my $command = shift(@ARGV);
my %func = (showALEN=>\&showALEN, pileup2fq=>\&pileup2fq, varFilter=>\&varFilter,
- unique=>\&unique, uniqcmp=>\&uniqcmp, sra2hdr=>\&sra2hdr);
+ unique=>\&unique, uniqcmp=>\&uniqcmp, sra2hdr=>\&sra2hdr, sam2fq=>\&sam2fq);
die("Unknown command \"$command\".\n") if (!defined($func{$command}));
&{$func{$command}};
# G close to a high-quality indel (SNP only)
# Q low RMS mapping quality (SNP only)
# g close to another indel with higher quality (indel only)
+# s low SNP quality (SNP only)
+# i low indel quality (indel only)
sub varFilter {
- my %opts = (d=>3, D=>100, l=>30, Q=>25, q=>10, G=>25, s=>100, w=>10, W=>10, N=>2, p=>undef);
- getopts('pq:d:D:l:Q:w:W:N:G:', \%opts);
+ my %opts = (d=>3, D=>100, l=>30, Q=>25, q=>10, G=>25, s=>100, w=>10, W=>10, N=>2, p=>undef, S=>'', i=>'');
+ getopts('pq:d:D:l:Q:w:W:N:G:S:i:', \%opts);
die(qq/
Usage: samtools.pl varFilter [options] <in.cns-pileup>
-q INT minimum RMS mapping quality for gaps [$opts{q}]
-d INT minimum read depth [$opts{d}]
-D INT maximum read depth [$opts{D}]
+ -S INT minimum SNP quality [$opts{S}]
+ -i INT minimum indel quality [$opts{i}]
-G INT min indel score for nearby SNP filtering [$opts{G}]
-w INT SNP within INT bp around a gap to be filtered [$opts{w}]
next if (uc($t[2]) eq uc($t[3]) || $t[3] eq '*/*'); # skip non-var sites
# clear the out-of-range elements
while (@staging) {
- last if ($staging[0][2] eq $t[0] && $staging[0][3] + $max_dist >= $t[1]);
+ # Still on the same chromosome and the first element's window still affects this position?
+ last if ($staging[0][3] eq $t[0] && $staging[0][4] + $staging[0][2] + $max_dist >= $t[1]);
varFilter_aux(shift(@staging), $opts{p}); # calling a function is a bit slower, not much
}
my ($flt, $score) = (0, -1);
} elsif ($t[7] > $opts{D}) {
$flt = 3;
}
+ if ($t[2] eq '*') { # an indel
+ if ($opts{i} && $opts{i}>$t[5]) { $flt = 8; }
+ }
+ elsif ($opts{S} && $opts{S}>$t[5]) { $flt = 7; } # SNP
+
# site dependent filters
+ my $len=0;
if ($flt == 0) {
if ($t[2] eq '*') { # an indel
+
+ # If deletion, remember the length of the deletion
+ my ($a,$b) = split(m{/},$t[3]);
+ my $alen = length($a) - 1;
+ my $blen = length($b) - 1;
+ if ( $alen>$blen )
+ {
+ if ( substr($a,0,1) eq '-' ) { $len=$alen; }
+ }
+ elsif ( substr($b,0,1) eq '-' ) { $len=$blen; }
+
$flt = 1 if ($t[6] < $opts{q});
# filtering SNPs
if ($t[5] >= $opts{G}) {
for my $x (@staging) {
- next if ($x->[0] >= 0 || $x->[3] + $ow < $t[1]);
+ # Is it a SNP and is it outside the SNP filter window?
+ next if ($x->[0] >= 0 || $x->[4] + $x->[2] + $ow < $t[1]);
$x->[1] = 5 if ($x->[1] == 0);
}
}
$score += $opts{s} * $t[11] if ($t[9] ne '*');
# check the staging list for indel filtering
for my $x (@staging) {
- next if ($x->[0] < 0 || $x->[3] + $ol < $t[1]);
+ # Is it a SNP and is it outside the gap filter window
+ next if ($x->[0] < 0 || $x->[4] + $x->[2] + $ol < $t[1]);
if ($x->[0] < $score) {
$x->[1] = 6;
} else {
# check adjacent SNPs
my $k = 1;
for my $x (@staging) {
- ++$k if ($x->[0] < 0 && $x->[3] + $oW >= $t[1] && ($x->[1] == 0 || $x->[1] == 4 || $x->[1] == 5));
+ ++$k if ($x->[0] < 0 && $x->[4] + $x->[2] + $oW >= $t[1] && ($x->[1] == 0 || $x->[1] == 4 || $x->[1] == 5));
}
# filtering is necessary
if ($k > $opts{N}) {
$flt = 4;
for my $x (@staging) {
- $x->[1] = 4 if ($x->[0] < 0 && $x->[3] + $oW >= $t[1] && $x->[1] == 0);
+ $x->[1] = 4 if ($x->[0] < 0 && $x->[4] + $x->[2] + $oW >= $t[1] && $x->[1] == 0);
}
} else { # then check gap filter
for my $x (@staging) {
- next if ($x->[0] < 0 || $x->[3] + $ow < $t[1]);
+ next if ($x->[0] < 0 || $x->[4] + $x->[2] + $ow < $t[1]);
if ($x->[0] >= $opts{G}) {
$flt = 5; last;
}
}
}
}
- push(@staging, [$score, $flt, @t]);
+ push(@staging, [$score, $flt, $len, @t]);
}
# output the last few elements in the staging list
while (@staging) {
sub varFilter_aux {
my ($first, $is_print) = @_;
if ($first->[1] == 0) {
- print join("\t", @$first[2 .. @$first-1]), "\n";
+ print join("\t", @$first[3 .. @$first-1]), "\n";
} elsif ($is_print) {
- print STDERR join("\t", substr("UQdDWGgX", $first->[1], 1), @$first[2 .. @$first-1]), "\n";
+ print STDERR join("\t", substr("UQdDWGgsiX", $first->[1], 1), @$first[3 .. @$first-1]), "\n";
}
}
}
}
+#
+# sam2fq
+#
+
+sub sam2fq {
+ my %opts = (n=>20, p=>'');
+ getopts('n:p:', \%opts);
+ die("Usage: samtools.pl sam2fq [-n 20] [-p <prefix>] <inp.sam>\n") if (@ARGV == 0 && -t STDIN);
+ if ($opts{p} && $opts{n} > 1) {
+ my $pre = $opts{p};
+ my @fh;
+ for (0 .. $opts{n}-1) {
+ open($fh[$_], sprintf("| gzip > $pre.%.3d.fq.gz", $_)) || die;
+ }
+ my $i = 0;
+ while (<>) {
+ next if (/^@/);
+ chomp;
+ my @t = split("\t");
+ next if ($t[9] eq '*');
+ my ($name, $seq, $qual);
+ if ($t[1] & 16) { # reverse strand
+ $seq = reverse($t[9]);
+ $qual = reverse($t[10]);
+ $seq =~ tr/ACGTacgt/TGCAtgca/;
+ } else {
+ ($seq, $qual) = @t[9,10];
+ }
+ $name = $t[0];
+ $name .= "/1" if ($t[1] & 0x40);
+ $name .= "/2" if ($t[1] & 0x80);
+ print {$fh[$i]} "\@$name\n$seq\n";
+ if ($qual ne '*') {
+ print {$fh[$i]} "+\n$qual\n";
+ }
+ $i = 0 if (++$i == $opts{n});
+ }
+ close($fh[$_]) for (0 .. $opts{n}-1);
+ } else {
+ die("To be implemented.\n");
+ }
+}
+
#
# sra2hdr
#
sub unique {
my %opts = (f=>250.0, q=>5, r=>2, a=>1, b=>3);
- getopts('Qf:q:r:a:b:', \%opts);
+ getopts('Qf:q:r:a:b:m', \%opts);
die("Usage: samtools.pl unique [-f $opts{f}] <in.sam>\n") if (@ARGV == 0 && -t STDIN);
my $last = '';
my $recal_Q = !defined($opts{Q});
+ my $multi_only = defined($opts{m});
my @a;
while (<>) {
my $score = -1;
}
$score = 1 if ($score < 1);
if ($t[0] ne $last) {
- &unique_aux(\@a, $opts{f}, $recal_Q) if (@a);
+ &unique_aux(\@a, $opts{f}, $recal_Q, $multi_only) if (@a);
$last = $t[0];
}
push(@a, [$score, \@t]);
}
- &unique_aux(\@a, $opts{f}, $recal_Q) if (@a);
+ &unique_aux(\@a, $opts{f}, $recal_Q, $multi_only) if (@a);
}
sub unique_aux {
- my ($a, $fac, $is_recal) = @_;
+ my ($a, $fac, $is_recal, $multi_only) = @_;
my ($max, $max2, $max_i) = (0, 0, -1);
for (my $i = 0; $i < @$a; ++$i) {
if ($a->[$i][0] > $max) {
}
}
if ($is_recal) {
- my $q = int($fac * ($max - $max2) / $max + .499);
- $q = 250 if ($q > 250);
- $a->[$max_i][1][4] = $q < 250? $q : 250;
+ if (!$multi_only || @$a > 1) {
+ my $q = int($fac * ($max - $max2) / $max + .499);
+ $q = 250 if ($q > 250);
+ $a->[$max_i][1][4] = $q < 250? $q : 250;
+ }
}
print join("\t", @{$a->[$max_i][1]});
@$a = ();
projects / samtools.git / blobdiff