From c7af593e1e00cfa4bad6f07bf8d2d85c79c23803 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sun, 8 Oct 2017 07:17:20 -0500
Subject: [PATCH] Fix bam syntax and file name.
---
workflow/scripts/map_reads.py | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/workflow/scripts/map_reads.py b/workflow/scripts/map_reads.py
index 7fd6baf..b36920c 100644
--- a/workflow/scripts/map_reads.py
+++ b/workflow/scripts/map_reads.py
@@ -98,7 +98,7 @@ def generate_sa(fastq, reference):
sai = '%s.sai' % (fastq_basename)
with open(sai, 'w') as sai_file:
- bwa_command = "bwa aln %s -t %d %s %s -f %s" \
+ bwa_command = "bwa aln %s -t %d %s %s" \
% (bwa_aln_params, cpu_count(),
reference, fastq, sai_file)
@@ -112,7 +112,7 @@ def align_se(fastq, sai, reference, fastq_basename):
'''Use BWA to align SE data.'''
sam_filename = "%s.sam" % (fastq_basename)
- bam_filename = '%s.bam' % (fastq_basename)
+ bam_filename = '%s.srt.bam' % (fastq_basename)
steps = [
"bwa samse %s %s %s"
@@ -132,7 +132,7 @@ def align_pe(fastq, sai, reference, fastq_basename):
sam_filename = "%s.sam" % (fastq_basename)
badcigar_filename = "%s.badReads" % (fastq_basename)
- bam_filename = '%s.bam' % (fastq_basename)
+ bam_filename = '%s.srt.bam' % (fastq_basename)
# Remove read pairs with bad CIGAR strings and sort by position
steps = [
@@ -197,7 +197,7 @@ def main():
bam_filename = align_se(fastq, sai, reference, fastq_basename)
- bam_mapstats_filename = '%s.raw.srt.bam.flagstat.qc' % (fastq_basename)
+ bam_mapstats_filename = '%s.srt.bam.flagstat.qc' % (fastq_basename)
with open(bam_mapstats_filename, 'w') as fh:
subprocess.check_call(
shlex.split("samtools flagstat %s" % (bam_filename)),
--
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