From: Heng Li <lh3@live.co.uk>
Date: Thu, 14 Oct 2010 03:32:12 +0000 (+0000)
Subject: improve the LD statistics
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=30d422313b3d1c4586c8c4098e3e6c3777dc521e

improve the LD statistics
---

diff --git a/bcftools/call1.c b/bcftools/call1.c
index 68b24f0..2b28452 100644
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -348,7 +348,7 @@ int bcfview(int argc, char *argv[])
 				kstring_t s;
 				s.m = s.l = 0; s.s = 0;
 				if (*b->info) kputc(';', &s);
-				ksprintf(&s, "NEIR=%.3lf", r2);
+				ksprintf(&s, "NEIR=%.3lf;NEIF=%.3lf,%.3lf", r2, f[0]+f[2], f[0]+f[1]);
 				bcf_append_info(b, s.s, s.l);
 				free(s.s);
 			}
diff --git a/bcftools/ld.c b/bcftools/ld.c
index 01145b8..aa7ec07 100644
--- a/bcftools/ld.c
+++ b/bcftools/ld.c
@@ -90,7 +90,7 @@ double bcf_ld_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4])
 	{ // calculate r^2
 		double p[2], q[2], D;
 		p[0] = f[0] + f[1]; q[0] = 1 - p[0];
-		p[1] = f[2] + f[3]; q[1] = 1 - p[1];
+		p[1] = f[0] + f[2]; q[1] = 1 - p[1];
 		D = f[0] * f[3] - f[1] * f[2];
 		r = sqrt(D * D / (p[0] * p[1] * q[0] * q[1]));
 		// fprintf(stderr, "R(%lf,%lf,%lf,%lf)=%lf\n", f[0], f[1], f[2], f[3], r2);
diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl
index 4caa846..d0b7971 100755
--- a/bcftools/vcfutils.pl
+++ b/bcftools/vcfutils.pl
@@ -104,38 +104,25 @@ sub fillac {
 }
 
 sub ldstats {
-  my %opts = (s=>0.01);
-  getopts('ps:', \%opts);
-  die("Usage: vcfutils.pl ldstats [-s $opts{s}] <in.vcf>\n") if (@ARGV == 0 && -t STDIN);
-  my ($lastchr, $lastpos) = ('', 0);
-  my @a;
-  my $is_print = defined($opts{p})? 1 : 0;
+  my %opts = (t=>0.9);
+  getopts('t:', \%opts);
+  die("Usage: vcfutils.pl ldstats [-t $opts{t}] <in.vcf>\n") if (@ARGV == 0 && -t STDIN);
+  my $cutoff = $opts{t};
+  my ($last, $lastchr) = (0x7fffffff, '');
+  my ($x, $y, $n) = (0, 0, 0);
   while (<>) {
-	next if (/^#/);
-	my @t = split;
-	if ($t[0] ne $lastchr) {
-	  $lastchr = $t[0];
-	} elsif (/NEIR=([\d\.]+)/) {
-	  push(@a, [$t[1] - $lastpos, $1, $t[1]]);
-	}
-	$lastpos = $t[1];
-  }
-  my $max = 1000000000;
-  push(@a, [$max, 0, 0]); # end marker
-  @a = sort {$a->[0]<=>$b->[0]} @a;
-  my $next = $opts{s};
-  my $last = $a[0];
-  my @c = (0, 0, 0, 0);
-  for my $p (@a) {
-	print STDERR "$p->[0]\t$p->[1]\t$p->[2]\n" if ($is_print);
-	if ($p->[0] == $max || ($p->[0] != $last && $c[0]/@a > $next)) {
-	  printf("%d\t%.2f\t%.4f\n", $c[1], $c[2]/$c[1], $c[3]/$c[1]);
-	  $c[1] = $c[2] = $c[3] = 0;
-	  $next = $c[0]/@a + $opts{s};
+	if (/^([^#\s]+)\s(\d+)/) {
+	  my ($chr, $pos) = ($1, $2);
+	  if (/NEIR=([\d\.]+)/) {
+		++$n;
+		++$y, $x += $pos - $last if ($lastchr eq $chr && $pos > $last && $1 > $cutoff);
+	  }
+	  $last = $pos; $lastchr = $chr;
 	}
-	++$c[0]; ++$c[1]; $c[2] += $p->[0]; $c[3] += $p->[1];
-	$last = $p->[0];
   }
+  print "Number of SNP intervals in strong LD (r > $opts{t}): $y\n";
+  print "Fraction: ", $y/$n, "\n";
+  print "Length: $x\n";
 }
 
 sub qstats {