comparison alignCustomAmplicon/alignCustomAmplicon.pl @ 4:22f35f830f48 draft

Uploaded

3:a72948f2c8c7

			-o	STR	filename for bam file
			-p	INT	number of threads [$OPTIONS{p}]
			-r		do not create stats report
			-s		sort the bam file
			-v		verbose progress
) if(@ARGV != 4);

my $Script = 'alignCustomAmplicon';
my $ref = shift @ARGV;
my $fastq1 = shift @ARGV;

	# Open the log file and redirect output to it
	open (STDERR, ">>$logfile") or die 'Couldn\'t create log file!\n';
	open (STDOUT, ">>$logfile") or die 'Couldn\'t create log file!\n';
	my $now = localtime time;
	print "Appending To Log File $now\n\n";
}

# print version of this script
print "Using $Script version $version \n\n";

$_->join() for @threadArray;

# sort the bam file
if(defined $OPTIONS{s}) {
	system("MergeSamFiles.sh  MAX_RECORDS_IN_RAM=2000000 I=$bam_to_sort O=$bamfile_out VALIDATION_STRINGENCY=LENIENT SO=coordinate USE_THREADING=true CREATE_INDEX=true");
	unlink $bam_to_sort;
}

if(!defined $OPTIONS{r}) {
	# print out statistics

4:22f35f830f48

			-o	STR	filename for bam file
			-p	INT	number of threads [$OPTIONS{p}]
			-r		do not create stats report
			-s		sort the bam file
			-v		verbose progress
			-j	STR	picard jar
) if(@ARGV != 4);

my $Script = 'alignCustomAmplicon';
my $ref = shift @ARGV;
my $fastq1 = shift @ARGV;

	# Open the log file and redirect output to it
	open (STDERR, ">>$logfile") or die 'Couldn\'t create log file!\n';
	open (STDOUT, ">>$logfile") or die 'Couldn\'t create log file!\n';
	my $now = localtime time;
	print "Appending To Log File $now\n\n";
}

if (defined $OPTIONS{j})
{
	my $JAR = $OPTIONS{j};

}

# print version of this script
print "Using $Script version $version \n\n";

$_->join() for @threadArray;

# sort the bam file
if(defined $OPTIONS{s}) {
	system("java -Xmx8g -jar $JAR  MAX_RECORDS_IN_RAM=2000000 I=$bam_to_sort O=$bamfile_out VALIDATION_STRINGENCY=LENIENT SO=coordinate USE_THREADING=true CREATE_INDEX=true");
	unlink $bam_to_sort;
}

if(!defined $OPTIONS{r}) {
	# print out statistics