[med-svn] [canu] 02/04: Match upstream source -- merge conflict didn't work out properly
Afif Elghraoui
afif at moszumanska.debian.org
Thu May 18 06:00:48 UTC 2017
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afif pushed a commit to branch master
in repository canu.
commit 744a6d9dabbc33bb666ffc69ca3f00ff122a1f8e
Author: Afif Elghraoui <afif at debian.org>
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];
--
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