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commit 744a6d9dabbc33bb666ffc69ca3f00ff122a1f8e Author: Afif Elghraoui <[email protected]> Date: Thu May 18 01:45:06 2017 -0400 Match upstream source -- merge conflict didn't work out properly re-extract conflicting files, pointed out by dpkg-source, on top of the current files. --- src/AS_global.C | 1 - src/bogart/AS_BAT_BestOverlapGraph.C | 2 - src/overlapInCore/overlapPair.C | 10 +-- src/pipelines/canu/Defaults.pm | 162 ----------------------------------- src/stores/ovStore.H | 6 -- 5 files changed, 5 insertions(+), 176 deletions(-) diff --git a/src/AS_global.C b/src/AS_global.C index d7aefbb..0b9304f 100644 --- a/src/AS_global.C +++ b/src/AS_global.C @@ -105,7 +105,6 @@ AS_configure(int argc, char **argv) { AS_UTL_installCrashCatcher(argv[0]); - // // Et cetera. // diff --git a/src/bogart/AS_BAT_BestOverlapGraph.C b/src/bogart/AS_BAT_BestOverlapGraph.C index 60e62e7..6030cd7 100644 --- a/src/bogart/AS_BAT_BestOverlapGraph.C +++ b/src/bogart/AS_BAT_BestOverlapGraph.C @@ -117,8 +117,6 @@ BestOverlapGraph::removeHighErrorBestEdges(void) { uint32 numThreads = omp_get_max_threads(); uint32 blockSize = (fiLimit < 100 * numThreads) ? numThreads : fiLimit / 99; - writeStatus("BestOverlapGraph()-- analyzing best edges to find useful edge error rate\n"); - stdDev<double> edgeStats; // Find the overlap for every best edge. diff --git a/src/overlapInCore/overlapPair.C b/src/overlapInCore/overlapPair.C index 3dce0d0..63571ea 100644 --- a/src/overlapInCore/overlapPair.C +++ b/src/overlapInCore/overlapPair.C @@ -802,12 +802,12 @@ 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; diff --git a/src/pipelines/canu/Defaults.pm b/src/pipelines/canu/Defaults.pm index c7a3df3..6e91966 100644 --- a/src/pipelines/canu/Defaults.pm +++ b/src/pipelines/canu/Defaults.pm @@ -1176,168 +1176,6 @@ sub checkGnuplot () { -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 checkParameters () { # diff --git a/src/stores/ovStore.H b/src/stores/ovStore.H index dfec980..fdaee47 100644 --- a/src/stores/ovStore.H +++ b/src/stores/ovStore.H @@ -329,12 +329,6 @@ public: return(new ovStoreHistogram(_storePath)); }; - // Return the statistics associated with this store - - ovStoreHistogram *getHistogram(void) { - return(new ovStoreHistogram(_gkp, _storePath)); - }; - private: char _storePath[FILENAME_MAX]; -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/canu.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
