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Fix get haplo #6

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Fix get haplo #6

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e917885
Add multi-threading + temporary directory assignment for sorting BAMs.
rsrivas84 Aug 8, 2018
be365f0
Added temporary directory path for use with samtools.
rsrivas84 Aug 8, 2018
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5 changes: 3 additions & 2 deletions bin/getHaplo_PE_cgOnly.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -46,8 +46,9 @@ sub main{
readCGTable($ARGV[1]);
my $bamfile = $ARGV[0];
my $start_time = time;
my $TEMP_PREFIX2 = $ARGV[2];
my ($last_list_pos, $last_list_calls, $last_id, $last_chr) = ("NA", "NA", "NA", "NA");
open(INFILE, "$samtools sort -n -O SAM $bamfile |") || die("Error running samtools to convert BAM file\n");
open(INFILE, "$samtools sort -T $TEMP_PREFIX2 -@ 4 -n -O SAM $bamfile |") || die("Error running samtools to convert BAM file\n");
while(my $line = <INFILE>){
next if($line =~ m/^@/);
chomp($line);
Expand Down Expand Up @@ -249,7 +250,7 @@ sub getAlignmentInfo{

sub printUsage{
print " Usage: \n";
print " getHaplo_PE_cgOnly.pl [cpg position list] < [sam file sorted by name] \n";
print " getHaplo_PE_cgOnly.pl [cpg position list] [sam file sorted by name] [temp_prefix]\n";
exit 0;
}

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