Math::Random is in package libmath-random-perl which is

Last-Update: Mon, 09 Jan 2017 11:13:13 +0100

unfortunately in non-free thus we can not use it for testing while building
this package.  Thus the occurrences of references and the surrounding code
is removed here.

Gbp-Pq: Name skip_test_requiring_non-free_libmath-random-perl.patch

2 files changed, 4 insertions, 120 deletions

diff --git a/Makefile b/Makefile
index 30887fb..b7753ab 100644
--- a/Makefile
+++ b/Makefile
@@ -527,12 +527,12 @@ install: all
 	done
 
 .PHONY: simple-test
-simple-test: perl-deps both both-debug both-sanitized
+simple-test: all
 	eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
 	sh ./scripts/test/simple_tests.sh
 
 .PHONY: random-test
-random-test: all perl-deps
+random-test: all
 	eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
 	sh ./scripts/sim/run.sh $(if $(NUM_CORES), $(NUM_CORES), 2)
 
@@ -543,8 +543,7 @@ perl-deps:
 	fi
 	DL=$$( ( which wget >/dev/null 2>&1 && echo "wget --no-check-certificate -O-" ) || echo "curl -L") ; \
 	$$DL http://cpanmin.us | perl - -l $(CURDIR)/.tmp App::cpanminus local::lib ; \
-	eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
-	$(CURDIR)/.tmp/bin/cpanm --force File::Which Math::Random Clone Test::Deep Sys::Info ; \
+	eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` 
 
 .PHONY: static-libs
 static-libs:
@@ -601,7 +600,7 @@ sra-deps:
 	 fi ;
 
 .PHONY: test
-test: simple-test random-test
+test: simple-test
 
 .PHONY: clean
 clean:
diff --git a/example/reads/simulate.pl b/example/reads/simulate.pl
index cdf7c51..ac80c04 100644
--- a/example/reads/simulate.pl
+++ b/example/reads/simulate.pl
@@ -33,7 +33,6 @@
 use strict;
 use warnings;
 use Carp;
-use Math::Random qw(random_normal random_exponential);
 use Getopt::Long;
 use List::Util qw(max min);
 
@@ -105,7 +104,6 @@ $rdlen_min = $rdlen_min || 40;    # min read length (added to exponential draw)
 $frag_av   = $frag_av   || 250;   # mean fragment len
 $frag_sd   = $frag_sd   || 45;    # s.d. when drawing frag len from normal dist
 my @fraglens  = ();     # fragment lengths (for paired)
-my @readlens  = ();     # read/end lengths
 
 if($long) {
 	$nreads = 6000;
@@ -134,77 +132,15 @@ for(0..length($rf)-1) {
 }
 
 print STDERR "Adding microindels...\n";
-my $microgap = 0;
-{
-	my $newrf = "";
-	my $nins = int(length($rf) * 0.0005 + 0.5);
-	my $ndel = int(length($rf) * 0.0005 + 0.5);
-	$microgap = $nins + $ndel;
-	my %indel = ();
-	for(1..$nins) {
-		my $off = int(rand(length($rf)));
-		$indel{$off}{ty} = "ins";
-		$indel{$off}{len} = int(random_exponential(1, 3))+1;
-	}
-	for(1..$ndel) {
-		my $off = int(rand(length($rf)));
-		$indel{$off}{ty} = "del";
-		$indel{$off}{len} = int(random_exponential(1, 3))+1;
-	}
-	my $lasti = 0;
-	for my $rfi (sort {$a <=> $b} keys %indel) {
-		if($rfi > $lasti) {
-			$newrf .= substr($rf, $lasti, $rfi - $lasti);
-			$lasti = $rfi;
-		}
-		if($indel{$rfi}{ty} eq "ins") {
-			$newrf .= rand_dna($indel{$rfi}{len});
-		} else {
-			$lasti += $indel{$rfi}{len};
-		}
-	}
-	if($lasti < length($rf)-1) {
-		$newrf .= substr($rf, $lasti, length($rf) - $lasti - 1);
-	}
-	$rf = $newrf;
-}
 
 print STDERR "Adding larger rearrangements...\n";
-my $nrearr = int(random_exponential(1, 3)+1);
-for(0..$nrearr) {
-	my $break = int(rand(length($rf)));
-	my $before = substr($rf, 0, $break);
-	my $after = substr($rf, $break);
-	$after = revcomp($after) if int(rand()) == 0;
-	$rf = $after.$before;
-}
 
 print STDERR "Added $nsnp SNPs\n";
-print STDERR "Added $microgap Microindels\n";
-print STDERR "Added $nrearr Rearrangements\n";
 
 #
 # Simulate reads
 #
 
-print STDERR "Picking read and fragment lengths...\n";
-# Pick random read lengths
-if(defined($rdlen_exact)) {
-	@readlens = ($rdlen_exact) x ($nreads * ($paired ? 2 : 1));
-} else {
-	@readlens = random_exponential($nreads * ($paired ? 2 : 1), $rdlen_av);
-	@readlens = map int, @readlens;
-	@readlens = map { int($_ + $rdlen_min) } @readlens;
-}
-if($paired) {
-	# Pick random fragment and read lengths
-	@fraglens = random_normal($nreads, $frag_av, $frag_sd);
-	@fraglens = map int, @fraglens;
-	for(my $i = 0; $i < scalar(@readlens); $i += 2) {
-		$fraglens[$i/2] = max($fraglens[$i/2], $readlens[$i] + $readlens[$i+1]);
-	}
-}
-
 sub rand_quals($) {
 	my $ret = "";
 	my $upper = (rand() < 0.2 ? 11 : 40);
@@ -259,61 +195,10 @@ if($paired) {
 		}
 		# Possibly reverse complement
 		$fstr = revcomp($fstr) if (int(rand(2)) == 0);
-		# Get reads 1 and 2
-		my $rdlen1 = min($readlens[2*$i], $flen);
-		my $rdlen2 = min($readlens[2*$i+1], $flen);
-		my $rd1 = substr($fstr, 0, $rdlen1);
-		my $rd2 = substr($fstr, length($fstr)-$rdlen2);
-		length($rd2) == $rdlen2 || die "Got ".length($rd2)." expected $rdlen2";
-		# Reverse complement 2 to simulate --fr orientation
-		$rd2 = revcomp($rd2);
-		# Generate random quality values
-		my $qu1 = rand_quals($rdlen1);
-		$rd1 = add_seq_errs($rd1, $qu1);
-		length($rd1) == length($qu1) || die;
-		my $qu2 = rand_quals($rdlen2);
-		$rd2 = add_seq_errs($rd2, $qu2);
-		length($rd2) == length($qu2) || die;
-		# Print
-		print RD1 "\@r".($i+1)."\n$rd1\n+\n$qu1\n";
-		print RD2 "\@r".($i+1)."\n$rd2\n+\n$qu2\n";
 	}
 	close(RD1);
 	close(RD2);
 	print STDERR "Made pairs: reads_1.fq/reads_2.fq\n";
-} else {
-	open(RD1, ">${prefix}.fq") || die;
-	for(my $i = 0; $i < scalar(@readlens); $i++) {
-		# Extract fragment
-		my $rdlen = $readlens[$i];
-		my $off = int(rand($rflen - ($rdlen-1)));
-		my $rd = substr($rf, $off, $rdlen);
-		# Check if it has too many Ns
-		my %ccnt = ();
-		for my $j (1..$rdlen) {
-			my $c = uc substr($rd, $j, 1);
-			$ccnt{tot}++;
-			$ccnt{non_acgt}++ if ($c ne "A" && $c ne "C" && $c ne "G" && $c ne "T");
-			$ccnt{$c}++;
-		}
-		# Skip if it has >10% Ns
-		if(1.0 * $ccnt{non_acgt} / $ccnt{tot} > 0.10) {
-			$i--;
-			next;
-		}
-		length($rd) == $rdlen || die;
-		# Possibly reverse complement
-		$rd = revcomp($rd) if int(rand(2)) == 0;
-		# Generate random quality values
-		my $qu = rand_quals($rdlen);
-		length($rd) == length($qu) || die "length(seq) = ".length($rd).", length(qual) = ".length($qu);
-		$rd = add_seq_errs($rd, $qu);
-		length($rd) == length($qu) || die "length(seq) = ".length($rd).", length(qual) = ".length($qu);
-		# Print
-		print RD1 "\@r".($i+1)."\n$rd\n+\n$qu\n";
-	}
-	close(RD1);
-	print STDERR "Made unpaired reads: $prefix.fq\n";
 }
 
 print STDERR "DONE\n";