Mercurial > repos > mcharles > rapsodyn
diff rapsodyn/mpileupfilterandstat.pl @ 29:7b8646f46010 draft
Uploaded
author | mcharles |
---|---|
date | Wed, 08 Oct 2014 09:06:53 -0400 |
parents | 39376c7204be |
children |
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--- a/rapsodyn/mpileupfilterandstat.pl Wed Sep 10 08:10:38 2014 -0400 +++ b/rapsodyn/mpileupfilterandstat.pl Wed Oct 08 09:06:53 2014 -0400 @@ -1,4 +1,5 @@ #!/usr/bin/perl +#V1.0.0 use strict; use Getopt::Long; @@ -29,6 +30,9 @@ my $ONLY_UNFILTERED_VARIANT="OFF"; my $DO_STAT="NO"; +my $nb_variant_checked=0; +my $nb_variant_selected=0; + my $STAT_MIN_DEPTH_MIN = 2; my $STAT_MIN_DEPTH_MAX = 10; @@ -83,6 +87,7 @@ #Extraction des variants my $nb_line=0; while (my $line=<IF>){ + $nb_variant_checked++; $nb_line++; if (($nb_line % 1000000 == 0)&&($VERBOSE==1)){ print "$nb_line\n"; @@ -151,6 +156,7 @@ my $error_code = check_error($tbl_line[$i],$before,$after,\%USR_PARAM); if ($error_code == 0){ print $line{"line"}; + $nb_variant_selected++; } else { push(@error,$error_code,"\t",$line{"line"}); @@ -159,8 +165,12 @@ ### LOG open(LF,">$logfile") or die ("Can't open $logfile\n"); - -if ($DO_STAT eq "YES"){ +print LF "\n####\t MPileup filtering \n"; +print LF "Variant checked :\t$nb_variant_checked\n"; +if ($DO_STAT eq "NO"){ + print LF "Variant selected :\t$nb_variant_selected\n"; +} +elsif ($DO_STAT eq "YES"){ for (my $idx_min_depth=$STAT_MIN_DEPTH_MIN;$idx_min_depth<=$STAT_MIN_DEPTH_MAX;$idx_min_depth = $idx_min_depth + $STAT_MIN_DEPTH_STEP ){ for (my $idx_max_depth=$STAT_MAX_DEPTH_MIN;$idx_max_depth<=$STAT_MAX_DEPTH_MAX;$idx_max_depth = $idx_max_depth + $STAT_MAX_DEPTH_STEP ){ for (my $idx_freq = $STAT_FREQ_MIN;$idx_freq<=$STAT_FREQ_MAX;$idx_freq= $idx_freq+$STAT_FREQ_STEP){ @@ -183,9 +193,9 @@ } -for (my $i=0;$i<=$#error;$i++){ - print LF $error[$i]; -} +#for (my $i=0;$i<=$#error;$i++){ +# print LF $error[$i]; +#} close (LF);