in convert_reads.py: assigned memory to working thread in damtool sort, similar to map_reads.py

workflow/scripts/convert_reads.py

@@ -106,9 +106,16 @@ def convert_mapped_pe(bam, bam_basename):
 
     # Name sort bam to make BEDPE
     nmsrt_bam_filename = bam_basename + ".nmsrt.bam"
+    # Allocate memory for each thread used during samtools sort.
+    # Determine the available memory on the host system (kB).
+    avail_sys_mem = int(subprocess.check_output("grep MemTotal /proc/meminfo | grep -o '[0-9]*'", shell=True).decode("utf-8").strip())
+    # Divide the total by the number of processors and apply a scaling factor (0.85) to not use all memory.
+    mem_per_thread = math.floor((avail_sys_mem // cpu_count()) * 0.85)
+    # DEBUGGING
+    mem_per_thread = mem_per_thread * 4
     samtools_sort_command = \
-        "samtools sort -n -@%d -o %s %s" \
-        % (cpu_count(), nmsrt_bam_filename, bam)
+        "samtools sort -m %d  -n -@%d -o %s %s" \
+        % (mem_per_thread, cpu_count(), nmsrt_bam_filename, bam)
 
     logger.info(samtools_sort_command)
     subprocess.check_output(shlex.split(samtools_sort_command))