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added clipping #21

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added clipping #21

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9eb1152
added clipping
lskatz Jun 1, 2024
1f15f79
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lskatz Jun 1, 2024
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52 changes: 51 additions & 1 deletion samclip
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ use constant {
SAM_CIGAR => 5,
SAM_TLEN => 8,
SAM_SEQ => 9,
SAM_QUAL => 10,
};

#----------------------------------------------------------------------
Expand All @@ -41,6 +42,7 @@ my $ref = '';
my $invert = 0;
my $debug = 0;
my $progress = 100_000;
my $clip = 0;

#----------------------------------------------------------------------
sub usage {
Expand All @@ -57,7 +59,8 @@ sub usage {
" --help This help\n",
" --version Print version and exit\n",
" --ref FASTA Reference genome - needs FASTA.fai index\n",
" --max NUM Maximum clip length to allow (default=$max)\n",
" --clip Clip any soft ends; convert to hard clip\n",
" --max NUM Maximum clip length to allow before filtering (default=$max)\n",
" --invert Output rejected SAM lines and ignore good ones\n",
" --debug Print verbose debug info to stderr\n",
" --progress N Print progress every NUM records (default=$progress,none=0)\n",
Expand All @@ -75,6 +78,7 @@ GetOptions(
"help" => \&usage,
"version" => \&version,
"ref=s" => \$ref,
"clip" => \$clip,
"max=i" => \$max,
"invert" => \$invert,
"debug" => \$debug,
Expand Down Expand Up @@ -128,6 +132,11 @@ while (my $line = <ARGV>) {
$L = 0 if $start <= 1+$L;
$R = 0 if $end >= $contiglen-$R;
my $info = $debug ? "CHROM=$sam[SAM_RNAME]:1..$contiglen POS=$start..$end CIGAR=$sam[SAM_CIGAR] L=$L R=$R | HL=$HL SL=$SL SR=$SR HR=$HR max=$max)" : "need --debug";
if($clip){
my $samArr = clip(\@sam, $HL, $SL, $SR, $HR);
@sam = @$samArr;
$line = join("\t", @sam);
}
if ($L > $max or $R > $max) {
msg("BAD! $info") if $debug;
$removed++;
Expand All @@ -145,6 +154,47 @@ msg("Total SAM records $total, removed $removed, allowed $kept, passed", $total-
msg("Header contained $header lines");
msg("Done.");

sub clip{
my($samArr, $HL, $SL, $SR, $HR) = @_;

# Avoid modifying the original array
my @sam = @$samArr;

# Trim the sequence and qual according to soft clips
$sam[SAM_SEQ] = substr($sam[SAM_SEQ], $SL, length($sam[SAM_SEQ])-$SL-$SR);
$sam[SAM_QUAL] = substr($sam[SAM_QUAL], $SL, length($sam[SAM_QUAL])-$SL-$SR);

# update the cigar line: we have now hard clipped the ends
my @cigar;
while($sam[SAM_CIGAR] =~ /(\d+)([MIDNSHP=X])/g){
my($len, $op) = ($1, $2);
if($op eq 'S'){
$op = 'H';
}
push @cigar, [$len, $op];
}
# Merge neighboring hard clips
for(my $i=0; $i<@cigar; $i++){
if($cigar[$i][1] eq 'H' and $i+1 < @cigar and $cigar[$i+1][1] eq 'H'){
$cigar[$i][0] += $cigar[$i+1][0];
splice(@cigar, $i+1, 1);
$i--;
}
}
# Recreate the cigar string
$sam[SAM_CIGAR] = '';
for(@cigar){
my $op = $$_[1];
my $len = $$_[0];
$sam[SAM_CIGAR] .= $len.$op;
}

# update the position of the mapping according to how much we clipped from the left
$sam[SAM_POS] += $SL;

return \@sam;
}

#----------------------------------------------------------------------
sub fai_to_dict {
my($fname) = @_;
Expand Down