/vGfx.h | 193 -
gbtools/src/include/blatSrc/vcf.h | 297 --
gbtools/src/include/blatSrc/vcfBits.h | 158 -
gbtools/src/include/blatSrc/verbose.h | 53 -
gbtools/src/include/blatSrc/wormdna.h | 245 -
gbtools/src/include/blatSrc/xAli.h | 73 -
gbtools/src/include/blatSrc/xa.h | 63 -
gbtools/src/include/blatSrc/xap.h | 78 -
gbtools/src/include/blatSrc/xenalign.h | 41 -
gbtools/src/include/blatSrc/xmlEscape.h | 17 -
gbtools/src/include/blatSrc/xp.h | 78 -
gbtools/src/include/blatSrc/zlibFace.h | 26 -
gbtools/src/include/json/json-forwards.h | 319 --
gbtools/src/include/json/json.h | 2241 ---------
gbtools/src/jsoncpp/Makefile.am | 15 -
gbtools/src/jsoncpp/Makefile.in | 723 ---
gbtools/src/jsoncpp/jsoncpp.cpp | 5247 ----------------------
457 files changed, 388 insertions(+), 120405 deletions(-)
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