[med-svn] [canu] 02/03: Merge tag 'upstream/1.5+dfsg'
Afif Elghraoui
afif at moszumanska.debian.org
Thu May 18 05:30:13 UTC 2017
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository canu.
commit a9101d36f75d05681f6bd16f71c63eaf6ce63abb
Merge: f6f924b 15ffcc1
Author: Afif Elghraoui <afif at debian.org>
Date: Thu May 18 01:18:32 2017 -0400
Merge tag 'upstream/1.5+dfsg'
Upstream version 1.5+dfsg
Conflicts:
src/bogart/buildGraph.mk
src/gfa/alignGFA.mk
src/meryl/maskMers.mk
src/pipelines/sanity/sanity.pl
src/pipelines/sanity/sanity.sh
README.licenses | 43 +
addCopyrights-BuildData.pl | 1 +
addCopyrights.dat | 729 +++++
addCopyrights.pl | 41 +-
buildRelease.sh | 39 +
documentation/reST-markup-hints | 10 +
documentation/source/conf.py | 4 +-
documentation/source/faq.rst | 95 +-
documentation/source/parameter-reference.rst | 418 ++-
documentation/source/quick-start.rst | 55 +-
documentation/source/tutorial.rst | 114 +-
src/AS_UTL/AS_UTL_fileIO.C | 149 +-
src/AS_UTL/AS_UTL_fileIO.H | 8 +-
src/AS_UTL/AS_UTL_stackTrace.C | 376 ++-
src/AS_UTL/AS_UTL_stackTrace.H | 2 +-
src/AS_UTL/bitPackedFile.C | 2 +-
src/AS_UTL/libbacktrace/LICENSE | 29 +
src/AS_UTL/libbacktrace/README | 15 +
src/AS_UTL/libbacktrace/atomic.c | 113 +
src/AS_UTL/libbacktrace/backtrace-supported.h | 66 +
src/AS_UTL/libbacktrace/backtrace.c | 129 +
src/AS_UTL/libbacktrace/backtrace.h | 182 ++
src/AS_UTL/libbacktrace/config.h | 128 +
src/AS_UTL/libbacktrace/dwarf.c | 3123 ++++++++++++++++++++
src/AS_UTL/libbacktrace/elf.c | 983 ++++++
src/AS_UTL/libbacktrace/fileline.c | 194 ++
src/AS_UTL/libbacktrace/internal.h | 294 ++
src/AS_UTL/libbacktrace/make.out | 26 +
src/AS_UTL/libbacktrace/make.sh | 22 +
src/AS_UTL/libbacktrace/mmap.c | 303 ++
src/AS_UTL/libbacktrace/mmapio.c | 100 +
src/AS_UTL/libbacktrace/posix.c | 100 +
src/AS_UTL/libbacktrace/print.c | 92 +
src/AS_UTL/libbacktrace/simple.c | 108 +
src/AS_UTL/libbacktrace/sort.c | 108 +
src/AS_UTL/libbacktrace/state.c | 72 +
src/AS_UTL/libbacktrace/unknown.c | 68 +
src/AS_global.C | 10 +-
src/Makefile | 227 +-
src/bogart/AS_BAT_BestOverlapGraph.C | 88 +-
src/bogart/AS_BAT_BestOverlapGraph.H | 10 +-
src/bogart/AS_BAT_ChunkGraph.C | 16 +-
src/bogart/AS_BAT_CreateUnitigs.C | 2 +-
src/bogart/AS_BAT_MergeOrphans.H | 6 +-
src/bogart/AS_BAT_OverlapCache.C | 70 +-
src/bogart/AS_BAT_TigGraph.C | 28 +-
src/bogart/bogart.C | 25 +-
src/canu_version_update.pl | 58 +-
src/correction/generateCorrectionLayouts.C | 63 +-
src/falcon_sense/falcon_sense.C | 21 +
src/falcon_sense/falcon_sense.mk | 2 +-
src/falcon_sense/libfalcon/falcon.C | 240 +-
src/falcon_sense/libfalcon/falcon.H | 75 +-
src/falcon_sense/libfalcon/kmer_lookup.C | 622 ----
src/fastq-utilities/fastqSimulate.C | 4 +-
src/gfa/alignGFA.C | 464 +++
.../falcon_sense.mk => gfa/alignGFA.mk} | 8 +-
src/gfa/gfa.C | 345 +++
src/gfa/gfa.H | 103 +
src/main.mk | 43 +-
src/merTrim/merTrim.C | 183 +-
.../falcon_sense.mk => merTrim/merTrim.mk} | 10 +-
src/merTrim/merTrimResult.H | 9 +-
src/meryl/compare-counts.C | 4 +
src/meryl/estimate-mer-threshold.C | 310 +-
src/meryl/existDB.C | 252 ++
.../falcon_sense.mk => meryl/existDB.mk} | 12 +-
src/meryl/libkmer/existDB-create-from-fasta.C | 304 ++
src/meryl/libkmer/existDB-create-from-meryl.C | 261 ++
src/meryl/libkmer/existDB-create-from-sequence.C | 293 ++
src/meryl/libkmer/existDB-state.C | 233 ++
src/meryl/libkmer/existDB.C | 211 ++
src/meryl/libkmer/existDB.H | 190 ++
src/meryl/libkmer/existDB.mk | 13 +
src/meryl/libkmer/percentCovered.C | 95 +
src/meryl/libkmer/percentCovered.mk | 13 +
src/meryl/libkmer/posDB.mk | 13 +
src/meryl/libkmer/positionDB-access.C | 376 +++
src/meryl/libkmer/positionDB-dump.C | 79 +
src/meryl/libkmer/positionDB-file.C | 318 ++
src/meryl/libkmer/positionDB-mismatch.C | 412 +++
src/meryl/libkmer/positionDB-sort.C | 182 ++
src/meryl/libkmer/positionDB.C | 1186 ++++++++
src/meryl/libkmer/positionDB.H | 273 ++
src/meryl/maskMers.C | 4 +
src/meryl/meryl-build.C | 20 +
src/meryl/positionDB.C | 308 ++
.../falcon_sense.mk => meryl/positionDB.mk} | 12 +-
src/mhap/mhapConvert.C | 33 +-
src/minimap/mmapConvert.C | 36 +-
src/overlapInCore/libedlib/edlib.C | 65 +-
src/overlapInCore/libedlib/edlib.H | 327 +-
.../prefixEditDistance-allocateMoreSpace.C | 13 +-
.../liboverlap/prefixEditDistance-extend.C | 18 +-
.../liboverlap/prefixEditDistance-forward.C | 36 +-
.../liboverlap/prefixEditDistance-reverse.C | 36 +-
src/overlapInCore/liboverlap/prefixEditDistance.H | 21 +-
.../overlapInCore-Process_String_Overlaps.C | 2 +-
src/overlapInCore/overlapPair.C | 700 +++--
src/pipelines/canu-object-store.pl | 152 +
src/pipelines/canu.pl | 405 +--
src/pipelines/canu/Configure.pm | 193 +-
src/pipelines/canu/Consensus.pm | 465 ++-
src/pipelines/canu/CorrectReads.pm | 688 +++--
src/pipelines/canu/Defaults.pm | 569 ++--
src/pipelines/canu/ErrorEstimate.pm | 102 +-
src/pipelines/canu/Execution.pm | 508 +++-
src/pipelines/canu/Gatekeeper.pm | 369 +--
src/pipelines/canu/Grid_Cloud.pm | 347 +++
src/pipelines/canu/Grid_DNANexus.pm | 104 +
src/pipelines/canu/Grid_LSF.pm | 3 -
src/pipelines/canu/Grid_PBSTorque.pm | 19 +-
src/pipelines/canu/Grid_SGE.pm | 34 +-
src/pipelines/canu/Grid_Slurm.pm | 3 -
src/pipelines/canu/HTML.pm | 214 +-
src/pipelines/canu/Meryl.pm | 573 ++--
src/pipelines/canu/Output.pm | 150 +-
src/pipelines/canu/OverlapBasedTrimming.pm | 165 +-
src/pipelines/canu/OverlapErrorAdjustment.pm | 345 ++-
src/pipelines/canu/OverlapInCore.pm | 216 +-
src/pipelines/canu/OverlapMMap.pm | 298 +-
src/pipelines/canu/OverlapMhap.pm | 352 ++-
src/pipelines/canu/OverlapStore.pm | 428 +--
src/pipelines/canu/Report.pm | 172 ++
src/pipelines/canu/Unitig.pm | 169 +-
src/pipelines/parallel-ovl-store-test.sh | 68 +
src/pipelines/sanity/sanity-all-done.pl | 240 --
src/pipelines/sanity/sanity-merge-qc.pl | 121 -
src/pipelines/sanity/sanity.pl | 382 ---
src/pipelines/sanity/sanity.sh | 50 -
src/pipelines/simple-repeat-test.pl | 107 +
src/stores/gatekeeperPartition.C | 82 +-
src/stores/gkStore.C | 35 +-
src/stores/gkStore.H | 3 +-
src/stores/ovOverlap.C | 13 +-
src/stores/ovOverlap.H | 18 +-
src/stores/ovStore.C | 115 +-
src/stores/ovStore.H | 14 +-
src/stores/ovStoreBucketizer.C | 4 +-
src/stores/ovStoreBuild.C | 13 +-
src/stores/ovStoreFile.C | 202 +-
src/stores/ovStoreFilter.C | 23 +-
src/stores/ovStoreHistogram.C | 28 +-
src/stores/ovStoreHistogram.H | 4 +-
src/stores/ovStoreWriter.C | 12 +-
src/stores/tgStore.C | 8 +-
src/stores/tgStoreCoverageStat.C | 4 +-
src/stores/tgStoreDump.C | 16 +-
src/stores/tgStoreLoad.C | 41 +-
src/stores/tgTig.C | 32 +
src/stores/tgTig.H | 2 +
src/stores/tgTigMultiAlignDisplay.C | 2 +-
src/utgcns/libNDFalcon/dw.C | 10 +
src/utgcns/libcns/unitigConsensus.C | 134 +-
src/utgcns/libcns/unitigConsensus.H | 3 +-
src/utgcns/libpbutgcns/LICENSE | 72 +-
src/utgcns/utgcns.C | 5 +-
157 files changed, 20800 insertions(+), 5840 deletions(-)
diff --cc src/AS_global.C
index 533f428,0b9304f..d7aefbb
--- a/src/AS_global.C
+++ b/src/AS_global.C
@@@ -102,9 -102,9 +102,10 @@@ AS_configure(int argc, char **argv)
// Install a signal handler to catch seg faults and errors.
- AS_UTL_installCrashCatcher();
+ AS_UTL_installCrashCatcher(argv[0]);
+
+
//
// Et cetera.
//
diff --cc src/overlapInCore/overlapPair.C
index bb7ac31,63571ea..3dce0d0
--- a/src/overlapInCore/overlapPair.C
+++ b/src/overlapInCore/overlapPair.C
@@@ -513,18 -802,18 +802,18 @@@ main(int argc, char **argv)
// Initialize thread work areas. Mirrored from overlapInCore.C
for (uint32 tt=0; tt<numThreads; tt++) {
- fprintf(stderr, "Initialize thread %u\n", tt);
+ fprintf(stderr, "Initialize thread %u\n", tt);
- WA[tt].threadID = tt;
- WA[tt].maxErate = maxErate;
- WA[tt].partialOverlaps = partialOverlaps;
- WA[tt].invertOverlaps = invertOverlaps;
+ WA[tt].threadID = tt;
+ WA[tt].maxErate = maxErate;
+ WA[tt].partialOverlaps = partialOverlaps;
+ WA[tt].invertOverlaps = invertOverlaps;
- WA[tt].gkpStore = gkpStore;
- WA[tt].overlaps = NULL;
+ WA[tt].gkpStore = gkpStore;
+ WA[tt].overlaps = NULL;
- // preallocate some work thread memory for common tasks to avoid allocation
- WA[tt].readSeq = new char[AS_MAX_READLEN+1];
+ // preallocate some work thread memory for common tasks to avoid allocation
+ WA[tt].readSeq = new char[AS_MAX_READLEN+1];
}
diff --cc src/pipelines/canu/Defaults.pm
index 0c3d69e,6e91966..c7a3df3
--- a/src/pipelines/canu/Defaults.pm
+++ b/src/pipelines/canu/Defaults.pm
@@@ -987,17 -998,32 +998,194 @@@ sub setDefaults ()
}
+ # Get the version information. Needs to be last so that pathMap can be defined.
+
+ sub setVersion ($) {
+ my $bin = shift @_;
+ my $version;
+
+ open(F, "$bin/gatekeeperCreate --version 2>&1 |");
+ while (<F>) {
+ $version = $_; chomp $version;
+ }
+ close(F);
+
+ $global{'version'} = $version;
+ }
+
+
+ sub checkJava () {
+ return if ((getGlobal("corOverlapper") ne "mhap") &&
+ (getGlobal("obtOverlapper") ne "mhap") &&
+ (getGlobal("utgOverlapper") ne "mhap"));
+
+ my $java = getGlobal("java");
+ my $versionStr = "unknown";
+ my $version = 0;
+
+ # Argh, we can't use runCommand() here, because we're included in Execution.pm. Try to check
++ # it with -x. Nope. Fails if $java == "java".
++
++ #if (! -x $java) {
++ # addCommandLineError("ERROR: java executable '$java' not found or not executable\n");
++ #}
++
++ open(F, "$java -Xmx1g -showversion 2>&1 |");
++ while (<F>) {
++ # First word is either "java" or "openjdk" or ...
++ if (m/^.*\s+version\s+\"(\d+.\d+)(.*)\".*$/) {
++ $versionStr = "$1$2";
++ $version = $1;
++ }
++ }
++ close(F);
++
++ if ($version < 1.8) {
++ addCommandLineError("ERROR: mhap overlapper requires java version at least 1.8.0; you have $versionStr (from '$java').\n");
++ addCommandLineError("ERROR: '$java -showversion' reports:\n");
++
++ open(F, "$java -showversion 2>&1 |");
++ while (<F>) {
++ chomp;
++ addCommandLineError("ERROR: '$_'\n");
++ }
++ close(F);
++
++ } else {
++ print STDERR "-- Detected Java(TM) Runtime Environment '$versionStr' (from '$java').\n";
++ }
++}
++
++
++
++sub checkGnuplot () {
++
++ return if (getGlobal("gnuPlotTested") == 1);
++
++ my $gnuplot = getGlobal("gnuplot");
++ my $format = getGlobal("gnuplotImageFormat");
++ my $version = undef;
++
++ # Check for existence of gnuplot.
++
++ open(F, "$gnuplot -V |");
++ while (<F>) {
++ chomp;
++ $version = $_;
++ $version = $1 if ($version =~ m/^gnuplot\s+(.*)$/);
++ }
++ close(F);
++
++ if (!defined($version)) {
++ addCommandLineError("ERROR: Failed to run gnuplot from '$gnuplot'.");
++ addCommandLineError("ERROR: Set option gnuplot=<path-to-gnuplot> or gnuplotTested=true to skip this test and not generate plots.\n");
++ return;
++ }
++
++ # Check for existence of a decent output format. Need to redirect in /dev/null to make gnuplot
++ # not use it's builtin pager.
++
++ if (!defined($format)) {
++ my $havePNG = 0;
++ my $haveSVG = 0;
++ my $haveGIF = 0;
++
++ open(F, "> /tmp/gnuplot-$$-test.gp");
++ print F "set terminal\n";
++ close(F);
++
++ system("cd /tmp && $gnuplot < /dev/null /tmp/gnuplot-$$-test.gp > /tmp/gnuplot-$$-test.err 2>&1");
++
++ open(F, "< /tmp/gnuplot-$$-test.err");
++ while (<F>) {
++ s/^\s+//;
++ s/\s+$//;
++
++ my @t = split '\s+', $_;
++
++ $havePNG = 1 if ($t[0] eq 'png');
++ $haveSVG = 1 if ($t[0] eq 'svg');
++ $haveGIF = 1 if ($t[0] eq 'gif');
++ }
++ close(F);
++
++ $format = "gif" if ($haveGIF);
++ $format = "svg" if ($haveSVG);
++ $format = "png" if ($havePNG);
++
++ setGlobal("gnuplotImageFormat", $format);
++
++ unlink "/tmp/gnuplot-$$-test.gp";
++ unlink "/tmp/gnuplot-$$-test.err";
++ }
++
++ if (!defined($format)) {
++ addCommandLineError("ERROR: Failed to detect a suitable output format for gnuplot.\n");
++ addCommandLineError("ERROR: Looked for png, svg and gif, found none of them.\n");
++ addCommandLineError("Set option gnuplotImageFormat=<type>, or gnuplotTested=true to skip this test and not generate plots.\n");
++ return;
++ }
++
++ # Test if we can actually make images.
++
++ open(F, "> /tmp/gnuplot-$$-test.gp");
++ print F "set title 'gnuplot test'\n";
++ print F "set xlabel 'X'\n";
++ print F "set xlabel 'Y'\n";
++ print F "\n";
++ print F "set terminal $format size 1024,1024\n";
++ print F "set output '/tmp/gnuplot-$$-test.1.$format'\n";
++ print F "\n";
++ print F "plot [-30:20] sin(x*20) * atan(x)\n\n";
++ print F "\n";
++ print F "set terminal $format size 256,256\n";
++ print F "set output '/tmp/gnuplot-$$-test.2.$format'\n";
++ print F "\n";
++ print F "bogus line\n";
++ close(F);
++
++ # Dang, we don't have runCommandSilently here, so have to do it the hard way.
++
++ system("cd /tmp && $gnuplot < /dev/null /tmp/gnuplot-$$-test.gp > /tmp/gnuplot-$$-test.err 2>&1");
++
++ if ((! -e "/tmp/gnuplot-$$-test.1.$format") ||
++ (! -e "/tmp/gnuplot-$$-test.2.$format")) {
++ addCommandLineError("ERROR: gnuplot failed to generate images.\n");
++
++ open(F, "< /tmp/gnuplot-$$-test.err");
++ while (<F>) {
++ chomp;
++ addCommandLineError("ERROR: gnuplot reports: $_\n");
++ }
++ close(F);
++
++ addCommandLineError("ERROR: Set option gnuplotImageFormat=<type>, or gnuplotTested=true to skip this test and not generate plots.\n");
++ return;
++ }
++
++ # Yay, gnuplot works!
++
++ print STDERR "-- Detected gnuplot version '$version' (from '$gnuplot') and image format '$format'.\n";
++ #addCommandLineOption("gnuplotTested=1");
++
++ unlink "/tmp/gnuplot-$$-test.gp";
++ unlink "/tmp/gnuplot-$$-test.err";
++ unlink "/tmp/gnuplot-$$-test.1.$format";
++ unlink "/tmp/gnuplot-$$-test.2.$format";
++}
++
++
+
+sub checkJava () {
+ return if ((getGlobal("corOverlapper") ne "mhap") &&
+ (getGlobal("obtOverlapper") ne "mhap") &&
+ (getGlobal("utgOverlapper") ne "mhap"));
+
+ my $java = getGlobal("java");
+ my $versionStr = "unknown";
+ my $version = 0;
+
+ # Argh, we can't use runCommand() here, because we're included in Execution.pm. Try to check
# it with -x. Nope. Fails if $java == "java".
#if (! -x $java) {
diff --cc src/stores/ovStore.H
index d86a6b1,fdaee47..dfec980
--- a/src/stores/ovStore.H
+++ b/src/stores/ovStore.H
@@@ -322,14 -322,13 +322,19 @@@ public
// of evalues must agree.
void addEvalues(vector<char *> &fileList);
- void addEvalues(uint32 bgnID, uint32 endID, uint16 *evalues, uint64 evaluesLen);
+
+ // Return the statistics associated with this store
+
+ ovStoreHistogram *getHistogram(void) {
+ return(new ovStoreHistogram(_storePath));
+ };
+ // Return the statistics associated with this store
+
+ ovStoreHistogram *getHistogram(void) {
+ return(new ovStoreHistogram(_gkp, _storePath));
+ };
+
private:
char _storePath[FILENAME_MAX];
--
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