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eris2.pl
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#!/usr/bin/perl -w
# SVfinder Eris Module - A.Gilly
# MA Madoui & JM Aury, Genoscope, 2011
use strict;
use Getopt::Long;
use POSIX qw(floor);
use Switch;
use List::Util qw[min max];
use Devel::Peek;
my $VERSION=0.1;
my $PICARD_PATH="/env/cns/src/picard/picard-tools-1.67";
# PARAMETERS
our @RERUNS;
our $NODISCORDANT="";
our ( $BAM , $OUTPUT_DIR , $LIB , $EXT , $MAX_COV , $COV_EXTENSION , $READ_SIZE , $SAMTOOLS_PATH , $DOC_MAD , $SPAN_MAD , $SAMPLE_SIZE , $SLC , $REFERENCE, $NOSORT, $NOLUTHER, $CONCORDANT, $DISCORDANT) = ( "", "" , "MP" , 20000 , 1000, 500, 76, "/env/cns/src/samtools/samtools-0.1.8/bin/samtools" , 4 , 4 , 1000000 , "/env/cns/proj/projet_AKL/slc/slclust", "", "", "", "no", "no");
our @TREAT_BAM=();
our $RUNDATA="";
our $MOCK="";
our $MAXMAP=10000;
our $MAXMIS=1;
our $CHAINLOAD="";
our $FILTER=100000;
my $MAN="";
my @args=@ARGV;
my $result = GetOptions ( 'bam=s' =>\$BAM,
'out=s' =>\$OUTPUT_DIR,
'lib=s' =>\$LIB,
'ext=i' =>\$EXT,
'maxcov=i' =>\$MAX_COV,
'covext=i' =>\$COV_EXTENSION,
'read=i' =>\$READ_SIZE,
'samtools=s' =>\$SAMTOOLS_PATH,
'dm=f' =>\$DOC_MAD,
'sm=f' =>\$SPAN_MAD,
'sample=i' =>\$SAMPLE_SIZE,
'nosort=s' =>\$NOSORT,
"noluther" =>\$NOLUTHER,
'concordant:s' =>\$CONCORDANT,
'discordant:s' =>\$DISCORDANT,
'treat_bam=s' =>\@TREAT_BAM,
'mock' =>\$MOCK,
'rundata=s' =>\$RUNDATA,
'maxmap=i' =>\$MAXMAP,
'maxmis=i' =>\$MAXMIS,
'nodiscordant' =>\$NODISCORDANT,
'chainload=s' =>\$CHAINLOAD,
'f1=s' =>\$FILTER,
'picard_path=s' =>\$PICARD_PATH,
'man' =>\$MAN
);
$| = 1;
man() if ($MAN ne "");
usage() if ( $BAM eq "" || $OUTPUT_DIR eq "" || $LIB !~/^MP$|^PE$/);
if(scalar @TREAT_BAM > 0 && $TREAT_BAM[0] ne ""){
foreach my $treat (@TREAT_BAM){
my @treat_modes=split(":", $treat);
die("Malformed treat_bam argument: should be [input|discordant|concordant]:i[-j].\n") if (scalar(@treat_modes) !=2);
if($treat_modes[0] ne "input" and $treat_modes[0] ne "concordant" and $treat_modes[0] ne "discordant"){
die("Malformed treat_bam argument, 1° member! Should be [input|concordant|discordant]\n");
}
if(!($treat_modes[1] =~ m/^\d(\-\d)?$/)){
die("Error in treat_bam parameter, 2° member! Must be of form i or i-j with i, j integers.\n");
}
}
}
if ($FILTER =~ /\D/ && $FILTER ne "disabled") {
die ("ERROR:\tThe f1 argument is a numerical filter. Please use an integer or the string value 'disabled'.\n");
}
die ("ERROR:\t Main BAM-file $BAM not found.\n") if(!-e $BAM);
die ("ERROR:\t Pre-sorted BAM-file $NOSORT not found.\n") if ($NOSORT ne "" && (!-e $NOSORT));
my $X;
my $Y;
my $MIN;
my $READS_LENGTH;
my $ISMEDIAN;
my $ISMAD;
my $DOCMEDIAN;
my $DOCMAD;
our $RERUN="NO";
print "\nSVfinder Eris module v. $VERSION - Detection of discordant reads\n\n";
#print "\n\"So, after all, there was not one Eris (Discord) alone, but all over the earth there are two. As for the one, a man would praise her when he came to understand her.\"\n";
#printf("%80s", 'Hesiod, Works and Days, 11-24');
print("\n\nInput BAM :\t$BAM\n");
print("Sorted input :\t$NOSORT\n") if $NOSORT ne "";
print("Output dir:\t$OUTPUT_DIR\n");
print("Using rundata:\t$RUNDATA\n");
print("Level-1 intrachromosomal filter:\t$FILTER\n");
print("\n");
if ($NOLUTHER ne ""){
print("-no-luther mode enabled. Not reforming reads.\n");
}
#print "-$MAXMIS mismatches allowed.\n";
print "-$MAXMAP mappings allowed.\n";
print("\n");
print("Estimation of insert size distribution\tscheduled.\nEstimation of coverage distribution\tscheduled.\n") if($RUNDATA eq "");
print("Detection of over-covered regions\tscheduled.\n") if (!-e "$OUTPUT_DIR/over_cov.txt");
print("Sorting of input file\t\tscheduled.\n") if ($NOSORT eq "");
print("Generation of discordant file\tscheduled.\n") if ($DISCORDANT ne "no");
print("Generation of concordant file\tscheduled.\n") if ($CONCORDANT ne "no");
foreach my $treat (@TREAT_BAM){
my $TREAT_MODE=(split(":", $treat))[0];
my $TREAT_ID=(split(":", $treat))[1];
if(defined($TREAT_MODE) && defined($TREAT_ID)){
print("Post-treatment of $TREAT_MODE file with $TREAT_ID mismatch filter\tscheduled.\n");
}
}
print("Chainloading execution to last treated BAM file\tscheduled.\n") if($CHAINLOAD eq "treated");
print("Chainloading execution to concordant BAM file\tscheduled.\n") if($CHAINLOAD eq "concordant");
print("Chainloading execution to discordant BAM file\tscheduled.\n") if($CHAINLOAD eq "discordant");
############################################################################
`mkdir -p $OUTPUT_DIR` if ( $OUTPUT_DIR && ! -d $OUTPUT_DIR );
############################################################################
my @DOC ;
my @SPAN ;
my $root_dir=$OUTPUT_DIR;
my $MAIN_RUN=1;
if ($RUNDATA ne "" && -e "$RUNDATA"){
open(IN, "$RUNDATA") or die "File $RUNDATA not found.\n";
my $line=<IN>;
chomp($line);
@DOC=split(":", $line);
print "INFO:\tRead DOC data: $line\n";
$line=<IN>;
@SPAN=split(":", $line);
close(IN);
print "INFO:\tRead insert size data: $line\n";
}else{
@DOC=get_DOC_distribution ( $BAM , $DOC_MAD );
@SPAN= get_insert_size_distribution ( $BAM , $SPAN_MAD );
open(OUT, ">$OUTPUT_DIR/rundata.dat");
print OUT join(":",@DOC), "\n";
print OUT join(":",@SPAN);
close(OUT);
}
my(@TRANS, @DEL);
my @CONCORDANTID;
my %OVER_COV = get_high_coverage_positions ( $BAM , $MAX_COV , $COV_EXTENSION , $READ_SIZE );
exit if($MOCK ne "");
our %CURRENT_DISCORDANT_PAIRS;
my $chemin_sorted;
if(scalar(@TREAT_BAM)>1 || !($TREAT_BAM[0]=~/input/)){
bam2discordant_pairs ( $BAM , $OUTPUT_DIR , $SPAN[2] , $SPAN[3] , $LIB , $EXT );
}
if(lc($DISCORDANT) eq "sorted"){
print("INFO:\tSorting discordant file...\n");
`samtools sort $root_dir/discordant.bam $root_dir/discordant.sorted`;
die("Samtools sort failed on $root_dir/discordant.bam.\n") if($? != 0);
# `rm $root_dir/discordant.bam; mv $root_dir/discordant.sorted.bam $root_dir/discordant.bam`;
}
if(lc($CONCORDANT) eq "sorted"){
print("INFO:\tSorting concordant file...\n");
`samtools sort $root_dir/concordant.bam $root_dir/discordant.sorted`;
die("Samtools sort failed on $root_dir/concordant.bam.\n") if($? != 0);
# `rm $root_dir/concordant.bam; mv $root_dir/concordant.sorted.bam $root_dir/concordant.bam`;
}
foreach my $treat (@TREAT_BAM){
my $TREAT_MODE=(split(":", $treat))[0];
my $TREAT_ID=(split(":", $treat))[1];
if(defined($TREAT_MODE) && defined($TREAT_ID)){
switch ($TREAT_MODE) {
case "input" {
if ($NOSORT eq "") {
print "INFO:\tSorting by name... (this step can be lengthy)\n";
sort_bam_by_name($BAM, "$OUTPUT_DIR/input_sortedby_name");
$chemin_sorted="$OUTPUT_DIR/input_sortedby_name.bam";
}
else{
$chemin_sorted=$NOSORT;
}
treat_bam($chemin_sorted, "$OUTPUT_DIR/input.$TREAT_ID.mismatch.ReadOrder.bam", $TREAT_ID);}
case "concordant" {treat_bam("$OUTPUT_DIR/concordant.bam", "$OUTPUT_DIR/concordant.$TREAT_ID.mismatch.ReadOrder.bam", $TREAT_ID);}
case "discordant" {treat_bam("$OUTPUT_DIR/discordant.bam", "$OUTPUT_DIR/discordant.$TREAT_ID.mismatch.ReadOrder.bam", $TREAT_ID);}
}
}
}
if($CHAINLOAD eq "treated"){
my $TREAT_MODE=(split(":", $TREAT_BAM[$#TREAT_BAM]))[0];
my $TREAT_ID=(split(":", $TREAT_BAM[$#TREAT_BAM]))[1];
if(defined($TREAT_MODE) && defined($TREAT_ID)){
my $mode=$TREAT_MODE;
print "INFO:\tSorting treated BAM...\n";
my $PICARD_SORT_TASK=`java -jar $PICARD_PATH/SortSam.jar INPUT=$OUTPUT_DIR/$TREAT_MODE.$TREAT_ID.mismatch.ReadOrder.bam OUTPUT=$OUTPUT_DIR/$TREAT_MODE.$TREAT_ID.mismatch.sorted.bam SORT_ORDER=coordinate VALIDATION_STRINGENCY=SILENT`;
($?>>8) and die "ERROR:\tTask exited with errorlevel: ", ($?>>8), ". Exiting.\n";
$NODISCORDANT="";
$BAM="$OUTPUT_DIR/$TREAT_MODE.$TREAT_ID.mismatch.sorted.bam";
$NOSORT="$OUTPUT_DIR/$TREAT_MODE.$TREAT_ID.mismatch.ReadOrder.bam";
$RUNDATA="$OUTPUT_DIR/rundata.dat";
if($RUNDATA eq ""){
open(IN, "$RUNDATA") or die "File $RUNDATA not found.\n";
my $line=<IN>;
chomp($line);
@DOC=split(":", $line);
$line=<IN>;
@SPAN=split(":", $line);
close(IN);
}
bam2discordant_pairs ( $BAM , $OUTPUT_DIR , $SPAN[2] , $SPAN[3] , $LIB , $EXT );
}
}
#############################################################################
# get_DOC_distribution
#----------------------------------------------------------------------------
# Take a SAM file, run samtools pileup
# Return an array that insert size distribution
sub get_DOC_distribution {
my ( $bam , $n_mad ) = @_;
# Depth of coverage analysis
my @cov;
open ( IN, "$SAMTOOLS_PATH pileup $bam |" ) || die "Cannot open $bam, $!\n";
while ( <IN> ){
last if ( $. > $SAMPLE_SIZE );
my @data = split /\t/, $_;
push ( @cov, $data[3] );
}
close (IN);
my @doc = get_limits ( \@cov , $n_mad );
$doc[2] = ( $doc[2] < 1 ) ? 1 : $doc[2] ;
print "INFO:\tDepth of coverage analysis\tDOC median: ",$doc[0],"\tDOC MAD: ",$doc[1],"\tDOC inf lim: ",$doc[2],"\tDOC sup lim: ",$doc[3],"\n";
return @doc;
}
#############################################################################
# get_insert_size_distribution
#----------------------------------------------------------------------------
# Take a BAM file, run samtools
# Return an array that contains insert size distribution (isd)
sub get_insert_size_distribution {
my ( $bam , $n_mad ) = @_;
# Insert size analysis
my @insert;
open ( IN, "$SAMTOOLS_PATH view $bam|" ) || die "Cannot open $bam, $!\n";
while (<IN>){
last if ( $. > $SAMPLE_SIZE );
my @data = split /\t/, $_;
if ( $data[6] eq "=" && $data[8] > 0 ){
push ( @insert, $data[8] );
}
}
close (IN);
my @isd = get_limits ( \@insert , $n_mad );
print "INFO:\tInsert size analysis\tInsert size median: ", $isd[0] ,"\tInsert size MAD: ", $isd[1] ,"\tInsert size inf lim: ", $isd[2] ,"\tInsert size sup lim: " , $isd[3],"\tInsert shift: ", 2 * $n_mad * $isd[1] , "\n";
return @isd;
}
###################################################################################
# get_limits
#----------------------------------------------------------------------------------
#takes an array of insert sizes
#returns the median, median + n.MAD, median - n.MAD
sub get_limits {
my ( $data , $n_mad ) = @_;
my @quartiles = getBoxPlot ( \@$data );
return ( $quartiles[1] , getMAD ( \@$data , $quartiles[1] ), $quartiles[1]- $n_mad * getMAD ( \@$data , $quartiles[1] ), $quartiles[1] + $n_mad * getMAD ( \@$data , $quartiles[1] ) );
}
###################################################################################
# getMAD
#----------------------------------------------------------------------------------
# Take an array
# Return the median absolute deviation (MAD)
sub getMAD {
my ( $array, $med ) = @_;
my @dev;
foreach ( @$array ){
push ( @dev, abs( $_ - $med ) );
}
my @MAD = getBoxPlot( \@dev );
return $MAD[1];
}
##################################################################################
# getBoxplot
#---------------------------------------------------------------------------------
# Take an array of value
# Return the quartiles Q1, Q2, Q3, inf and sup limit values
sub getBoxPlot {
my ( $array ) = @_;
my @sorted_array = sort { $a <=> $b } @$array;
my @results = (quartile ( 1, \@sorted_array ) , quartile ( 2, \@sorted_array ), quartile ( 3, \@sorted_array ));
return ( $results[0] , $results[1] , $results[2] , $results[0] - 1.5 * ( $results[1] - $results[0] ) , $results[2] + 1.5 * ( $results[2] - $results[1] ) );
}
#############################################################################
# quartile
#----------------------------------------------------------------------------
# Take a value and an integer (1, 2 or 3)
# Return the quartile value Q1, Q2 or Q3
sub quartile {
my ( $quart, $array ) = @_ ;
my $K_quantile = ( ( $quart / 4 ) * ( $#{@$array} - 1 ) + 1 );
my $F_quantile = $K_quantile - POSIX::floor($K_quantile); #decimal part
$K_quantile = POSIX::floor($K_quantile); #entire part
my $aK_quantile = $array->[ $K_quantile - 1 ];
return $aK_quantile if ( $F_quantile == 0 ); #if the decimal part is null
my $aKPlus_quantile = $array->[$K_quantile];
my $quantile = $aK_quantile + ( $F_quantile * ( $aKPlus_quantile - $aK_quantile ) );#if the decimal part is not null
return $quantile;
}
###################################################################################
# get_high_coverage_positions
#----------------------------------------------------------------------------------
# Take a BAM file
# Return a hash of overcovered region
sub get_high_coverage_positions {
my ( $bam_file , $max_cov, $ext, $read_length ) = @_;
my %over_cov;
if (-e "$OUTPUT_DIR/over_cov.txt"){
print "INFO:\tPrevious run detected. Fetching over-covered regions...";
open(IN, "$OUTPUT_DIR/over_cov.txt");
while (<IN>){
chomp;
my @data=split /\t/;
push ( @{$over_cov{$data[0]}}, [$data[1], $data[2]]);
}
close(IN);
my $CMD=`cat $OUTPUT_DIR/over_cov.txt | wc -l`;
chomp $CMD;
print "Fetched ", $CMD, " lines.\n";
}else{
print "INFO:\tCalculating over-covered ( > $max_cov ) regions...";
open ( IN , "$SAMTOOLS_PATH pileup $bam_file | awk '{if ( \$4 > $max_cov ){ print \$1\"\\t\"\$2\"\\t\"\$4 } }' |" ) || die "$!\n";
my $end;
my ( $ref , $start ) = ( "" , 0 );
while ( <IN> ){
chomp;
my @data = split /\t/;
if ( $ref eq "" ){
( $ref , $start , $end ) = ( $data[0] , $data[1] , $data[1] );
}
elsif ( $ref eq $data[0] ){
if ( $end + $ext >= $data[1] ) {
$end = $data[1];
}
else{
push ( @{$over_cov{$ref}}, [$start, $end + $read_length] );
# print $ref,"\t",$start,"\t",$end,"\n";
( $start , $end ) = ( $data[1] , $data[1] );
}
}
else{
( $ref , $start , $end ) = ( $data[0] , $data[1] , $data[1] );
}
}
print "Done.\n";
open ( OV , ">$OUTPUT_DIR/over_cov.txt") || die "Cannot open $OUTPUT_DIR/over_cov.txt, $!\n";
foreach my $ref ( keys %over_cov ) {
foreach my $i ($#{@{$over_cov{$ref}}}){
print OV $ref,"\t",$over_cov{$ref}->[$i]->[0],"\t",$over_cov{$ref}->[$i]->[1],"\n";
}
}
close (OV);
}
return %over_cov;
}
#############################################################################
# sort_BAM_by_name
#----------------------------------------------------------------------------
# Accessory function: sorts the bam file by name using samtools. output in
# global variable NOSORT.
sub sort_bam_by_name{
my($input, $output)=@_;
my $cmd=`$SAMTOOLS_PATH sort -n $input $output`;
die ("samtools exited abnormally: $!\n") if ($? !=0);
}
sub bam2discordant_pairs {
my ( $bam , $output_dir , $lim_inf , $lim_sup , $lib_type , $extend_overlap ) = @_;
opendir ( my $open_dir , $output_dir ) || die "Cannot open $output_dir, $!\n";
my @filelist= grep (/chr.\.[\+\-]\.(del|ins|dup|inv|trans)\.init/, readdir($open_dir));
if (scalar(@filelist) > 0){
print "QUERY:\tPrevious run detected. ",scalar(@filelist)," discordant pair files were found. Do you want to reuse them to spare time?(y/N)\n";
print "\t(Beware, there is no guarantee that the previous run was complete or used the same parameters you did)";
my $input=<>;
chomp($input);
if ($input eq "y" or $input eq "Y"){
print "Skipping...\n";
$RERUN="YES";
return;
}
}
print "INFO:\tDetection of discordant reads\n";
if ($NOSORT eq "") {
print "INFO:\tSorting by name... (this step can be lengthy)\n";
sort_bam_by_name($BAM, "$OUTPUT_DIR/input_sortedby_name");
$chemin_sorted="$output_dir/input_sortedby_name.bam";
}
else{
$chemin_sorted=$NOSORT;
}
my $ref = "";
my @multiple_hits;
my $disc_HANDLE;
my $conc_HANDLE;
if($CONCORDANT ne "no"){
open ($conc_HANDLE, "|-", "$SAMTOOLS_PATH view -bS - -o $OUTPUT_DIR/concordant.bam") or die("open: $!");
}
if($DISCORDANT ne "no"){
open ($disc_HANDLE, "|-", "$SAMTOOLS_PATH view -bS - -o $OUTPUT_DIR/discordant.bam") or die("open: $!");
}
my $total=`$SAMTOOLS_PATH view -c $chemin_sorted`;
open ( IN, "$SAMTOOLS_PATH view -h $chemin_sorted |" ) || die "$!\n";
my $flag="";
use Time::HiRes qw( gettimeofday tv_interval );
my $startime=[Time::HiRes::gettimeofday()];
my $maxsize=0;
my $count=0;
my $progress;
my $remaining;
my $line="";
my @data;
my $memory="";
while ( <IN> ){
chomp;
$line=$_;
# Following line to remove duplicates in SAM file
if($memory eq $line){next;} else {$memory=$line;};
if($count % 1000 == 0){
$progress=sprintf('%.2f', ($count/$total)*100);
$remaining=$progress !=0 ?((100-$progress)/$progress)*tv_interval($startime):0;
$remaining=int($remaining/3600) .':'. int(($remaining-(int($remaining/3600)*3600))/60);
print "INFO:\tTreated ",$progress,"% of reads. Estimated time remaining: $remaining.\r";}#, " Size: ", sprintf('%.2f', total_size(\%CURRENT_DISCORDANT_PAIRS)/1000000000) , "Go.\r";}
$count++;
# Following block writes the headers for conc and disc files.
if($line =~ m/^\@/){
print $conc_HANDLE $line, "\n" if $CONCORDANT ne "no";
print $disc_HANDLE $line, "\n" if $DISCORDANT ne "no";
next;
}
@data = split /\t/ , $line;
next if ( $data[5] eq "*" || $data[6] eq "*" || ( ( $data[3] == $data[7] ) && ( $data[6] eq "=" ) ) );#|| $data[4] == 0 ); #on avance jusqu'à la première ligne intéressante suivante
if ( $ref eq "" ){ #au début on prend la première bonne séquence comme référence et on ajoute tous ses mappings au format perso
$ref = $data[0];
push ( @{$multiple_hits[0]} , get_sam_multiple_records ( \@data ) );
}
elsif ( $data[0] eq $ref ){# si une référence existe on ajoute les mappings du read apparié à la suite dans multiple_h
push ( @{$multiple_hits[1]} , get_sam_multiple_records ( \@data ) ) ;
}
else{ # une référence existe mais on tombe sur une autre paire valide
# on envoie tous les multiple hits déjà trouvés à analyse_one_pair...
if(defined($multiple_hits[0]) && defined($multiple_hits[1]) && scalar(@{$multiple_hits[0]}) < $MAXMAP && scalar(@{$multiple_hits[1]})<$MAXMAP) {
analyse_one_pair_mapping_results ( \@multiple_hits, $lim_inf , $lim_sup , $lib_type , $output_dir, $extend_overlap, $conc_HANDLE, $disc_HANDLE);
}
$ref = $data[0];
undef(@multiple_hits);
push ( @{$multiple_hits[0]} , get_sam_multiple_records ( \@data ) ) ;
}
}
analyse_one_pair_mapping_results ( \@multiple_hits, $lim_inf , $lim_sup , $lib_type , $output_dir, $extend_overlap, $conc_HANDLE, $disc_HANDLE);
$remaining=tv_interval($startime);
$remaining=int($remaining/3600) .'h '. int(($remaining-(int($remaining/3600)*3600))/60)."min";
print "INFO:\tTreated $count reads in $remaining. Writing results to disk... \n";
close($disc_HANDLE) if $DISCORDANT ne "no";
close($conc_HANDLE) if $CONCORDANT ne "no";
close (IN);
print_discordant_pairs ( \%CURRENT_DISCORDANT_PAIRS , $output_dir ) if ($NODISCORDANT eq "");
print "INFO:\tDone.\n";
}
sub DIAGNOSE_printhit{
my ($pairs)=@_;
for my $i (0..1){
print "Mate $i: ", $#{$pairs->[$i]}, " mappings found.";
print "(Pair ",$pairs->[$i]->[0]->[5], ")\n" if ($#{$pairs->[$i]}>0);
# for my $j (1..$#{$pairs->[$i]}){
# push (@{$clean_matches[$i]}, $pairs->[$i]->[$j]) if($pairs->[$i]->[$j]->[7] <= $MAXMIS);
# print "Mapping treated: ", join('.', @{$pairs->[$i]->[$j]}), "\n";
# }
}
}
##########################################################################################################
# get_sam_multiple_records
#---------------------------------------------------------------------------------------------------------
# prend en entrée un tableau de colonnes SAM
# retourne un tableau à un format personnalisé:
# reference sequence name
# position
# une partie du FLAG (uniqt sens)
# séquence
# read name
# qualité
# ==============
# s'il existe d'autres mappings, pour chaque mapping
# ==============
# le chromosome
# la position
# le sens
# le sens du père
# séquence du père
# read name du père
# qualité du père
# distance
sub get_sam_multiple_records {
my ( $data ) = @_;
my @records;
my $pos = $data->[3];
my $sens = ( ( $data->[1] & 0x10 ) == 16 ) ? "-" : "+";
my $cigar = $data->[5];
my $edit;
for (my $ch=10;$ch<=$#{@$data};$ch++){
if($data->[$ch] =~/^NM\:i\:/){
$edit = $data->[$ch];
$edit =~s/NM\:i\://;
print $edit , "\n";
last;
}
}
push @records , [ $data->[2] , $pos , $sens, $data->[9], $data->[10] , $data->[0] , $data->[4], $data->[1], $data->[5], $data->[6], $data->[7], $data->[8], @{$data}[11..$#{$data}] ];
my $line = join "\t" , @$data;
if ( $line =~/\t(XA\:.+\;)/){
my @mult = split ( /\;/ , $1);
my @new_data=();
for (my $j=0; $j<=$#mult; $j++){
# foreach my $j ( 0..$#mult ){
$mult[$j] =~s/.+\://g; #pour chaque autre mapping, on supprime les noms des champs et on parse (chr, pos, cigar, nm)
@new_data = split ( /\,/ , $mult[$j] );
$sens = $new_data[1];
$sens =~s/\w*//g;
$pos = $new_data[1];
$pos =~s/[\+\-]//;
my $mult_edit = $new_data[3];
print $mult_edit,"\n";
$cigar = $new_data[2];
if ( $mult_edit == $edit ){
push @records , [ $new_data[0], $pos, $sens, $data->[9], $data->[10] , $data->[0] , $data->[4] , $new_data[3], $cigar ] ;
}
# Attention le CIGAR n'est jamais utilisé.
undef ( @new_data );
}
undef ( @mult );
}
undef $data;
return @records;
undef @records;
}
#############################################################################################
# analyse_one_pair_mapping_results
#-------------------------------------------------------------------------------------------
# take: an array of array containing one pair mapping features
# load: the selected pair hash of array, keys are pair case (chr_a.sens_a.chr_b.sens_b), values are array of pair features (pair name, pos_a, pos_b)
sub analyse_one_pair_mapping_results {
my ( $pair_to_analyse , $lim_inf , $lim_sup , $lib , $output_dir , $overlap_limit, $conc_handle, $disc_handle) = @_;
# print "Records 1 - ", $#{@$pair_to_analyse->[0]}, "\n";
# print "Records 2 - ", $#{@$pair_to_analyse->[1]}, "\n";
my $check = is_proper_mapped ( $pair_to_analyse , $lim_inf, $lim_sup , $lib );
# print "##DIAGNOSE: Size of array: ", sprintf('%.2f', total_size($check)/1000000000) , "Go.\n" if(total_size($check)>100000000);
# print "Proper mapped : ", $#{@$check}, "\n";
if ((!defined($check)) || (!defined($check->[0])) || ! @{$check->[0]} ){ # si la paire ne mappe pas (discordante) alors le tableau est vide
my %non_overlapping_cases = get_classified_multiple_hits ( $pair_to_analyse, $lim_inf, $lim_sup , $overlap_limit );
# print "Records 1 - ", join "::", keys(%non_overlapping_cases), "\n";
if($DISCORDANT ne "no"){
print({$disc_handle} join("\t", $pair_to_analyse->[0]->[0]->[5], $pair_to_analyse->[0]->[0]->[7],$pair_to_analyse->[0]->[0]->[0], $pair_to_analyse->[0]->[0]->[1], $pair_to_analyse->[0]->[0]->[6], $pair_to_analyse->[0]->[0]->[8],$pair_to_analyse->[0]->[0]->[9], $pair_to_analyse->[0]->[0]->[10], $pair_to_analyse->[0]->[0]->[11], $pair_to_analyse->[0]->[0]->[3], $pair_to_analyse->[0]->[0]->[4], @{$pair_to_analyse->[0]->[0]}[12..$#{$pair_to_analyse->[0]->[0]}]), "\n");
print ({$disc_handle} join("\t", $pair_to_analyse->[1]->[0]->[5], $pair_to_analyse->[1]->[0]->[7], $pair_to_analyse->[1]->[0]->[0], $pair_to_analyse->[1]->[0]->[1], $pair_to_analyse->[1]->[0]->[6], $pair_to_analyse->[1]->[0]->[8], $pair_to_analyse->[1]->[0]->[9], $pair_to_analyse->[1]->[0]->[10], $pair_to_analyse->[1]->[0]->[11], $pair_to_analyse->[1]->[0]->[3], $pair_to_analyse->[1]->[0]->[4], @{$pair_to_analyse->[1]->[0]}[12..$#{$pair_to_analyse->[1]->[0]}]), "\n");# if defined($pair_to_analyse->[1]);
}
foreach my $case ( keys %non_overlapping_cases ){
foreach my $i ( 0 .. $#{@{$non_overlapping_cases{$case} } } ){
push @{$CURRENT_DISCORDANT_PAIRS{$case}} , [ $non_overlapping_cases{$case}->[$i]->[0] , $non_overlapping_cases{$case}->[$i]->[1] , $non_overlapping_cases{$case}->[$i]->[2] ];
}
}
undef %non_overlapping_cases;
}
elsif (@{$check->[0]} and scalar(@{$check->[0]})==1 && $CONCORDANT ne "no") # sinon ce ne sont que les MP matches uniques qui nous intéressent
{
my @splitted=split('\t', $check->[0]->[0]);
my $i=$splitted[1];
my $j=$splitted[2];
if($splitted[1]!=0){ #Si le mapping correct n'est pas le mapping principal, remplacer par les données du XA
my $flag= $pair_to_analyse->[0]->[0]->[7];
my $length=max($pair_to_analyse->[1]->[$j]->[1], $pair_to_analyse->[0]->[$i]->[1])-min($pair_to_analyse->[1]->[$j]->[1], $pair_to_analyse->[0]->[$i]->[1]); #unsure about this calculation, supposed to be #rightmost_base - #leftmost_base, here max(pos1, 2)-min(pos1, 2)
if($pair_to_analyse->[0]->[0]->[1] ne $pair_to_analyse->[0]->[$i]->[1]){
$flag=($pair_to_analyse->[0]->[$i]->[1] eq "-")? ($flag | 0x10) : ($flag ^ 0x10);
}
if($NOLUTHER eq ""){
print({$conc_handle} join("\t", $pair_to_analyse->[0]->[0]->[5],
$flag,
$pair_to_analyse->[0]->[$i]->[0],
$pair_to_analyse->[0]->[$i]->[1],
255,
$pair_to_analyse->[0]->[0]->[8],
'=',
$pair_to_analyse->[0]->[0]->[10],
$length,
$pair_to_analyse->[0]->[0]->[3],
$pair_to_analyse->[0]->[0]->[4],
"NM:i:$pair_to_analyse->[0]->[$i]->[7]\n"));
}
}else {
print({$conc_handle} join("\t", $pair_to_analyse->[0]->[0]->[5], $pair_to_analyse->[0]->[0]->[7],$pair_to_analyse->[0]->[0]->[0], $pair_to_analyse->[0]->[0]->[1], $pair_to_analyse->[0]->[0]->[6], $pair_to_analyse->[0]->[0]->[8],$pair_to_analyse->[0]->[0]->[9], $pair_to_analyse->[0]->[0]->[10], $pair_to_analyse->[0]->[0]->[11], $pair_to_analyse->[0]->[0]->[3], $pair_to_analyse->[0]->[0]->[4], @{$pair_to_analyse->[0]->[0]}[12..$#{$pair_to_analyse->[0]->[0]}]), "\n");
}
if($splitted[2]!=0){#Idem pour le read '2'
my $flag= $pair_to_analyse->[1]->[0]->[7];
my $length=max($pair_to_analyse->[1]->[$j]->[1], $pair_to_analyse->[0]->[$i]->[1])-min($pair_to_analyse->[1]->[$j]->[1], $pair_to_analyse->[0]->[$i]->[1]); #unsure about this calculation, supposed to be #rightmost_base - #leftmost_base, here max(pos1, 2)-min(pos1, 2)
if($pair_to_analyse->[1]->[0]->[1] ne $pair_to_analyse->[1]->[$j]->[1]){
$flag=($pair_to_analyse->[1]->[$j]->[1] eq "-")? ($flag | 0x10) : ($flag ^ 0x10);
}
if($NOLUTHER eq ""){
print({$conc_handle} join("\t", $pair_to_analyse->[0]->[0]->[5],
$flag,
$pair_to_analyse->[0]->[$i]->[0],
$pair_to_analyse->[0]->[$i]->[1],
255,
$pair_to_analyse->[0]->[0]->[8],
'=',
$pair_to_analyse->[0]->[0]->[10],
$length,
$pair_to_analyse->[0]->[0]->[3],
$pair_to_analyse->[0]->[0]->[4],
"NM:i:$pair_to_analyse->[0]->[$i]->[7]\n"));
}
}
else{
print ({$conc_handle} join("\t", $pair_to_analyse->[1]->[0]->[5], $pair_to_analyse->[1]->[0]->[7], $pair_to_analyse->[1]->[0]->[0], $pair_to_analyse->[1]->[0]->[1], $pair_to_analyse->[1]->[0]->[6], $pair_to_analyse->[1]->[0]->[8], $pair_to_analyse->[1]->[0]->[9], $pair_to_analyse->[1]->[0]->[10], $pair_to_analyse->[1]->[0]->[11], $pair_to_analyse->[1]->[0]->[3], $pair_to_analyse->[1]->[0]->[4], @{$pair_to_analyse->[1]->[0]}[12..$#{$pair_to_analyse->[1]->[0]}]), "\n");
}
}
undef $pair_to_analyse;
undef @$check;
}
###############################################################################################
# is_proper_mapped
#-------------------------------------------------------------------------------------------
# take: 1. an array of array containing one pair mapping results (each hit is an array element containing a tab split SAM lines ),
# 2. the lower fragment size limit (bp),
# 3. the upper fragment size limit (bp),
# 4. the type of library (MP or PE)
# return: "" si la paire est discordante, "MP suivi d'un tab-split string:
#
sub is_proper_mapped {
my ( $pairs, $lim_inf, $lim_sup, $lib ) = @_;
my @alignments=();
# nouvel algorithme: retourner uniquement les paires qui possèdent un mapping concordant UNIQUE en MP.
# retourner ici un array au lieu d'une ligne
#plus haut: si l'array MP contient plus d'une ligne, discard
# s'il ne contient qu'une ligne et que cette ligne correspond à l'alignement principal pour 1 : écrire 1 sans XA
# s'il ne contient qu'une ligne et que cette ligne correspond à l'alignement principal pour 2 ! écrire 2 sans XA
# s'il ne contient qu'une ligne et que l'alignement est dans XA pour l'un des deux: récrire l'alignement principal avec les infos de XA et écrire.
for my $i ( 0 .. $#{@{$pairs->[0]}}){
for my $j ( 0 .. $#{@{$pairs->[1]}} ) {
#test MP - looking for proper mapped pair (MP reverse forward, and size > lim inf , size < lim sup
if ( $LIB eq "MP" && $pairs->[0]->[$i]->[0] eq $pairs->[1]->[$j]->[0] && ( ($pairs->[0]->[$i]->[1] > $pairs->[1]->[$j]->[1] && $pairs->[0]->[$i]->[2] eq "+" && $pairs->[1]->[$j]->[2] eq "-" && $pairs->[0]->[$i]->[1] - $pairs->[1]->[$j]->[1] > $lim_inf && $pairs->[0]->[$i]->[1] - $pairs->[1]->[$j]->[1] < $lim_sup ) || ($pairs->[0]->[$i]->[1] < $pairs->[1]->[$j]->[1] && $pairs->[0]->[$i]->[2] eq "-" && $pairs->[1]->[$j]->[2] eq "+" && $pairs->[1]->[$j]->[1] - $pairs->[0]->[$i]->[1] >$lim_inf && $pairs->[1]->[$j]->[1] - $pairs->[0]->[$i]->[1] < $lim_sup) ) ){
push(@{$alignments[0]},"MP\t".$i."\t".$j."\t".join ( "\t" , @{$pairs->[0]->[$i]} )."\t".join ("\t", @{$pairs->[1]->[$j]})."\n");
}
#test PE - looking for proper mapped pair (PE forward reverse, and size > lim inf , size < lim sup
elsif ( $LIB eq "PE" && $pairs->[0]->[$i]->[0] eq $pairs->[1]->[$j]->[0] && ( ($pairs->[0]->[$i]->[1] > $pairs->[1]->[$j]->[1] && $pairs->[0]->[$i]->[2] eq "-" && $pairs->[1]->[$j]->[2] eq "+" && $pairs->[0]->[$i]->[1] - $pairs->[1]->[$j]->[1] > 100 && $pairs->[0]->[$i]->[1] - $pairs->[1]->[$j]->[1] < 700 ) || ($pairs->[0]->[$i]->[1] < $pairs->[1]->[$j]->[1] && $pairs->[0]->[$i]->[2] eq "+" && $pairs->[1]->[$j]->[2] eq "-" && $pairs->[1]->[$j]->[1] - $pairs->[0]->[$i]->[1] >100 && $pairs->[1]->[$j]->[1] - $pairs->[0]->[$i]->[1] < 700) ) ){
push(@{$alignments[1]}, "PE\t".join ( "\t" , @{$pairs->[0]->[$i]} )."\t".join ("\t", @{$pairs->[1]->[$j]})."\n");
}
}
}
return \@alignments;
}
##############################################################################################
# get_classified_multiple_hits
#------------------------------------------------------------------------------------------
# take: an array of array containing one pair mapping results ( each hit is an array element, each array element is an array containing a tab split SAM lines
# return: an hash of non overlapped cases of pairs
sub get_classified_multiple_hits {
my ( $pairs, $lim_inf, $lim_sup , $overlap_limit ) = @_;
my %pair_cases=();
my $read_name = $pairs->[0]->[0]->[5];
my @clean_matches;
# # remove all mappings with Edit Distance > $MAXMIS
# for my $i (0..1){
# my $xm=(split("XM:i:", join("\t", @{$pairs->[$i]->[0]})))[1];
# $xm=(split("\t", $xm))[0];
# push (@{$clean_matches[$i]}, $pairs->[$i]->[0]) if($xm <= $MAXMIS);
# for my $j (1..$#{$pairs->[$i]}){
# push (@{$clean_matches[$i]}, $pairs->[$i]->[$j]) if($pairs->[$i]->[$j]->[7] <= $MAXMIS);
# }
# }
# if(!defined($clean_matches[1]) || !defined($clean_matches[0]) || scalar(@{$clean_matches[0]})==0 || scalar(@{$clean_matches[1]})==0){
# return %pair_cases;
# }
# $pairs=\@clean_matches;
# # Reduce the number of mappings by clustering nearby ones
# my @isolat_array;
# my $isolats=\@isolat_array;
# my $REPEAT_THRESHOLD=20000;
# for my $mate (0..1){
# next if(!defined($pairs->[$mate]));
# my @pair1_sortedchrpos=sort {$a->[0] cmp $b->[0] || $a->[1] <=> $b->[1]} @{$pairs->[$mate]};
# my ($firstplus, $firstminus, $lastplus, $lastminus, $chr);
# $chr="";
# foreach my $alignment (@pair1_sortedchrpos){
# $chr=$alignment->[0] if($chr eq "");
# if($chr ne $alignment->[0]){
# push( @{$isolat_array[$mate]}, [ @{$firstplus} ]) if(defined($firstplus));
# push( @{$isolat_array[$mate]}, [ @{$firstminus} ]) if(defined($firstminus));
# undef($firstplus);undef($firstminus);
# if($alignment->[1] eq "+"){$firstplus=$alignment;$lastplus=$alignment;}
# else{$firstminus=$alignment; $lastminus=$alignment;};
# $chr=$alignment->[0];
# }
# else{ # même chromosome
# if($alignment->[2] eq "+"){
# #plus case
# if(!defined($firstplus)){$firstplus=$alignment; $lastplus=$alignment;next;};
# if($alignment->[1] > $lastplus->[1]+$REPEAT_THRESHOLD){
# push( @{$isolat_array[$mate]}, [ @{$firstplus} ]);
# $firstplus=$alignment;$lastplus=$alignment;
# }else{
# $lastplus=$alignment;
# }
# }
# else{
# #minus case
# if(!defined($firstminus)){$firstminus=$alignment; $lastminus=$alignment;next;};
# if($alignment->[1] > $lastminus->[1]+$REPEAT_THRESHOLD){
# push( @{$isolat_array[$mate]}, [ @{$firstminus} ]);
# $firstminus=$alignment;$lastminus=$alignment;
# }else{
# $lastminus=$alignment;
# }
# }
# }
# }
# push( @{$isolat_array[$mate]}, [ @{$firstplus} ]) if(defined($firstplus));
# push( @{$isolat_array[$mate]}, [ @{$firstminus} ]) if(defined($firstminus));
# }
# $pairs=\@isolat_array;
for my $i ( 0 .. $#{@{$pairs->[0]}} ){
for my $j ( 0 .. $#{@{$pairs->[1]}} ) {
my ( $chr_a , $chr_b , $pos_a , $pos_b , $sens_a , $sens_b ) = ( $pairs->[0]->[$i]->[0] , $pairs->[1]->[$j]->[0] , $pairs->[0]->[$i]->[1] , $pairs->[1]->[$j]->[1], $pairs->[0]->[$i]->[2] , $pairs->[1]->[$j]->[2] );
if ( $chr_a ne $chr_b ){
if ( exists $pair_cases{"$chr_b.$sens_b.$chr_a.$sens_a.trans"} ){
push @{$pair_cases{"$chr_b.$sens_b.$chr_a.$sens_a.trans"}}, [ $pos_b, $pos_a ] ;
}
else{
push @{$pair_cases{"$chr_a.$sens_a.$chr_b.$sens_b.trans"}}, [ $pos_a, $pos_b ] ;
}
}
else{
if ( $pos_a > $pos_b ){
my ( $chr_c , $sens_c , $pos_c ) = ( $chr_a , $sens_a , $pos_a );
( $chr_a , $sens_a , $pos_a ) = ( $chr_b , $sens_b , $pos_b );
( $chr_b , $sens_b , $pos_b ) = ( $chr_c , $sens_c , $pos_c );
undef($chr_c);undef($sens_c);undef($pos_c);
}
if ( $pos_b-$pos_a >= $lim_sup && $sens_a eq "-" && $sens_b eq "+" && $pos_a != $pos_b){
push @{$pair_cases{"$chr_a.$sens_a.$chr_b.$sens_b.del"}}, [ $pos_a, $pos_b ] ;
}
elsif ( $pos_b-$pos_a <= $lim_sup && $sens_a eq "-" && $sens_b eq "+" && $pos_a != $pos_b ){
push @{$pair_cases{"$chr_a.$sens_a.$chr_b.$sens_b.ins"}}, [ $pos_a, $pos_b ] ;
}
elsif ( $sens_a eq $sens_b && $pos_a != $pos_b ){
push @{$pair_cases{"$chr_a.$sens_a.$chr_b.$sens_b.inv"}}, [ $pos_a, $pos_b ] ;
}
elsif ( $sens_a eq "+" && $sens_b eq "-" && $pos_a != $pos_b ){
push @{$pair_cases{"$chr_a.$sens_a.$chr_b.$sens_b.dup"}}, [ $pos_a, $pos_b ] ;
}
}
}
}
foreach my $key (keys %pair_cases){
}
# Get non overlapping pairs
my %non_overlapped_pair;
foreach my $case ( keys %pair_cases ){
my @good_pairs;
my @sorted_pair_case = sort { $a->[0] <=> $b->[0] } @{$pair_cases{$case}};
if ( $#{@{$pair_cases{$case}}} > 0 ){
@good_pairs = get_pair_cluster ( \@sorted_pair_case, $case , $overlap_limit );
foreach my $i ( 0 .. $#good_pairs ){
push @{$non_overlapped_pair{$case}} , [ $good_pairs[$i]->[0], $good_pairs[$i]->[1] , $read_name ] ;
}
}
else {
push @{$non_overlapped_pair{$case}} , [ $pair_cases{$case}[0]->[0], $pair_cases{$case}[0]->[1] , $read_name ] ;
}
undef ( @good_pairs );
undef ( @sorted_pair_case);
}
undef ( %pair_cases );
undef ( $pairs );
if($FILTER ne "disabled"){
# Get likely discordant pairs for low complexity regions
my $good_case = "";
my $flag = 0;
foreach my $case ( keys %non_overlapped_pair ) {
if ( $case =~/del|inv|dup|ins/ ){
foreach my $i ( 0 .. $#{@{$non_overlapped_pair{$case} } } ){
if ( ( $non_overlapped_pair{$case}[$i]->[1] - $non_overlapped_pair{$case}[$i]->[0] ) <= $FILTER ){
$good_case = $case ;
$flag = 1;
last;
}
}
}
last if ( $flag == 1 );
}
# remove artefactual cases
if ( $good_case ne "" ){
foreach my $case ( keys %non_overlapped_pair ){
delete $non_overlapped_pair{$case} if ( $case ne $good_case && $case =~/del|inv|dup|ins/);
}
}
}
return %non_overlapped_pair;
}
sub sort_for_pairs ($$){
my ($premier, $deuxieme)=@_;
if($premier->[0] ne $deuxieme->[0]) {return $premier->[0] cmp $deuxieme->[0];}
else{return $premier->[1] <=> $deuxieme->[1];}
}
############################################################################################################
# get_pair_cluster
#-----------------------------------------------------------------------------------------------------------
# take: array of [pos_a, pos_b], corresponding to a signature
# return:
sub get_pair_cluster{
my ( $pair , $case , $overlap_limit ) = @_;
my @clust;
my $n_clust = 0;
# initialize cluster
push @{$clust[$n_clust]} , $pair->[0]; #begin by taking the first (posa, posb)
for my $k ( 1 .. $#{@$pair} ){
my @overlap = is_overlapping ($pair->[$k]->[0], $pair->[$k]->[0] + $overlap_limit, $pair->[$k-1]->[0], $pair->[$k-1]->[0] + $overlap_limit, 0 );
if ( $overlap[0] > 0 ){
push @{$clust[$n_clust]} , $pair->[$k];
}
else{
++$n_clust;
push @{$clust[$n_clust]} , $pair->[$k];
}
}
# take a random pair from overlapping region
my @non_overlapped_pair;
for my $k ( 0 .. $#clust ){
my $rand = int ( rand ( $#{@{$clust[$k]}} ) );
push ( @non_overlapped_pair , [ $clust[$k]->[$rand]->[0], $clust[$k]->[$rand]->[1] ] );
}
undef @clust;
return @non_overlapped_pair;
}
###############################################################################
# print_discordant_pairs
#------------------------------------------------------------------------------
# take: a hash of discordant pair
# return: print the result in files
sub print_discordant_pairs{
my ( $pair, $output_dir ) = @_;
foreach my $case ( keys %$pair ){
my $A = 0;
my $B = 1;
my $different_chr = $case;
$different_chr =~/chr(\w+)\.[\-\+]\.chr(\w+)\.[\-\+]\..+/;
my $chr1 = $1;
my $chr2 = $2;
my @discordant_pairs = sort { $a->[0] <=> $b->[0] } @{$pair->{$case}};
if ( $chr1 ne $chr2 ){
if ( $chr1 =~/\d/ && $chr2=~/\d/ && $chr1 > $chr2 ){
$A = 1;
$B = 0;
$case =~s/chr(\w+)\.([\-\+])\.chr(\w+)\.([\-\+])\.(.+)/chr$3.$4.chr$1.$2.$5/;
}
if ( $chr1=~/\D/ || $chr2=~/\D/ ){
my @order = ( $chr1 , $chr2 );
@order = sort { $a cmp $b } @order;
if ( $order[0] ne $chr1 ){
$A = 1;
$B = 0;
$case =~s/chr(\w+)\.([\-\+])\.chr(\w+)\.([\-\+])\.(.+)/chr$3.$4.chr$1.$2.$5/;
}
}
}
open ( OUT ,">>$output_dir/$case.init" );
foreach my $i ( 0 .. $#discordant_pairs ){
print OUT $discordant_pairs[$i]->[$A] , "\t" , $discordant_pairs[$i]->[$B] , "\t", $discordant_pairs[$i]->[2] , "\n" ;
}
close ( OUT );
}
# sort and uniq
opendir ( my $open_dir , $output_dir ) || die "Cannot open $output_dir, $!\n";
my @files = readdir ( $open_dir );
foreach my $file ( @files ){
if ( $file=~/.\.init$/ ){
`sort -k1,1n $output_dir/$file | awk '{if ( vu[\$1"@"\$2]!=1 ){print \$0;vu[\$1"@"\$2]=1}}' > $output_dir/$file.sorted;rm $output_dir/$file; mv $output_dir/$file.sorted $output_dir/$file`;
}
}
closedir ($open_dir);
}
#############################################################################
# treat_BAM
#----------------------------------------------------------------------------
# Accessory function: redefines the bam file so that it contains only perfect
# matches. Lone mates are also removed. Works only on ordered-by-name files.
sub treat_bam{
my ( $input, $output, $regx ) = @_;
# preprocesses the bam file to remove all reads that do not map perfectly at least once
print "INFO:\tTreating file $input with mismatch parameters $regx.\n";
my $m=$READ_SIZE."M";
my $newfilename="$output";
open (OUT, "| $SAMTOOLS_PATH view -Sb - -o $newfilename");
my %reads;
my $first="";
open ( IN, "$SAMTOOLS_PATH view -h $input |" ) || die "Cannot open $input, $!\n";
while ( <IN> ){
chomp;
if ($_ =~ m/^\@/ ) {
print OUT $_, "\n";
next;
}
my $data=$_;
my @tab=split('\t', $data);
if($data =~ m/XT:A:M/){
my @multiples=split('XA:Z:', $data);
if(scalar(@multiples)>1 && $multiples[1] =~ m/$m,[$regx]/){
#Sometimes in case of discordant reads the main mapping is quite bad (rescued mate)
#In this case the secondary mappings contain worthy information
if($first ne "" && (split('\t', $first))[0] eq $tab[0]){
print OUT (split('\n', $first))[0], "\n";
print OUT (split('\n', $data))[0], "\n";
$first="";
}else{
$first=$data;
}
}
}
elsif ($tab[5] eq $m && $data =~ m/XM:i:[$regx]/ ) {
if($first ne "" && (split('\t', $first))[0] eq $tab[0]){
print OUT (split('\n', $first))[0], "\n";
print OUT (split('\n', $data))[0], "\n";
$first="";
}else{