[med-svn] [amos] 06/08: Merge tag 'upstream/3.1.0'
Afif Elghraoui
afif-guest at moszumanska.debian.org
Wed Aug 12 07:58:47 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository amos.
commit 5ddeb89fad5d13111ed15dd426c00f2d8ee904c0
Merge: aaa5e5e 060e85d
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Tue Aug 11 22:57:07 2015 -0700
Merge tag 'upstream/3.1.0'
Upstream version 3.1.0
AUTHORS | 22 +
COPYING | 114 +
INSTALL | 302 +
Makefile.am | 11 +
Makefile.in | 736 ++
NEWS | 124 +
README | 199 +
THANKS | 31 +
aclocal.m4 | 957 ++
config.h.in | 254 +
config/amos.m4 | 577 ++
config/amos.mk | 81 +
config/compile | 136 +
config/config.guess | 1561 +++
config/config.rpath | 548 +
config/config.sub | 1686 ++++
config/depcomp | 630 ++
config/getopt.m4 | 47 +
config/install-sh | 520 +
config/missing | 376 +
config/mkinstalldirs | 162 +
config/onceonly_2_57.m4 | 86 +
config/perlmodules.m4 | 36 +
config/strtod.m4 | 24 +
config/strtol.m4 | 21 +
configure | 10016 +++++++++++++++++++
configure.ac | 310 +
doc/AMOScmp.README | 109 +
doc/Makefile.am | 14 +
doc/Makefile.in | 475 +
doc/amosvalidate.README | 1 +
doc/hawkeye.README | 1 +
doc/minimus.README | 114 +
doc/portability.README | 20 +
doc/runAmos.README | 215 +
src/AMOS/BankStream_AMOS.cc | 379 +
src/AMOS/BankStream_AMOS.hh | 494 +
src/AMOS/Bank_AMOS.cc | 1326 +++
src/AMOS/Bank_AMOS.hh | 1283 +++
src/AMOS/ContigEdge_AMOS.cc | 85 +
src/AMOS/ContigEdge_AMOS.hh | 144 +
src/AMOS/ContigIterator_AMOS.cc | 252 +
src/AMOS/ContigIterator_AMOS.hh | 328 +
src/AMOS/ContigLink_AMOS.cc | 81 +
src/AMOS/ContigLink_AMOS.hh | 146 +
src/AMOS/Contig_AMOS.cc | 545 +
src/AMOS/Contig_AMOS.hh | 449 +
src/AMOS/Edge_AMOS.cc | 167 +
src/AMOS/Edge_AMOS.hh | 219 +
src/AMOS/Feature_AMOS.cc | 143 +
src/AMOS/Feature_AMOS.hh | 208 +
src/AMOS/Fragment_AMOS.cc | 212 +
src/AMOS/Fragment_AMOS.hh | 255 +
src/AMOS/Group_AMOS.cc | 147 +
src/AMOS/Group_AMOS.hh | 169 +
src/AMOS/IDMap_AMOS.cc | 669 ++
src/AMOS/IDMap_AMOS.hh | 717 ++
src/AMOS/Index_AMOS.cc | 327 +
src/AMOS/Index_AMOS.hh | 437 +
src/AMOS/Kmer_AMOS.cc | 247 +
src/AMOS/Kmer_AMOS.hh | 358 +
src/AMOS/Layout_AMOS.cc | 142 +
src/AMOS/Layout_AMOS.hh | 155 +
src/AMOS/Library_AMOS.cc | 89 +
src/AMOS/Library_AMOS.hh | 127 +
src/AMOS/Link_AMOS.cc | 241 +
src/AMOS/Link_AMOS.hh | 291 +
src/AMOS/Makefile.am | 127 +
src/AMOS/Makefile.in | 1191 +++
src/AMOS/Message_AMOS.cc | 240 +
src/AMOS/Message_AMOS.hh | 554 +
src/AMOS/Motif_AMOS.cc | 87 +
src/AMOS/Motif_AMOS.hh | 115 +
src/AMOS/Overlap_AMOS.cc | 199 +
src/AMOS/Overlap_AMOS.hh | 270 +
src/AMOS/Read_AMOS.cc | 297 +
src/AMOS/Read_AMOS.hh | 318 +
src/AMOS/ScaffoldEdge_AMOS.cc | 85 +
src/AMOS/ScaffoldEdge_AMOS.hh | 145 +
src/AMOS/ScaffoldLink_AMOS.cc | 80 +
src/AMOS/ScaffoldLink_AMOS.hh | 144 +
src/AMOS/Scaffold_AMOS.cc | 187 +
src/AMOS/Scaffold_AMOS.hh | 203 +
src/AMOS/Sequence_AMOS.cc | 335 +
src/AMOS/Sequence_AMOS.hh | 458 +
src/AMOS/Universal_AMOS.cc | 216 +
src/AMOS/Universal_AMOS.hh | 267 +
src/AMOS/banktest.cc | 231 +
src/AMOS/databanks_AMOS.hh | 16 +
src/AMOS/datatypes_AMOS.cc | 360 +
src/AMOS/datatypes_AMOS.hh | 473 +
src/AMOS/exceptions_AMOS.hh | 279 +
src/AMOS/foundation_AMOS.hh | 25 +
src/AMOS/inttypes_AMOS.hh | 209 +
src/AMOS/maptest.cc | 28 +
src/AMOS/messages_AMOS.hh | 15 +
src/AMOS/msgtest.cc | 88 +
src/AMOS/streamtest.cc | 88 +
src/AMOS/umdtest.cc | 21 +
src/AMOS/universals_AMOS.cc | 165 +
src/AMOS/universals_AMOS.hh | 610 ++
src/AMOS/utility_AMOS.cc | 88 +
src/AMOS/utility_AMOS.hh | 380 +
src/Align/Makefile.am | 300 +
src/Align/Makefile.in | 1216 +++
src/Align/align.cc | 7169 +++++++++++++
src/Align/align.hh | 771 ++
src/Align/align_poly.cc | 6929 +++++++++++++
src/Align/align_poly.hh | 760 ++
src/Align/arrive.cc | 87 +
src/Align/arrive2.cc | 697 ++
src/Align/count-kmers.cc | 499 +
src/Align/count-qmers.cc | 544 +
src/Align/find-tandem.cc | 310 +
src/Align/frg-umd-merge.cc | 256 +
src/Align/gap-links.cc | 114 +
src/Align/genome-complexity-fast.cc | 1144 +++
src/Align/hash-overlap.cc | 1374 +++
src/Align/hash-overlap.hh | 161 +
src/Align/kmer-count.cc | 162 +
src/Align/kmer-cov-plot.cc | 377 +
src/Align/kmer-cov.cc | 546 +
src/Align/make-consensus.cc | 1321 +++
src/Align/make-consensus_poly.cc | 1262 +++
src/Align/maligntest.cc | 202 +
src/Align/matrix.hh | 53 +
src/Align/merge-contigs.cc | 920 ++
src/Align/missing-reads.cc | 280 +
src/Align/overlap-align.cc | 364 +
src/Align/ovl-degr-dist.cc | 329 +
src/Align/qmer-filter.cc | 32 +
src/Align/readinfo2cam.cc | 1294 +++
src/Align/running-cmp.cc | 91 +
src/Align/show-ma-asm.cc | 1332 +++
src/Align/sim-cover-depth.cc | 251 +
src/Align/sim-cover2.cc | 633 ++
src/Align/sim-shotgun.cc | 347 +
src/Align/simple-overlap.cc | 437 +
src/Align/simple-overlap.hh | 52 +
src/Align/test-align.cc | 176 +
src/Align/verify-layout.cc | 130 +
src/Bambus/Bundler/Bundler.cc | 377 +
src/Bambus/Bundler/Chainer.pl | 365 +
src/Bambus/Bundler/FilterEdgesByCluster.cc | 313 +
src/Bambus/Bundler/Joiner.pl | 145 +
src/Bambus/Bundler/Makefile.am | 85 +
src/Bambus/Bundler/Makefile.in | 823 ++
src/Bambus/Bundler/MarkRepeats.cc | 400 +
src/Bambus/Bundler/OrientContigs.cc | 1831 ++++
src/Bambus/Bundler/Utilities_Bundler.cc | 457 +
src/Bambus/Bundler/Utilities_Bundler.hh | 129 +
src/Bambus/Bundler/clk.cc | 370 +
src/Bambus/Makefile.am | 16 +
src/Bambus/Makefile.in | 570 ++
src/Bambus/Output/Linearize.cc | 323 +
src/Bambus/Output/Makefile.am | 55 +
src/Bambus/Output/Makefile.in | 648 ++
src/Bambus/Output/OutputMotifs.cc | 354 +
src/Bambus/Output/OutputResults.cc | 176 +
src/Bambus/Output/OutputScaffolds.cc | 232 +
src/Bambus/Output/Output_Utils.cc | 665 ++
src/Bambus/Output/Output_Utils.hh | 23 +
src/Bambus/Output/Position.cc | 146 +
src/Bambus/Output/Position.hh | 41 +
src/Bambus/Untangler/AsmLib.pm | 434 +
src/Bambus/Untangler/DotLib.pm | 238 +
src/Bambus/Untangler/Makefile.am | 20 +
src/Bambus/Untangler/Makefile.in | 608 ++
src/Bambus/Untangler/printScaff.pl | 1022 ++
src/Bambus/Untangler/untangle.pl | 544 +
src/Bank/Makefile.am | 313 +
src/Bank/Makefile.in | 1263 +++
src/Bank/bank-clean.cc | 234 +
src/Bank/bank-combine.cc | 93 +
src/Bank/bank-mapping.cc | 251 +
src/Bank/bank-report.cc | 502 +
src/Bank/bank-transact.cc | 509 +
src/Bank/bank-tutorial.cc | 174 +
src/Bank/bank-unlock.pl | 94 +
src/Bank/bank2contig.cc | 546 +
src/Bank/bank2coverage.cc | 299 +
src/Bank/bank2fasta.cc | 272 +
src/Bank/bank2lib.cc | 188 +
src/Bank/bank2scaff.cc | 370 +
src/Bank/dumpContigsAsReads.cc | 202 +
src/Bank/dumpFeatures.cc | 221 +
src/Bank/dumpmates.cc | 207 +
src/Bank/dumpreads.cc | 332 +
src/Bank/extractContig.cc | 124 +
src/Bank/findMissingMates.cc | 512 +
src/Bank/grow-readbank.cc | 275 +
src/Bank/listGCContent.cc | 269 +
src/Bank/listReadPlacedStatus.cc | 217 +
src/Bank/load-overlaps.cc | 502 +
src/Bank/loadFeatures.cc | 220 +
src/Bank/normalizeScaffold.cc | 224 +
src/Bank/partitionBank.cc | 218 +
src/Bank/renameReads.cc | 124 +
src/Bank/resetFragLibrary.cc | 70 +
src/Bank/revScaffold.cc | 173 +
src/Bank/select-reads.cc | 554 +
src/Bank/simpleContigLoader.cc | 286 +
src/Bank/simplifyLibraries.cc | 122 +
src/Bank/updateBankPositions.cc | 143 +
src/Bank/updateClrRanges.cc | 97 +
src/Bank/updateLibSizes.cc | 83 +
src/Casm/Makefile.am | 42 +
src/Casm/Makefile.in | 608 ++
src/Casm/casm-breaks.cc | 918 ++
src/Casm/casm-layout.cc | 2368 +++++
src/Casm/casm-libsize.cc | 93 +
src/CelMsg/CelMsg.cc | 2563 +++++
src/CelMsg/CelMsg.hh | 847 ++
src/CelMsg/Makefile.am | 24 +
src/CelMsg/Makefile.in | 611 ++
src/Common/Makefile.am | 34 +
src/Common/Makefile.in | 629 ++
src/Common/alloc.hh | 108 +
src/Common/amp.cc | 84 +
src/Common/amp.hh | 55 +
src/Common/delcher.cc | 265 +
src/Common/delcher.hh | 142 +
src/Common/delta.cc | 1229 +++
src/Common/delta.hh | 618 ++
src/Common/fasta.cc | 422 +
src/Common/fasta.hh | 51 +
src/Common/fastq.cc | 92 +
src/Common/fastq.hh | 31 +
src/Common/prob.cc | 101 +
src/Common/prob.hh | 23 +
src/Compare/Makefile.am | 22 +
src/Compare/Makefile.in | 564 ++
src/Compare/contig-cmp.cc | 588 ++
src/Contig/ContigUtils.cc | 955 ++
src/Contig/ContigUtils.hh | 46 +
src/Contig/CoverageStats.cc | 184 +
src/Contig/CoverageStats.hh | 59 +
src/Contig/DataStore.cc | 925 ++
src/Contig/DataStore.hh | 137 +
src/Contig/Insert.cc | 279 +
src/Contig/Insert.hh | 96 +
src/Contig/InsertStats.cc | 121 +
src/Contig/InsertStats.hh | 32 +
src/Contig/Makefile.am | 45 +
src/Contig/Makefile.in | 698 ++
src/Contig/olapsFromContig.cc | 637 ++
src/Converters/Makefile.am | 65 +
src/Converters/Makefile.in | 686 ++
src/Converters/ace2contig.pl | 244 +
src/Converters/agp2amos.pl | 80 +
src/Converters/amos2ace.pl | 467 +
src/Converters/amos2frg.pl | 216 +
src/Converters/amos2mates.pl | 123 +
src/Converters/amos2sq.pl | 123 +
src/Converters/arachne2ctg.pl | 87 +
src/Converters/arachne2scaff.pl | 98 +
src/Converters/benchmark2arachne.pl | 274 +
src/Converters/benchmark2ca.pl | 303 +
src/Converters/benchmark2mates.pl | 205 +
src/Converters/benchmark2ta.pl | 183 +
src/Converters/blasr2coords.pl | 30 +
src/Converters/blat2nucmer.pl | 154 +
src/Converters/ca2ctg.pl | 249 +
src/Converters/ca2mates.pl | 156 +
src/Converters/ca2scaff.pl | 257 +
src/Converters/ca2singletons.pl | 168 +
src/Converters/ca2ta.pl | 865 ++
src/Converters/castats.pl | 740 ++
src/Converters/cgb2ctg.pl | 124 +
src/Converters/contig2contig.pl | 77 +
src/Converters/ctg2fasta.pl | 19 +
src/Converters/ctg2umdcontig.pl | 104 +
src/Converters/frg2fasta.pl | 24 +
src/Converters/frg2fastq.pl | 31 +
src/Converters/frg2ta.pl | 312 +
src/Converters/parsecasm.pl | 656 ++
src/Converters/phd2afg.pl | 466 +
src/Converters/scaff2fasta.pl | 314 +
src/Converters/ta2ace.pl | 628 ++
src/Converters/tarchive2amos.pl | 1172 +++
src/Converters/tarchive2ca.pl | 612 ++
src/Converters/toAmos.pl | 2101 ++++
src/Converters/toAmos_new.cc | 1433 +++
src/Converters/toArachne.pl | 768 ++
src/CtgTrim/Makefile.am | 20 +
src/CtgTrim/Makefile.in | 494 +
src/CtgTrim/excl_seqs.pl | 52 +
src/CtgTrim/findChimeras.pl | 196 +
src/CtgTrim/find_ends.pl | 94 +
src/CtgTrim/fixfrg.pl | 46 +
src/CtgTrim/iterate.pl | 70 +
src/CtgTrim/kmers.pl | 46 +
src/CtgTrim/singles.pl | 23 +
src/CtgTrim/tab2ovls.pl | 113 +
src/CtgTrim/trimends.pl | 232 +
src/CtgTrim/trimfrg.pl | 70 +
src/CtgTrim/vecfix.pl | 46 +
src/Experimental/ContigFattener.cc | 1373 +++
src/Experimental/ContigFattener.hh | 83 +
src/Experimental/ContigSequence.cc | 353 +
src/Experimental/ContigSequence.hh | 56 +
src/Experimental/Makefile.am | 293 +
src/Experimental/Makefile.in | 1116 +++
src/Experimental/PersistentUtils.hh | 147 +
src/Experimental/aj_evaluateSequenceOverlaps.pl | 1146 +++
src/Experimental/aj_joinContigs.pl | 712 ++
src/Experimental/aj_lowcomplexityfilter.pl | 73 +
src/Experimental/aj_scaff2amos.pl | 69 +
src/Experimental/aj_scaff2fasta.pl | 176 +
src/Experimental/aligncestat.pl | 133 +
src/Experimental/aligndist.pl | 248 +
src/Experimental/alignextend.pl | 325 +
src/Experimental/analyzeHaplotypes.cc | 444 +
src/Experimental/auto-fix-contigs.cc | 347 +
src/Experimental/autoJoiner.pl | 1869 ++++
src/Experimental/barcode-graph.cc | 232 +
src/Experimental/blasr_alignquality.pl | 131 +
src/Experimental/build-persistent-bank.cc | 264 +
src/Experimental/coords_best.pl | 34 +
src/Experimental/coords_depth.pl | 66 +
src/Experimental/ctg_gc.pl | 54 +
src/Experimental/fasta_filter_raw.pl | 47 +
src/Experimental/fastq_to_mates.pl | 34 +
src/Experimental/fattenContig.cc | 229 +
src/Experimental/filterfastadups.pl | 62 +
src/Experimental/gap-closure-reads.cc | 333 +
src/Experimental/insertGapColumn.cc | 47 +
src/Experimental/link2reads.pl | 147 +
src/Experimental/manageContigs.cc | 238 +
src/Experimental/mate-evolution.cc | 313 +
src/Experimental/persistent-assembly.pl | 80 +
src/Experimental/persistent-fix-contigs.cc | 588 ++
src/Experimental/persistent-fix.pl | 97 +
src/Experimental/persistent-plot-breaks.pl | 82 +
src/Experimental/persistent-read-dist.cc | 417 +
src/Experimental/persistent-unitig.pl | 81 +
src/Experimental/po-align.cc | 812 ++
src/Experimental/read-evolution.cc | 340 +
src/Experimental/revContig.cc | 61 +
src/Experimental/rotateContig.cc | 151 +
src/Experimental/splitContig.cc | 435 +
src/Experimental/splitscafffa.pl | 44 +
src/Experimental/stitchContigs.cc | 230 +
src/Experimental/sw_align.cc | 632 ++
src/Experimental/sw_align.hh | 339 +
src/Experimental/sw_alignscore.hh | 141 +
src/Experimental/tigrinc.cc | 237 +
src/Experimental/tigrinc.hh | 41 +
src/Experimental/trimContig.cc | 171 +
src/Experimental/zipContigs.cc | 572 ++
src/Experimental/zipalign.pl | 510 +
src/Foundation/AMOS_Foundation.cc | 243 +
src/Foundation/AMOS_Foundation.hh | 60 +
src/Foundation/CategoryInformation.cc | 142 +
src/Foundation/CategoryInformation.hh | 71 +
src/Foundation/ConfigFile.cc | 191 +
src/Foundation/ConfigFile.hh | 47 +
src/Foundation/ConfigSection.cc | 588 ++
src/Foundation/ConfigSection.hh | 77 +
src/Foundation/Exceptions.cc | 127 +
src/Foundation/Exceptions.hh | 151 +
src/Foundation/FileSystem.cc | 202 +
src/Foundation/FileSystem.hh | 51 +
src/Foundation/LogCategory.cc | 375 +
src/Foundation/LogCategory.hh | 119 +
src/Foundation/LogMsg.cc | 184 +
src/Foundation/LogMsg.hh | 76 +
src/Foundation/Logger.cc | 705 ++
src/Foundation/Logger.hh | 155 +
src/Foundation/Makefile.am | 35 +
src/Foundation/Makefile.in | 644 ++
src/Foundation/MessageLevel.hh | 37 +
src/Foundation/OptionResult.cc | 483 +
src/Foundation/OptionResult.hh | 132 +
src/Foundation/Options.cc | 736 ++
src/Foundation/Options.hh | 140 +
src/GNU/Makefile.am | 40 +
src/GNU/Makefile.in | 502 +
src/GNU/getopt.c | 1161 +++
src/GNU/getopt1.c | 79 +
src/GNU/getopt_.h | 191 +
src/GNU/getopt_int.h | 129 +
src/GNU/gettext.h | 68 +
src/GNU/gnu.c | 0
src/GNU/strtod.c | 189 +
src/GNU/strtol.c | 432 +
src/Graph/CompositeNode.cc | 1 +
src/Graph/CompositeNode.hh | 43 +
src/Graph/Edge.cc | 44 +
src/Graph/Edge.hh | 93 +
src/Graph/Graph.cc | 291 +
src/Graph/Graph.hh | 119 +
src/Graph/IEdge.hh | 73 +
src/Graph/IGraph.hh | 95 +
src/Graph/INode.hh | 74 +
src/Graph/Makefile.am | 43 +
src/Graph/Makefile.in | 645 ++
src/Graph/Node.cc | 1 +
src/Graph/Node.hh | 116 +
src/Graph/SubGraph.cc | 42 +
src/Graph/SubGraph.hh | 54 +
src/Graph/Test.cc | 138 +
src/Makefile.am | 77 +
src/Makefile.in | 626 ++
src/Message/Makefile.am | 38 +
src/Message/Makefile.in | 596 ++
src/Message/message-count.cc | 187 +
src/Message/message-extract.cc | 191 +
src/Message/message-validate.cc | 146 +
src/PerlModules/AmosFoundation.pm | 375 +
src/PerlModules/AmosLib.pm | 460 +
src/PerlModules/FASTAgrammar.pm | 361 +
src/PerlModules/FASTAiterator.pm | 750 ++
src/PerlModules/FASTAreader.pm | 930 ++
src/PerlModules/FASTArecord.pm | 479 +
src/PerlModules/FASTAwriter.pm | 408 +
src/PerlModules/Foundation.pm | 1863 ++++
src/PerlModules/Makefile.am | 21 +
src/PerlModules/Makefile.in | 536 +
src/PerlModules/ParseFasta.pm | 163 +
src/PerlModules/xfig.pm | 315 +
.../AMOScmp-shortReads-alignmentTrimmed.acf | 87 +
src/Pipeline/AMOScmp-shortReads.acf | 66 +
src/Pipeline/AMOScmp.acf | 42 +
src/Pipeline/FRCurve.acf | 48 +
src/Pipeline/Makefile.am | 38 +
src/Pipeline/Makefile.in | 503 +
src/Pipeline/Minimo.acf | 141 +
src/Pipeline/assembleRNAs.acf | 27 +
src/Pipeline/gene_asm.acf | 34 +
src/Pipeline/goBambus2.py | 391 +
src/Pipeline/minimus.acf | 34 +
src/Pipeline/minimus2-blat.acf | 85 +
src/Pipeline/minimus2.acf | 84 +
src/PythonModules/AMOS.py | 127 +
src/PythonModules/Makefile.am | 7 +
src/PythonModules/Makefile.in | 486 +
src/Sim/Makefile.am | 56 +
src/Sim/Makefile.in | 676 ++
src/Sim/pyrosim.cc | 456 +
src/Sim/rerunMultiTest.pl | 24 +
src/Sim/runMultiTest.pl | 69 +
src/Sim/runTest.pl | 335 +
src/Sim/shotgunSim.cc | 611 ++
src/Sim/summarizeMultiTest.pl | 35 +
src/Sim/tandemCollapse.cc | 439 +
src/Slice/Makefile.am | 27 +
src/Slice/Makefile.in | 617 ++
src/Slice/Slice.h | 284 +
src/Slice/getConsQC.c | 434 +
src/Slice/getConsQV.c | 1356 +++
src/Slice/newmem.c | 68 +
src/Slice/utility.c | 77 +
src/Slice/version.h | 11 +
src/Staden/Makefile.am | 5 +
src/Staden/Makefile.in | 566 ++
src/Staden/progs/Makefile.am | 39 +
src/Staden/progs/Makefile.in | 625 ++
src/Staden/progs/trace_comment.c | 151 +
src/Staden/progs/trace_comments.c | 173 +
src/Staden/progs/trace_convert.c | 613 ++
src/Staden/progs/trace_scf_dump.c | 125 +
src/Staden/progs/trace_seq.c | 188 +
src/Staden/read/Makefile.am | 68 +
src/Staden/read/Makefile.in | 601 ++
src/Staden/read/README | 114 +
src/Staden/read/Read.c | 472 +
src/Staden/read/Read.h | 230 +
src/Staden/read/abi.h | 52 +
src/Staden/read/alf.h | 51 +
src/Staden/read/array.c | 145 +
src/Staden/read/array.h | 85 +
src/Staden/read/calc_crc.h | 20 +
src/Staden/read/compress.c | 620 ++
src/Staden/read/compress.h | 71 +
src/Staden/read/compression.c | 1633 +++
src/Staden/read/compression.h | 271 +
src/Staden/read/ctfCompress.c | 1452 +++
src/Staden/read/error.c | 40 +
src/Staden/read/error.h | 21 +
src/Staden/read/expFileIO.c | 1184 +++
src/Staden/read/expFileIO.h | 327 +
src/Staden/read/files.c | 104 +
src/Staden/read/find.c | 103 +
src/Staden/read/fpoint.c | 68 +
src/Staden/read/fpoint.h | 20 +
src/Staden/read/mach-io.c | 197 +
src/Staden/read/mach-io.h | 112 +
src/Staden/read/misc.h | 120 +
src/Staden/read/misc_scf.c | 281 +
src/Staden/read/open_trace_file.c | 467 +
src/Staden/read/open_trace_file.h | 53 +
src/Staden/read/os.h | 117 +
src/Staden/read/plain.h | 51 +
src/Staden/read/read_alloc.c | 271 +
src/Staden/read/read_scf.c | 462 +
src/Staden/read/scf.h | 435 +
src/Staden/read/scf_extras.c | 234 +
src/Staden/read/scf_extras.h | 22 +
src/Staden/read/seqIOABI.c | 1084 ++
src/Staden/read/seqIOABI.h | 133 +
src/Staden/read/seqIOALF.c | 425 +
src/Staden/read/seqIOCTF.c | 101 +
src/Staden/read/seqIOCTF.h | 36 +
src/Staden/read/seqIOPlain.c | 249 +
src/Staden/read/strings.c | 168 +
src/Staden/read/tar_format.h | 62 +
src/Staden/read/traceType.c | 229 +
src/Staden/read/traceType.h | 76 +
src/Staden/read/translate.c | 887 ++
src/Staden/read/translate.h | 92 +
src/Staden/read/write_scf.c | 461 +
src/Staden/read/xalloc.c | 74 +
src/Staden/read/xalloc.h | 24 +
src/Staden/read/ztr.c | 771 ++
src/Staden/read/ztr.h | 121 +
src/Staden/read/ztr_translate.c | 890 ++
src/Tigger/Contig.hh | 31 +
src/Tigger/Makefile.am | 29 +
src/Tigger/Makefile.in | 585 ++
src/Tigger/Overlap.hh | 62 +
src/Tigger/Read.hh | 40 +
src/Tigger/TiggerIO.cc | 245 +
src/Tigger/Unitigger.cc | 917 ++
src/Tigger/Unitigger.hh | 80 +
src/Utils/Makefile.am | 122 +
src/Utils/Makefile.in | 833 ++
src/Utils/analyzeSNPs.cc | 435 +
src/Utils/benchmark_qual.pl | 44 +
src/Utils/benchmark_seq.pl | 167 +
src/Utils/ctgovl.pl | 270 +
src/Utils/cvgChop.pl | 407 +
src/Utils/cvgStat.cc | 527 +
src/Utils/delta2clr.pl | 146 +
src/Utils/delta2cvg.pl | 129 +
src/Utils/fasta_select_len.pl | 49 +
src/Utils/fasta_to_fastq.pl | 54 +
src/Utils/fastq_rename.pl | 63 +
src/Utils/fastq_to_fasta_fast.pl | 16 +
src/Utils/fastqqc.pl | 233 +
src/Utils/filter_contig.pl | 52 +
src/Utils/filter_seq.pl | 150 +
src/Utils/filterfrg.pl | 69 +
src/Utils/fixfastq.pl | 50 +
src/Utils/gccontent.pl | 46 +
src/Utils/getN50.pl | 65 +
src/Utils/getlengths.pl | 45 +
src/Utils/ktrimfrg.pl | 274 +
src/Utils/listcontigreads.sh | 3 +
src/Utils/nucmer2ovl.pl | 214 +
src/Utils/nucmerAnnotate.pl | 109 +
src/Utils/ovl2OVL.pl | 78 +
src/Utils/preTA.pl | 317 +
src/Utils/preassembleFrgs.pl | 90 +
src/Utils/pullTArchive.pl | 132 +
src/Utils/recallConsensus.cc | 275 +
src/Utils/revFasta.pl | 93 +
src/Utils/runAmos.cc | 792 ++
src/Utils/runTA.pl | 145 +
src/Utils/sort2.pl | 88 +
src/Utils/stats.pl | 266 +
src/Utils/tagsum-reduce.cc | 33 +
src/Utils/translate-fasta.pl | 83 +
src/Utils/trimByOvl.cc | 289 +
src/Utils/updateDeltaClr.pl | 119 +
src/Validation/Makefile.am | 169 +
src/Validation/Makefile.in | 905 ++
src/Validation/amosvalidate.acf | 68 +
src/Validation/analyze-read-depth.cc | 306 +
src/Validation/asmQC.cc | 1852 ++++
src/Validation/asmQC2.cc | 777 ++
src/Validation/astats.cc | 383 +
src/Validation/cavalidate.acf | 38 +
src/Validation/cestat-cov.cc | 368 +
src/Validation/clusterSnps.pl | 112 +
src/Validation/coords2cam.pl | 197 +
src/Validation/find-duplicate-reads.cc | 144 +
src/Validation/find-query-breaks.pl | 305 +
src/Validation/findTcovSnp.pl | 255 +
src/Validation/fixlib.pl | 1325 +++
src/Validation/getFRCvalues.cc | 462 +
src/Validation/getFRCvalues.hh | 55 +
src/Validation/insert-sizes.cc | 374 +
src/Validation/library-histogram.cc | 235 +
src/Validation/list-linked-contigs.cc | 220 +
src/Validation/listSingletonMates.cc | 204 +
src/Validation/listSurrogates.pl | 85 +
src/Validation/postCAqc.pl | 196 +
src/Validation/read-cov-plot.cc | 173 +
src/Validation/scaffoldRange2Ungapped.cc | 220 +
src/Validation/suspiciousfeat2region.pl | 88 +
src/Validation/tiling2cam.pl | 81 +
src/hawkeye/AlignmentInfo.hh | 43 +
src/hawkeye/AssemblyStats.cc | 265 +
src/hawkeye/AssemblyStats.hh | 6 +
src/hawkeye/BufferedLineEdit.cc | 14 +
src/hawkeye/BufferedLineEdit.hh | 22 +
src/hawkeye/CGraphContig.cc | 90 +
src/hawkeye/CGraphContig.hh | 25 +
src/hawkeye/CGraphEdge.cc | 12 +
src/hawkeye/CGraphEdge.hh | 18 +
src/hawkeye/CGraphView.cc | 34 +
src/hawkeye/CGraphView.hh | 27 +
src/hawkeye/CGraphWindow.cc | 251 +
src/hawkeye/CGraphWindow.hh | 46 +
src/hawkeye/ChromoField.cc | 315 +
src/hawkeye/ChromoField.hh | 40 +
src/hawkeye/ChromoPicker.cc | 157 +
src/hawkeye/ChromoPicker.hh | 45 +
src/hawkeye/ChromoStore.cc | 169 +
src/hawkeye/ChromoStore.hh | 45 +
src/hawkeye/ConsensusField.cc | 414 +
src/hawkeye/ConsensusField.hh | 85 +
src/hawkeye/ContigCanvasItem.cc | 22 +
src/hawkeye/ContigCanvasItem.hh | 20 +
src/hawkeye/ContigPicker.cc | 310 +
src/hawkeye/ContigPicker.hh | 6 +
src/hawkeye/CoverageCanvasItem.cc | 50 +
src/hawkeye/CoverageCanvasItem.hh | 38 +
src/hawkeye/CoverageRectCanvasItem.cc | 61 +
src/hawkeye/CoverageRectCanvasItem.hh | 41 +
src/hawkeye/DetailWidget.cc | 67 +
src/hawkeye/DetailWidget.hh | 39 +
src/hawkeye/FeatureBrowser.cc | 312 +
src/hawkeye/FeatureBrowser.hh | 6 +
src/hawkeye/FeatureCanvasItem.cc | 39 +
src/hawkeye/FeatureCanvasItem.hh | 26 +
src/hawkeye/HistogramWidget.cc | 282 +
src/hawkeye/HistogramWidget.hh | 38 +
src/hawkeye/HistogramWindow.cc | 75 +
src/hawkeye/HistogramWindow.hh | 28 +
src/hawkeye/InsertCanvasItem.cc | 86 +
src/hawkeye/InsertCanvasItem.hh | 40 +
src/hawkeye/InsertField.cc | 610 ++
src/hawkeye/InsertField.hh | 87 +
src/hawkeye/InsertPosition.cc | 134 +
src/hawkeye/InsertPosition.hh | 35 +
src/hawkeye/InsertWidget.cc | 1923 ++++
src/hawkeye/InsertWidget.hh | 233 +
src/hawkeye/InsertWindow.cc | 446 +
src/hawkeye/InsertWindow.hh | 97 +
src/hawkeye/LaunchPad.cc | 524 +
src/hawkeye/LaunchPad.hh | 140 +
src/hawkeye/LaunchPadBase.cc | 619 ++
src/hawkeye/LaunchPadBase.hh | 156 +
src/hawkeye/LibraryPicker.cc | 275 +
src/hawkeye/LibraryPicker.hh | 6 +
src/hawkeye/MainWindow.cc | 512 +
src/hawkeye/MainWindow.hh | 126 +
src/hawkeye/Makefile.am | 123 +
src/hawkeye/Makefile.in | 818 ++
src/hawkeye/NChartStats.cc | 106 +
src/hawkeye/NChartStats.hh | 40 +
src/hawkeye/NChartWidget.cc | 572 ++
src/hawkeye/NChartWidget.hh | 55 +
src/hawkeye/NChartWindow.cc | 23 +
src/hawkeye/NChartWindow.hh | 17 +
src/hawkeye/NChartWindowBase.cc | 113 +
src/hawkeye/NChartWindowBase.hh | 61 +
src/hawkeye/NetworkCom.cc | 126 +
src/hawkeye/NetworkCom.hh | 78 +
src/hawkeye/OverviewField.cc | 42 +
src/hawkeye/OverviewField.hh | 36 +
src/hawkeye/QueryWidget.cc | 444 +
src/hawkeye/QueryWidget.hh | 99 +
src/hawkeye/RangeScrollBar.cc | 734 ++
src/hawkeye/RangeScrollBar.hh | 226 +
src/hawkeye/ReadInfo.cc | 51 +
src/hawkeye/ReadInfo.hh | 31 +
src/hawkeye/ReadPicker.cc | 250 +
src/hawkeye/ReadPicker.hh | 6 +
src/hawkeye/RenderSeq.cc | 344 +
src/hawkeye/RenderSeq.hh | 71 +
src/hawkeye/ScaffoldPicker.cc | 250 +
src/hawkeye/ScaffoldPicker.hh | 6 +
src/hawkeye/SelectionWidget.cc | 101 +
src/hawkeye/SelectionWidget.hh | 46 +
src/hawkeye/SplashScreen.cc | 48 +
src/hawkeye/SplashScreen.hh | 27 +
src/hawkeye/TilingField.cc | 797 ++
src/hawkeye/TilingField.hh | 92 +
src/hawkeye/TilingFrame.cc | 565 ++
src/hawkeye/TilingFrame.hh | 104 +
src/hawkeye/UIElements.cc | 169 +
src/hawkeye/UIElements.hh | 68 +
src/hawkeye/hawkeye.pro | 107 +
src/hawkeye/icons/AAI.xpm | 549 +
src/hawkeye/icons/Hawkeye.jpg | Bin 0 -> 94816 bytes
src/hawkeye/icons/Hawkeye.xpm | 562 ++
src/hawkeye/icons/fontdecrease.xpm | 23 +
src/hawkeye/icons/fontincrease.xpm | 23 +
src/hawkeye/icons/pointer_tool.xpm | 21 +
src/hawkeye/icons/rangearrow_down.png | Bin 0 -> 326 bytes
src/hawkeye/icons/rangearrow_down.xpm | 47 +
src/hawkeye/icons/rangearrow_left.png | Bin 0 -> 347 bytes
src/hawkeye/icons/rangearrow_left.xpm | 47 +
src/hawkeye/icons/rangearrow_right.png | Bin 0 -> 337 bytes
src/hawkeye/icons/rangearrow_right.xpm | 47 +
src/hawkeye/icons/rangearrow_up.png | Bin 0 -> 317 bytes
src/hawkeye/icons/rangearrow_up.xpm | 47 +
src/hawkeye/icons/rangebar_horiz.png | Bin 0 -> 242 bytes
src/hawkeye/icons/rangebar_horiz.xpm | 37 +
src/hawkeye/icons/rangebar_vert.png | Bin 0 -> 226 bytes
src/hawkeye/icons/rangebar_vert.xpm | 37 +
src/hawkeye/icons/rangegrip_down.png | Bin 0 -> 276 bytes
src/hawkeye/icons/rangegrip_down.xpm | 25 +
src/hawkeye/icons/rangegrip_left.png | Bin 0 -> 295 bytes
src/hawkeye/icons/rangegrip_left.xpm | 35 +
src/hawkeye/icons/rangegrip_right.png | Bin 0 -> 272 bytes
src/hawkeye/icons/rangegrip_right.xpm | 35 +
src/hawkeye/icons/rangegrip_up.png | Bin 0 -> 262 bytes
src/hawkeye/icons/rangegrip_up.xpm | 25 +
src/hawkeye/icons/rangegroove_horiz.png | Bin 0 -> 210 bytes
src/hawkeye/icons/rangegroove_horiz.xpm | 29 +
src/hawkeye/icons/rangegroove_vert.png | Bin 0 -> 200 bytes
src/hawkeye/icons/rangegroove_vert.xpm | 29 +
src/hawkeye/icons/zoom_in.xpm | 22 +
src/hawkeye/icons/zoom_out.xpm | 22 +
src/hawkeye/main.cc | 145 +
test/minimus/influenza-A/influenza-A.afg | 6002 +++++++++++
test/minimus/influenza-A/influenza-A.qual | 4979 +++++++++
test/minimus/influenza-A/influenza-A.seq | 1587 +++
.../influenza-A/influenza-output.bnk.old/CTG.0.fix | Bin 0 -> 176 bytes
.../influenza-A/influenza-output.bnk.old/CTG.0.var | Bin 0 -> 29764 bytes
.../influenza-A/influenza-output.bnk.old/CTG.ifo | 9 +
.../influenza-A/influenza-output.bnk.old/CTG.map | 9 +
.../influenza-A/influenza-output.bnk.old/FRG.0.fix | Bin 0 -> 3081 bytes
.../influenza-A/influenza-output.bnk.old/FRG.0.var | Bin 0 -> 79 bytes
.../influenza-A/influenza-output.bnk.old/FRG.ifo | 9 +
.../influenza-A/influenza-output.bnk.old/FRG.map | 80 +
.../influenza-A/influenza-output.bnk.old/LAY.0.fix | Bin 0 -> 144 bytes
.../influenza-A/influenza-output.bnk.old/LAY.0.var | Bin 0 -> 3008 bytes
.../influenza-A/influenza-output.bnk.old/LAY.ifo | 9 +
.../influenza-A/influenza-output.bnk.old/LAY.map | 1 +
.../influenza-A/influenza-output.bnk.old/LIB.0.fix | Bin 0 -> 1106 bytes
.../influenza-A/influenza-output.bnk.old/LIB.0.var | Bin 0 -> 711 bytes
.../influenza-A/influenza-output.bnk.old/LIB.ifo | 9 +
.../influenza-A/influenza-output.bnk.old/LIB.map | 80 +
.../influenza-A/influenza-output.bnk.old/OVL.0.fix | Bin 0 -> 23902 bytes
.../influenza-A/influenza-output.bnk.old/OVL.0.var | Bin 0 -> 703 bytes
.../influenza-A/influenza-output.bnk.old/OVL.ifo | 9 +
.../influenza-A/influenza-output.bnk.old/OVL.map | 1 +
.../influenza-A/influenza-output.bnk.old/RED.0.fix | Bin 0 -> 8305 bytes
.../influenza-A/influenza-output.bnk.old/RED.0.var | Bin 0 -> 95290 bytes
.../influenza-A/influenza-output.bnk.old/RED.ifo | 9 +
.../influenza-A/influenza-output.bnk.old/RED.map | 152 +
.../influenza-A/influenza-output.bnk.old/UNV.0.fix | Bin 0 -> 14 bytes
.../influenza-A/influenza-output.bnk.old/UNV.0.var | Bin 0 -> 69 bytes
.../influenza-A/influenza-output.bnk.old/UNV.ifo | 9 +
.../influenza-A/influenza-output.bnk.old/UNV.map | 2 +
.../influenza-A/influenza-output.bnk/CTG.0.0.fix | Bin 0 -> 208 bytes
.../influenza-A/influenza-output.bnk/CTG.0.0.var | Bin 0 -> 30364 bytes
.../influenza-A/influenza-output.bnk/CTG.0.map | 9 +
.../influenza-A/influenza-output.bnk/CTG.ifo | 10 +
.../influenza-A/influenza-output.bnk/FRG.0.0.fix | Bin 0 -> 3081 bytes
.../influenza-A/influenza-output.bnk/FRG.0.0.var | Bin 0 -> 79 bytes
.../influenza-A/influenza-output.bnk/FRG.0.map | 80 +
.../influenza-A/influenza-output.bnk/FRG.ifo | 10 +
.../influenza-A/influenza-output.bnk/LAY.0.0.fix | Bin 0 -> 144 bytes
.../influenza-A/influenza-output.bnk/LAY.0.0.var | Bin 0 -> 3608 bytes
.../influenza-A/influenza-output.bnk/LAY.0.map | 1 +
.../influenza-A/influenza-output.bnk/LAY.ifo | 10 +
.../influenza-A/influenza-output.bnk/LIB.0.0.fix | Bin 0 -> 1106 bytes
.../influenza-A/influenza-output.bnk/LIB.0.0.var | Bin 0 -> 711 bytes
.../influenza-A/influenza-output.bnk/LIB.0.map | 80 +
.../influenza-A/influenza-output.bnk/LIB.ifo | 10 +
.../influenza-A/influenza-output.bnk/OVL.0.0.fix | Bin 0 -> 23902 bytes
.../influenza-A/influenza-output.bnk/OVL.0.0.var | Bin 0 -> 703 bytes
.../influenza-A/influenza-output.bnk/OVL.0.map | 1 +
.../influenza-A/influenza-output.bnk/OVL.ifo | 10 +
.../influenza-A/influenza-output.bnk/RED.0.0.fix | Bin 0 -> 8305 bytes
.../influenza-A/influenza-output.bnk/RED.0.0.var | Bin 0 -> 190429 bytes
.../influenza-A/influenza-output.bnk/RED.0.map | 152 +
.../influenza-A/influenza-output.bnk/RED.ifo | 10 +
.../influenza-A/influenza-output.bnk/UNV.0.0.fix | Bin 0 -> 14 bytes
.../influenza-A/influenza-output.bnk/UNV.0.0.var | Bin 0 -> 69 bytes
.../influenza-A/influenza-output.bnk/UNV.0.map | 2 +
.../influenza-A/influenza-output.bnk/UNV.ifo | 10 +
test/minimus/influenza-A/influenza-output.fasta | 234 +
test/minimus/zgene/zgene2-output.bnk.old/CTG.0.fix | Bin 0 -> 352 bytes
test/minimus/zgene/zgene2-output.bnk.old/CTG.0.var | Bin 0 -> 45674 bytes
test/minimus/zgene/zgene2-output.bnk.old/CTG.ifo | 9 +
test/minimus/zgene/zgene2-output.bnk.old/CTG.map | 17 +
test/minimus/zgene/zgene2-output.bnk.old/LAY.0.fix | Bin 0 -> 288 bytes
test/minimus/zgene/zgene2-output.bnk.old/LAY.0.var | Bin 0 -> 3036 bytes
test/minimus/zgene/zgene2-output.bnk.old/LAY.ifo | 9 +
test/minimus/zgene/zgene2-output.bnk.old/LAY.map | 1 +
test/minimus/zgene/zgene2-output.bnk.old/OVL.0.fix | Bin 0 -> 26486 bytes
test/minimus/zgene/zgene2-output.bnk.old/OVL.0.var | Bin 0 -> 779 bytes
test/minimus/zgene/zgene2-output.bnk.old/OVL.ifo | 9 +
test/minimus/zgene/zgene2-output.bnk.old/OVL.map | 1 +
test/minimus/zgene/zgene2-output.bnk.old/RED.0.fix | Bin 0 -> 8415 bytes
test/minimus/zgene/zgene2-output.bnk.old/RED.0.var | Bin 0 -> 104217 bytes
test/minimus/zgene/zgene2-output.bnk.old/RED.ifo | 9 +
test/minimus/zgene/zgene2-output.bnk.old/RED.map | 154 +
test/minimus/zgene/zgene2-output.bnk.old/UNV.0.fix | Bin 0 -> 14 bytes
test/minimus/zgene/zgene2-output.bnk.old/UNV.0.var | Bin 0 -> 69 bytes
test/minimus/zgene/zgene2-output.bnk.old/UNV.ifo | 9 +
test/minimus/zgene/zgene2-output.bnk.old/UNV.map | 2 +
test/minimus/zgene/zgene2-output.bnk/CTG.0.0.fix | Bin 0 -> 416 bytes
test/minimus/zgene/zgene2-output.bnk/CTG.0.0.var | Bin 0 -> 46278 bytes
test/minimus/zgene/zgene2-output.bnk/CTG.0.map | 17 +
test/minimus/zgene/zgene2-output.bnk/CTG.ifo | 10 +
test/minimus/zgene/zgene2-output.bnk/LAY.0.0.fix | Bin 0 -> 288 bytes
test/minimus/zgene/zgene2-output.bnk/LAY.0.0.var | Bin 0 -> 3640 bytes
test/minimus/zgene/zgene2-output.bnk/LAY.0.map | 1 +
test/minimus/zgene/zgene2-output.bnk/LAY.ifo | 10 +
test/minimus/zgene/zgene2-output.bnk/OVL.0.0.fix | Bin 0 -> 26486 bytes
test/minimus/zgene/zgene2-output.bnk/OVL.0.0.var | Bin 0 -> 779 bytes
test/minimus/zgene/zgene2-output.bnk/OVL.0.map | 1 +
test/minimus/zgene/zgene2-output.bnk/OVL.ifo | 10 +
test/minimus/zgene/zgene2-output.bnk/RED.0.0.fix | Bin 0 -> 8415 bytes
test/minimus/zgene/zgene2-output.bnk/RED.0.0.var | Bin 0 -> 208281 bytes
test/minimus/zgene/zgene2-output.bnk/RED.0.map | 154 +
test/minimus/zgene/zgene2-output.bnk/RED.ifo | 10 +
test/minimus/zgene/zgene2-output.bnk/UNV.0.0.fix | Bin 0 -> 14 bytes
test/minimus/zgene/zgene2-output.bnk/UNV.0.0.var | Bin 0 -> 69 bytes
test/minimus/zgene/zgene2-output.bnk/UNV.0.map | 2 +
test/minimus/zgene/zgene2-output.bnk/UNV.ifo | 10 +
test/minimus/zgene/zgene2-output.fasta | 373 +
test/minimus/zgene/zgene2.afg | 4987 +++++++++
test/minimus/zgene/zgene2.afg.runAmos.log.orig | 66 +
test/minimus/zgene/zgene2.seq | 1955 ++++
823 files changed, 249601 insertions(+)
--
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