use warnings;
use Getopt::Std;
-my $version = '0.2.3';
+my $version = '0.3.0';
&usage if (@ARGV < 1);
my $command = shift(@ARGV);
-my %func = (snpFilter=>\&snpFilter, indelFilter=>\&indelFilter, showALEN=>\&showALEN, pileup2fq=>\&pileup2fq);
+my %func = (showALEN=>\&showALEN, pileup2fq=>\&pileup2fq, varFilter=>\&varFilter);
die("Unknown command \"$command\".\n") if (!defined($func{$command}));
&{$func{$command}};
}
#
-# indelFilter
+# varFilter
#
-sub indelFilter {
- my %opts = (D=>100, m=>10, r=>undef, s=>100);
- getopts('D:m:rs:', \%opts); # -s for scaling factor in score calculation
-
+sub varFilter {
+ my %opts = (d=>3, D=>100, l=>30, Q=>25, G=>20, s=>100, w=>10, W=>10, N=>2);
+ getopts('d:D:l:Q:w:W:N:G:', \%opts);
die(qq/
-Usage: samtools.pl indelFilter [options] <in.indel>\n
-Options: -D INT maximum read depth [$opts{D}]
- -m INT minimum distance between two adjacent indels [$opts{m}]
-\n/) if (@ARGV == 0 && -t STDIN);
-
- my (@arr1, @arr2);
- my ($curr, $last) = (\@arr1, \@arr2);
- my $is_ref = defined($opts{r})? 1 : 0;
+Usage: samtools.pl varFilter [options] <in.cns-pileup>
+
+Options: -Q INT minimum RMS mapping quality [$opts{Q}]
+ -d INT minimum read depth [$opts{d}]
+ -D INT maximum read depth [$opts{D}]
+
+ -G INT min indel score for nearby SNP filtering [$opts{G}]
+ -w INT SNP within INT bp around a gap to be filtered [$opts{w}]
+
+ -W INT window size for filtering dense SNPs [$opts{W}]
+ -N INT max number of SNPs in a window [$opts{W}]
+
+ -l INT window size for filtering adjacent gaps [$opts{l}]\n
+/) if (@ARGV == 0 && -t STDIN);
+
+ # calculate the window size
+ my ($ol, $ow, $oW) = ($opts{l}, $opts{w}, $opts{W});
+ my $max_dist = $ol > $ow? $ol : $ow;
+ $max_dist = $oW if ($max_dist < $oW);
+ # the core loop
+ my @staging; # (indel_filtering_score, flt_tag)
while (<>) {
my @t = split;
- next if ($t[2] ne '*');
- if (!$is_ref) {
- next if ($t[3] eq '*/*');
- next if ($t[5] == 0);
- }
- next if ($t[7] > $opts{D});
- # calculate indel score
- my $score = $t[5];
- $score += $opts{s} * $t[10] if ($t[8] ne '*');
- $score += $opts{s} * $t[11] if ($t[9] ne '*');
- @$curr = ($t[0], $t[1], $score, $_);
- my $do_swap = 1;
- if (defined $last->[0]) {
- if ($curr->[0] eq $last->[0] && $last->[1] + $opts{m} > $curr->[1]) {
- $do_swap = 0 if ($last->[2] > $curr->[2]);
- } else { # then print
- print $last->[3];
+ next if ($t[2] eq $t[3] || $t[3] eq '*/*'); # skip non-var sites
+ # clear the out-of-range elements
+ while (@staging) {
+ if ($staging[0][2] ne $t[0] || $staging[0][3] + $max_dist < $t[1]) {
+ varFilter_aux(shift @staging);
+ } else {
+ last;
}
}
- if ($do_swap) {
- my $tmp = $curr; $curr = $last; $last = $tmp;
+ my ($flt, $score) = (0, -1);
+ # first a simple filter
+ if ($t[6] < $opts{Q}) {
+ $flt = 1;
+ } elsif ($t[7] < $opts{d}) {
+ $flt = 2;
+ } elsif ($t[7] > $opts{D}) {
+ $flt = 3;
}
- }
- print $last->[3] if (defined $last->[0]);
-}
-
-#
-# snpFilter
-#
-
-sub snpFilter {
- my %opts = (f=>'', Q=>40, d=>3, w=>10, D=>0, N=>2, W=>10, q=>20, s=>50);
- getopts('f:s:w:q:Q:d:D:W:N:', \%opts);
- die(qq{
-Usage: samtools.pl snpFilter [options] <cns2snp.snp>
-
-Options: -d INT minimum depth to call a SNP [$opts{d}]
- -D INT maximum depth, 0 to ignore [$opts{D}]
- -Q INT required max mapping quality of the reads covering the SNP [$opts{Q}]
- -q INT minimum SNP quality [$opts{q}]
-
- -f FILE filtered samtools indels [null]
- -s INT minimum samtols indel score [$opts{s}]
- -w INT SNP within INT bp around an indel to be filtered [$opts{w}]
-
- -W INT window size for filtering dense SNPs [$opts{W}]
- -N INT maximum number of SNPs in a window [$opts{N}]
-\n}) unless (@ARGV);
- my (%hash, $fh);
- my $skip = $opts{w};
- $opts{D} = 100000000 if ($opts{D} == 0);
- if ($opts{f}) { # filtered samtools indel
- my $n = 0;
- open($fh, $opts{f}) || die;
- while (<$fh>) {
- my @t = split;
- next if ($t[2] ne '*' || $t[3] eq '*/*' || $t[5] < $opts{s});
- for (my $x = $t[1] - $skip + 1; $x < $t[1] + $skip; ++$x) {
- $hash{$t[0],$x} = 1;
+ # site dependent filters
+ if ($flt == 0) {
+ if ($t[2] eq '*') { # an indel
+ # filtering SNPs
+ if ($t[5] >= $opts{G}) {
+ for my $x (@staging) {
+ next if ($x->[0] >= 0 || $x->[3] + $ow < $t[1]);
+ $x->[1] = 5 if ($x->[1] == 0);
+ }
+ }
+ # calculate the filtering score (different from indel quality)
+ $score = $t[5];
+ $score += $opts{s} * $t[10] if ($t[8] ne '*');
+ $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 < $t[1]);
+ if ($x->[0] < $score) {
+ $x->[1] = 6;
+ } else {
+ $flt = 6; last;
+ }
+ }
+ } else { # a SNP
+ # 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 || $x->[1] == 5));
+ }
+ # filtering is necessary
+ if ($k > $opts{N}) {
+ $flt = 4;
+ for my $x (@staging) {
+ $x->[1] = 4 if ($x->[0] < 0 && $x->[3] + $oW >= $t[1] && $x->[1] == 0);
+ }
+ } else { # then check gap filter
+ for my $x (@staging) {
+ next if ($x->[0] < 0 || $x->[3] + $ow < $t[1]);
+ if ($x->[0] >= $opts{G}) {
+ $flt = 5; last;
+ }
+ }
+ }
}
}
- close($fh);
+ push(@staging, [$score, $flt, @t]);
}
- my (@last, $last_chr);
- $last_chr = '';
- while (<>) {
- my @t = split;
- next if ($t[2] eq '*' || $hash{$t[0],$t[1]});
- next if ($t[2] eq $t[3]);
- my $is_good = ($t[7] >= $opts{d} && $t[7] <= $opts{D} && $t[6] >= $opts{Q} && $t[5] >= $opts{q})? 1 : 0;
- next unless ($is_good); # drop
- if ($t[0] ne $last_chr) { # a different chr, print
- map { print $_->{L} if ($_->{F}) } @last;
- @last = ();
- $last_chr = $t[0];
- }
- # The following block implemented by Nathans Weeks.
- push(@last, {L => $_, X => $t[1], F => 1}); # Enqueue current SNP
- if ($#last == $opts{N}) { # number of SNPs in queue is N+1
- if ($last[$#last]{X} - $last[0]{X} < $opts{W}) { # if all within window W
- map {$_->{F} = 0} @last; # all SNPs in the window of size W are "bad"
- }
- print STDOUT $last[0]{L} if ($last[0]{F}); # print first SNP if good
- shift @last # dequeue first SNP
- }
+ # output the last few elements in the staging list
+ while (@staging) {
+ varFilter_aux(shift @staging);
}
- # print the last few lines if applicable
- map { print $_->{L} if ($_->{F}) } @last;
}
+sub varFilter_aux {
+ my $first = shift;
+ if ($first->[1] == 0) {
+ print join("\t", @$first[2 .. @$first-1]), "\n";
+ } else {
+ print STDERR join("\t", substr("UQdDWGgX", $first->[1], 1), @$first[2 .. @$first-1]), "\n";
+ }
+}
+
+#
+# pileup2fq
+#
+
sub pileup2fq {
my %opts = (d=>3, D=>255, Q=>25, G=>50, l=>10);
getopts('d:D:Q:G:l:', \%opts);
-D INT maximum depth [$opts{D}]
-Q INT min RMS mapQ [$opts{Q}]
-G INT minimum indel score [$opts{G}]
- -l INT indel filter winsize [$opts{l}]
+ -l INT indel filter winsize [$opts{l}]\n
/) if (@ARGV == 0 && -t STDIN);
my ($last_chr, $seq, $qual, @gaps, $last_pos);
Version: $version
Contact: Heng Li <lh3\@sanger.ac.uk>\n
Usage: samtools.pl <command> [<arguments>]\n
-Command: indelFilter filter indels generated by `pileup -c'
- snpFilter filter SNPs generated by `pileup -c'
+Command: varFilter filtering SNPs and short indels
pileup2fq generate fastq from `pileup -c'
showALEN print alignment length (ALEN) following CIGAR
\n/);
projects / samtools.git / commitdiff