use warnings;
use Getopt::Std;
-my $version = '0.1.1';
+my $version = '0.3.1';
&usage if (@ARGV < 1);
my $command = shift(@ARGV);
-my %func = (indelFilter=>\&indelFilter, showALEN=>\&showALEN);
+my %func = (showALEN=>\&showALEN, pileup2fq=>\&pileup2fq, varFilter=>\&varFilter);
die("Unknown command \"$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=>25, s=>100, w=>10, W=>10, N=>2, p=>undef);
+ getopts('pd: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}]
+
+ -p print filtered variants
+/) 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[2] eq $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]);
+ varFilter_aux(shift(@staging), $opts{p}); # calling a function is a bit slower, not much
+ }
+ my ($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}) {
+ $flt = 3;
}
- next if ($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 $last->[3];
+ # site dependent filters
+ if ($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}) {
+ $flt = 5; last;
+ }
+ }
+ }
}
}
- if ($do_swap) {
- my $tmp = $curr; $curr = $last; $last = $tmp;
+ push(@staging, [$score, $flt, @t]);
+ }
+ # output the last few elements in the staging list
+ while (@staging) {
+ varFilter_aux(shift @staging, $opts{p});
+ }
+}
+
+sub varFilter_aux {
+ my ($first, $is_print) = @_;
+ if ($first->[1] == 0) {
+ print join("\t", @$first[2 .. @$first-1]), "\n";
+ } elsif ($is_print) {
+ print STDERR join("\t", substr("UQdDWGgX", $first->[1], 1), @$first[2 .. @$first-1]), "\n";
+ }
+}
+
+#
+# pileup2fq
+#
+
+sub pileup2fq {
+ my %opts = (d=>3, D=>255, Q=>25, G=>25, l=>10);
+ getopts('d:D:Q:G:l:', \%opts);
+ die(qq/
+Usage: samtools.pl pileup2fq [options] <in.cns-pileup>
+
+Options: -d INT minimum depth [$opts{d}]
+ -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}]\n
+/) if (@ARGV == 0 && -t STDIN);
+
+ my ($last_chr, $seq, $qual, @gaps, $last_pos);
+ my $_Q = $opts{Q};
+ my $_d = $opts{d};
+ my $_D = $opts{D};
+
+ $last_chr = '';
+ while (<>) {
+ my @t = split;
+ if ($last_chr ne $t[0]) {
+ &p2q_post_process($last_chr, \$seq, \$qual, \@gaps, $opts{l}) if ($last_chr);
+ $last_chr = $t[0];
+ $last_pos = 0;
+ $seq = ''; $qual = '';
+ @gaps = ();
}
+ if ($t[1] - $last_pos != 1) {
+ $seq .= 'n' x ($t[1] - $last_pos - 1);
+ $qual .= '!' x ($t[1] - $last_pos - 1);
+ }
+ if ($t[2] eq '*') {
+ push(@gaps, $t[1]) if ($t[5] >= $opts{G});
+ } else {
+ $seq .= ($t[6] >= $_Q && $t[7] >= $_d && $t[7] <= $_D)? uc($t[3]) : lc($t[3]);
+ my $q = $t[4] + 33;
+ $q = 126 if ($q > 126);
+ $qual .= chr($q);
+ }
+ $last_pos = $t[1];
+ }
+ &p2q_post_process($last_chr, \$seq, \$qual, \@gaps, $opts{l});
+}
+
+sub p2q_post_process {
+ my ($chr, $seq, $qual, $gaps, $l) = @_;
+ &p2q_filter_gaps($seq, $gaps, $l);
+ print "\@$chr\n"; &p2q_print_str($seq);
+ print "+\n"; &p2q_print_str($qual);
+}
+
+sub p2q_filter_gaps {
+ my ($seq, $gaps, $l) = @_;
+ for my $g (@$gaps) {
+ my $x = $g > $l? $g - $l : 0;
+ substr($$seq, $x, $l + $l) = lc(substr($$seq, $x, $l + $l));
}
- print $last->[3] if (defined $last->[0]);
}
+sub p2q_print_str {
+ my ($s) = @_;
+ my $l = length($$s);
+ for (my $i = 0; $i < $l; $i += 60) {
+ print substr($$s, $i, 60), "\n";
+ }
+}
+
+#
+# Usage
+#
+
sub usage {
die(qq/
+Program: samtools.pl (helper script for SAMtools)
+Version: $version
+Contact: Heng Li <lh3\@sanger.ac.uk>\n
Usage: samtools.pl <command> [<arguments>]\n
-Command: indelFilter filter indels 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 / blobdiff