Commit aa4a7a63 authored by Maxime Manno's avatar Maxime Manno 🍜
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Update insertssizes.py : update java parameters for Process inserts sizes...

Update insertssizes.py : update java parameters for Process inserts sizes metrics from production file
parent 13d8b68a
......@@ -45,7 +45,7 @@ def inserts_metrics(bam_file, pairs_count_file, metrics_file, hist_file, log_fil
if properly_paired_nb > 0 :
# Process inserts sizes metrics
command = Popen( ["-c", "java "+xmx+" -jar " + collectinsertsizemetrics_path + " " +options + " HISTOGRAM_FILE=" + hist_file + " INPUT=" + bam_file + " OUTPUT=" + metrics_file + " 2> " + log_file], shell=True, stdout=PIPE, stderr=PIPE )
command = Popen( ["-c", "java -Xmx4g -jar " + collectinsertsizemetrics_path + " " +options + " HISTOGRAM_FILE=" + hist_file + " INPUT=" + bam_file + " OUTPUT=" + metrics_file + " 2> " + log_file], shell=True, stdout=PIPE, stderr=PIPE )
stdout, stderr = command.communicate()
# Count nb pairs in bam file
command = Popen( ["-c", samtools_path + " view -F384 " + bam_file + " | wc -l"], shell=True, stdout=PIPE, stderr=PIPE) # First read in pair
......
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