--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/samtools-0.1.19/misc/samtools.pl	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,528 @@
+#!/usr/bin/perl -w
+
+# Author: lh3
+
+use strict;
+use warnings;
+use Getopt::Std;
+
+my $version = '0.3.3';
+&usage if (@ARGV < 1);
+
+my $command = shift(@ARGV);
+my %func = (showALEN=>\&showALEN, pileup2fq=>\&pileup2fq, varFilter=>\&varFilter, plp2vcf=>\&plp2vcf,
+			unique=>\&unique, uniqcmp=>\&uniqcmp, sra2hdr=>\&sra2hdr, sam2fq=>\&sam2fq);
+
+die("Unknown command \"$command\".\n") if (!defined($func{$command}));
+&{$func{$command}};
+exit(0);
+
+#
+# showALEN
+#
+
+sub showALEN {
+  die(qq/Usage: samtools.pl showALEN <in.sam>\n/) if (@ARGV == 0 && -t STDIN);
+  while (<>) {
+	my @t = split;
+	next if (/^\@/ || @t < 11);
+	my $l = 0;
+	$_ = $t[5];
+	s/(\d+)[MI]/$l+=$1/eg;
+	print join("\t", @t[0..5]), "\t$l\t", join("\t", @t[6..$#t]), "\n";
+  }
+}
+
+#
+# varFilter
+#
+
+#
+# Filtration code:
+#
+# d low depth
+# D high depth
+# W too many SNPs in a window (SNP only)
+# G close to a high-quality indel (SNP only)
+# Q low RMS mapping quality (SNP only)
+# g close to another indel with higher quality (indel only)
+# s low SNP quality (SNP only)
+# i low indel quality (indel only)
+
+sub varFilter {
+  my %opts = (d=>3, D=>100, l=>30, Q=>25, q=>10, G=>25, s=>100, w=>10, W=>10, N=>2, p=>undef, S=>'', i=>'');
+  getopts('pq:d:D:l:Q:w:W:N:G:S:i:', \%opts);
+  die(qq/
+Usage:   samtools.pl varFilter [options] <in.cns-pileup>
+
+Options: -Q INT    minimum RMS mapping quality for SNPs [$opts{Q}]
+         -q INT    minimum RMS mapping quality for gaps [$opts{q}]
+         -d INT    minimum read depth [$opts{d}]
+         -D INT    maximum read depth [$opts{D}]
+         -S INT    minimum SNP quality [$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 [$opts{w}]
+
+         -W INT    window size for filtering dense SNPs [$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);
+
+  # 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 < $oW);
+  # the core loop
+  my @staging; # (indel_filtering_score, flt_tag)
+  while (<>) {
+	my @t = split;
+	next if (uc($t[2]) eq uc($t[3]) || $t[3] eq '*/*'); # skip non-var sites
+	# clear the out-of-range elements
+	while (@staging) {
+      # Still on the same chromosome and the first element's window still affects this position?  
+	  last if ($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, $score) = (0, -1);
+	# first a simple filter
+	if ($t[7] < $opts{d}) {
+	  $flt = 2;
+	} elsif ($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 $x (@staging) {
+            # Is it a SNP and is it outside the SNP filter window?
+			next if ($x->[0] >= 0 || $x->[4] + $x->[2] + $ow < $t[1]);
+			$x->[1] = 5 if ($x->[1] == 0);
+		  }
+		}
+		# 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 $x (@staging) {
+          # Is it a SNP and is it outside the gap filter window
+		  next if ($x->[0] < 0 || $x->[4] + $x->[2] + $ol < $t[1]);
+		  if ($x->[0] < $score) {
+			$x->[1] = 6;
+		  } else {
+			$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->[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->[4] + $x->[2] + $oW >= $t[1] && $x->[1] == 0);
+		  }
+		} else { # then check gap filter
+		  for my $x (@staging) {
+			next if ($x->[0] < 0 || $x->[4] + $x->[2] + $ow < $t[1]);
+			if ($x->[0] >= $opts{G}) {
+			  $flt = 5; last;
+			}
+		  }
+		}
+	  }
+	}
+	push(@staging, [$score, $flt, $len, @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", @$first[3 .. @$first-1]), "\n";
+  } elsif ($is_print) {
+	print STDERR join("\t", substr("UQdDWGgsiX", $first->[1], 1), @$first[3 .. @$first-1]), "\n";
+  }
+}
+
+#
+# pileup2fq
+#
+
+sub pileup2fq {
+  my %opts = (d=>3, D=>255, Q=>25, G=>25, l=>10);
+  getopts('d:D:Q:G:l:', \%opts);
+  die(qq/
+Usage:   samtools.pl pileup2fq [options] <in.cns-pileup>
+
+Options: -d INT    minimum depth        [$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 + $l));
+  }
+}
+
+sub p2q_print_str {
+  my ($s) = @_;
+  my $l = length($$s);
+  for (my $i = 0; $i < $l; $i += 60) {
+	print substr($$s, $i, 60), "\n";
+  }
+}
+
+#
+# sam2fq
+#
+
+sub sam2fq {
+  my %opts = (n=>20, p=>'');
+  getopts('n:p:', \%opts);
+  die("Usage: samtools.pl sam2fq [-n 20] [-p <prefix>] <inp.sam>\n") if (@ARGV == 0 && -t STDIN);
+  if ($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
+#
+
+# This subroutine does not use an XML parser. It requires that the SRA
+# XML files are properly formated.
+sub sra2hdr {
+  my %opts = ();
+  getopts('', \%opts);
+  die("Usage: samtools.pl sra2hdr <SRA.prefix>\n") if (@ARGV == 0);
+  my $pre = $ARGV[0];
+  my $fh;
+  # read sample
+  my $sample = 'UNKNOWN';
+  open($fh, "$pre.sample.xml") || die;
+  while (<$fh>) {
+	$sample = $1 if (/<SAMPLE.*alias="([^"]+)"/i);
+  }
+  close($fh);
+  # read experiment
+  my (%exp2lib, $exp);
+  open($fh, "$pre.experiment.xml") || die;
+  while (<$fh>) {
+	if (/<EXPERIMENT.*accession="([^\s"]+)"/i) {
+	  $exp = $1;
+	} elsif (/<LIBRARY_NAME>\s*(\S+)\s*<\/LIBRARY_NAME>/i) {
+	  $exp2lib{$exp} = $1;
+	}
+  }
+  close($fh);
+  # read run
+  my ($run, @fn);
+  open($fh, "$pre.run.xml") || die;
+  while (<$fh>) {
+	if (/<RUN.*accession="([^\s"]+)"/i) {
+	  $run = $1; @fn = ();
+	} elsif (/<EXPERIMENT_REF.*accession="([^\s"]+)"/i) {
+	  print "\@RG\tID:$run\tSM:$sample\tLB:$exp2lib{$1}\n";
+	} elsif (/<FILE.*filename="([^\s"]+)"/i) {
+	  push(@fn, $1);
+	} elsif (/<\/RUN>/i) {
+	  if (@fn == 1) {
+		print STDERR "$fn[0]\t$run\n";
+	  } else {
+		for (0 .. $#fn) {
+		  print STDERR "$fn[$_]\t$run", "_", $_+1, "\n";
+		}
+	  }
+	}
+  }
+  close($fh);
+}
+
+#
+# unique
+#
+
+sub unique {
+  my %opts = (f=>250.0, q=>5, r=>2, a=>1, b=>3);
+  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;
+	print $_ if (/^\@/);
+	$score = $1 if (/AS:i:(\d+)/);
+	my @t = split("\t");
+	next if (@t < 11);
+	if ($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...
+	}
+	$score = 1 if ($score < 1);
+	if ($t[0] ne $last) {
+	  &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, $multi_only) if (@a);
+}
+
+sub unique_aux {
+  my ($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) {
+	  $max2 = $max; $max = $a->[$i][0]; $max_i = $i;
+	} elsif ($a->[$i][0] > $max2) {
+	  $max2 = $a->[$i][0];
+	}
+  }
+  if ($is_recal) {
+	if (!$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 = ();
+}
+
+#
+# uniqcmp: compare two SAM files
+#
+
+sub uniqcmp {
+  my %opts = (q=>10, s=>100);
+  getopts('pq:s:', \%opts);
+  die("Usage: samtools.pl uniqcmp <in1.sam> <in2.sam>\n") if (@ARGV < 2);
+  my ($fh, %a);
+  warn("[uniqcmp] read the first file...\n");
+  &uniqcmp_aux($ARGV[0], \%a, 0);
+  warn("[uniqcmp] read the second file...\n");
+  &uniqcmp_aux($ARGV[1], \%a, 1);
+  warn("[uniqcmp] stats...\n");
+  my @cnt;
+  $cnt[$_] = 0 for (0..9);
+  for my $x (keys %a) {
+	my $p = $a{$x};
+	my $z;
+	if (defined($p->[0]) && defined($p->[1])) {
+	  $z = ($p->[0][0] == $p->[1][0] && $p->[0][1] eq $p->[1][1] && abs($p->[0][2] - $p->[1][2]) < $opts{s})? 0 : 1;
+	  if ($p->[0][3] >= $opts{q} && $p->[1][3] >= $opts{q}) {
+		++$cnt[$z*3+0];
+	  } elsif ($p->[0][3] >= $opts{q}) {
+		++$cnt[$z*3+1];
+	  } elsif ($p->[1][3] >= $opts{q}) {
+		++$cnt[$z*3+2];
+	  }
+	  print STDERR "$x\t$p->[0][1]:$p->[0][2]\t$p->[0][3]\t$p->[0][4]\t$p->[1][1]:$p->[1][2]\t$p->[1][3]\t$p->[1][4]\t",
+		$p->[0][5]-$p->[1][5], "\n" if ($z && defined($opts{p}) && ($p->[0][3] >= $opts{q} || $p->[1][3] >= $opts{q}));
+	} elsif (defined($p->[0])) {
+	  ++$cnt[$p->[0][3]>=$opts{q}? 6 : 7];
+	  print STDERR "$x\t$p->[0][1]:$p->[0][2]\t$p->[0][3]\t$p->[0][4]\t*\t0\t*\t",
+		$p->[0][5], "\n" if (defined($opts{p}) && $p->[0][3] >= $opts{q});
+	} else {
+	  print STDERR "$x\t*\t0\t*\t$p->[1][1]:$p->[1][2]\t$p->[1][3]\t$p->[1][4]\t",
+		-$p->[1][5], "\n" if (defined($opts{p}) && $p->[1][3] >= $opts{q});
+	  ++$cnt[$p->[1][3]>=$opts{q}? 8 : 9];
+	}
+  }
+  print "Consistent (high, high):   $cnt[0]\n";
+  print "Consistent (high, low ):   $cnt[1]\n";
+  print "Consistent (low , high):   $cnt[2]\n";
+  print "Inconsistent (high, high): $cnt[3]\n";
+  print "Inconsistent (high, low ): $cnt[4]\n";
+  print "Inconsistent (low , high): $cnt[5]\n";
+  print "Second missing (high):     $cnt[6]\n";
+  print "Second missing (low ):     $cnt[7]\n";
+  print "First  missing (high):     $cnt[8]\n";
+  print "First  missing (low ):     $cnt[9]\n";
+}
+
+sub uniqcmp_aux {
+  my ($fn, $a, $which) = @_;
+  my $fh;
+  $fn = "samtools view $fn |" if ($fn =~ /\.bam/);
+  open($fh, $fn) || die;
+  while (<$fh>) {
+	my @t = split;
+	next if (@t < 11);
+#	my $l = ($t[5] =~ /^(\d+)S/)? $1 : 0;
+	my $l = 0;
+	my ($x, $nm) = (0, 0);
+	$nm = $1 if (/NM:i:(\d+)/);
+	$_ = $t[5];
+	s/(\d+)[MI]/$x+=$1/eg;
+	@{$a->{$t[0]}[$which]} = (($t[1]&0x10)? 1 : 0, $t[2], $t[3]-$l, $t[4], "$x:$nm", $x - 4 * $nm);
+  }
+  close($fh);
+}
+
+sub plp2vcf {
+  while (<>) {
+	my @t = split;
+	next if ($t[3] eq '*/*');
+	if ($t[2] eq '*') { # indel
+	  my @s = split("/", $t[3]);
+	  my (@a, @b);
+	  my ($ref, $alt);
+	  for (@s) {
+		next if ($_ eq '*');
+		if (/^-/) {
+		  push(@a, 'N'.substr($_, 1));
+		  push(@b, 'N');
+		} elsif (/^\+/) {
+		  push(@a, 'N');
+		  push(@b, 'N'.substr($_, 1));
+		}
+	  }
+	  if ($a[0] && $a[1]) {
+		if (length($a[0]) < length($a[1])) {
+		  $ref = $a[1];
+		  $alt = ($b[0] . ('N' x (length($a[1]) - length($a[0])))) . ",$b[1]";
+		} elsif (length($a[0]) > length($a[1])) {
+		  $ref = $a[0];
+		  $alt = ($b[1] . ('N' x (length($a[0]) - length($a[1])))) . ",$b[0]";
+		} else {
+		  $ref = $a[0];
+		  $alt = ($b[0] eq $b[1])? $b[0] : "$b[0],$b[1]";
+		}
+	  } else {
+		$ref = $a[0]; $alt = $b[0];
+	  }
+	  print join("\t", @t[0,1], '.', $ref, $alt, $t[5], '.', '.'), "\n";
+	} else { # SNP
+	}
+  }
+}
+
+#
+# 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: varFilter     filtering SNPs and short indels
+         pileup2fq     generate fastq from `pileup -c'
+         showALEN      print alignment length (ALEN) following CIGAR
+\n/);
+}