use warnings;
use Getopt::Std;
-my $version = '0.2.1';
+my $version = '0.3.2 (r321)';
&usage if (@ARGV < 1);
my $command = shift(@ARGV);
-my %func = (snpFilter=>\&snpFilter, indelFilter=>\&indelFilter, showALEN=>\&showALEN);
+my %func = (showALEN=>\&showALEN, pileup2fq=>\&pileup2fq, varFilter=>\&varFilter, unique=>\&unique);
die("Unknown command \"$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, q=>10, 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}]
+Usage: samtools.pl varFilter [options] <in.cns-pileup>
+
+Options: -Q INT minimum RMS mapping quality for SNPs [$opts{Q}]
+ -q INT minimum RMS mapping quality for gaps [$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{N}]
+
+ -l INT window size for filtering adjacent gaps [$opts{l}]
+
+ -p print filtered variants
\n/) if (@ARGV == 0 && -t STDIN);
- my (@arr1, @arr2);
- my ($curr, $last) = (\@arr1, \@arr2);
- my $is_ref = defined($opts{r})? 1 : 0;
+ # 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), $opts{p}); # calling a function is a bit slower, not much
}
- next if ($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 $last->[3];
- }
+ my ($flt, $score) = (0, -1);
+ # first a simple filter
+ if ($t[7] < $opts{d}) {
+ $flt = 2;
+ } elsif ($t[7] > $opts{D}) {
+ $flt = 3;
}
- if ($do_swap) {
- my $tmp = $curr; $curr = $last; $last = $tmp;
+ # site dependent filters
+ if ($flt == 0) {
+ if ($t[2] eq '*') { # an indel
+ $flt = 1 if ($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]);
+ $x->[1] = 5 if ($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
+ $flt = 1 if ($t[6] < $opts{Q});
+ # 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}) {
+ $flt = 5; last;
+ }
+ }
+ }
+ }
}
+ push(@staging, [$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";
}
- print $last->[3] if (defined $last->[0]);
}
#
-# snpFilter
+# pileup2fq
#
-sub snpFilter {
- my %opts = (f=>'', Q=>40, d=>3, w=>10, D=>0, N=>2, W=>10, q=>20, s=>50);
- getopts('f:s:w:q:Q:d:D:W:N:', \%opts);
- die(qq{
-Usage: samtools.pl snpFilter [options] <cns2snp.snp>
-
-Options: -d INT minimum depth to call a SNP [$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],$x} = 1;
- }
- }
- close($fh);
- }
- my (@last, $last_chr);
+sub pileup2fq {
+ my %opts = (d=>3, D=>255, Q=>25, G=>25, l=>10);
+ getopts('d:D:Q:G:l:', \%opts);
+ die(qq/
+Usage: samtools.pl pileup2fq [options] <in.cns-pileup>
+
+Options: -d INT minimum depth [$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};
+
$last_chr = '';
while (<>) {
my @t = split;
- next if ($t[2] eq '*' || $hash{$t[0],$t[1]});
- 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 = ();
+ 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 = ();
}
- # 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
+ 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];
}
- # print the last few lines if applicable
- map { print $_->{L} if ($_->{F}) } @last;
+ &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 + $l));
+ }
+}
+
+sub p2q_print_str {
+ my ($s) = @_;
+ my $l = length($$s);
+ for (my $i = 0; $i < $l; $i += 60) {
+ print substr($$s, $i, 60), "\n";
+ }
+}
+
+#
+# unique
+#
+
+sub unique {
+ my %opts = (f=>5.0, q=>5, r=>2, a=>1, b=>3);
+ getopts('f:', \%opts);
+ die("Usage: samtools.pl unique [-f $opts{f}] <in.sam>\n") if (@ARGV == 0 && -t STDIN);
+ my $last = '';
+ my @a;
+ while (<>) {
+ my $score = -1;
+ print $_ if (/^\@/);
+ $score = $1 if (/AS:i:(\d+)/);
+ my @t = split("\t");
+ if ($score < 0) { # AS tag is unavailable
+ my $cigar = $t[5];
+ my ($mm, $go, $ge) = (0, 0, 0);
+ $cigar =~ s/(\d+)[ID]/++$go,$ge+=$1/eg;
+ $cigar = $t[5];
+ $cigar =~ s/(\d+)M/$mm+=$1/eg;
+ $score = $mm * $opts{a} - $go * $opts{q} - $ge * $opts{r}; # no mismatches...
+ }
+ $score = 0 if ($score < 0);
+ if ($t[0] ne $last) {
+ &unique_aux(\@a, $opts{f}) if (@a);
+ $last = $t[0];
+ }
+ push(@a, [$score, \@t]);
+ }
+ &unique_aux(\@a, $opts{f}) if (@a);
+}
+
+sub unique_aux {
+ my ($a, $fac) = @_;
+ my ($max, $max2, $max_i) = (-1, -1, -1);
+ for (my $i = 0; $i < @$a; ++$i) {
+ if ($a->[$i][0] > $max) {
+ $max2 = $max; $max = $a->[$i][0]; $max_i = $i;
+ } elsif ($a->[$i][0] > $max2) {
+ $max2 = $a->[$i][0];
+ }
+ }
+ my $q = int($fac * ($max - $max2) + .499);
+ $a->[$max_i][1][4] = $q < 250? $q : 250;
+ print join("\t", @{$a->[$max_i][1]});
+ @$a = ();
+}
+
+#
+# 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'
- 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 / blobdiff