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fixing samtools sort output #111

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fixing samtools sort output #111

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3dd4f70
fixing samtools sort output
baileyglen Aug 16, 2017
7828fcc
Update sam_to_bam.py
baileyglen Aug 16, 2017
02a1150
Update sam_to_bam.py
baileyglen Aug 16, 2017
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8 changes: 4 additions & 4 deletions misopy/sam_to_bam.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,14 +24,14 @@ def sam_to_bam(sam_filename, output_dir,

# Sort
print "Sorting BAM file..."
sorted_filename = "%s.sorted" %(bam_filename.split(".bam")[0])
cmd = "samtools sort %s %s" %(bam_filename,
sorted_filename)
sorted_filename = "%s.sorted.bam" %(bam_filename.split(".bam")[0])
cmd = "samtools sort -o %s %s" %(sorted_filename,
bam_filename)
print " - Executing: %s" %(cmd)
os.system(cmd)

# Index
final_filename = "%s.bam" %(sorted_filename)
final_filename = "%s" %(sorted_filename)
print "Indexing BAM..."
cmd = "samtools index %s" %(final_filename)
print " - Executing: %s" %(cmd)
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