From 1b918e88bfce4bd04f6f6b2d2130f6b620d78fab Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sat, 7 Oct 2017 22:06:42 -0500
Subject: [PATCH] Fix order of sai and fastq arguments.
---
workflow/scripts/map_reads.py | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/workflow/scripts/map_reads.py b/workflow/scripts/map_reads.py
index 972a816..7fd6baf 100644
--- a/workflow/scripts/map_reads.py
+++ b/workflow/scripts/map_reads.py
@@ -98,9 +98,9 @@ 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" \
+ bwa_command = "bwa aln %s -t %d %s %s -f %s" \
% (bwa_aln_params, cpu_count(),
- reference, fastq)
+ reference, fastq, sai_file)
logger.info("Running bwa with %s", bwa_command)
subprocess.check_call(shlex.split(bwa_command), stdout=sai_file)
@@ -116,7 +116,7 @@ def align_se(fastq, sai, reference, fastq_basename):
steps = [
"bwa samse %s %s %s"
- % (reference, fastq[0], sai[0]),
+ % (reference, sai[0], fastq[0]),
"samtools view -@%d -Su -" % (cpu_count()),
"samtools sort -@%d -o %s"
% (cpu_count(), bam_filename)]
@@ -137,8 +137,8 @@ def align_pe(fastq, sai, reference, fastq_basename):
# Remove read pairs with bad CIGAR strings and sort by position
steps = [
"bwa sampe -P %s %s %s %s %s"
- % (reference, fastq[0], fastq[1],
- sai[0], sai[1]),
+ % (reference, sai[0], sai[1],
+ fastq[0], fastq[1]),
"tee %s" % (sam_filename),
r"""awk 'BEGIN {FS="\t" ; OFS="\t"} ! /^@/ && $6!="*" { cigar=$6; gsub("[0-9]+D","",cigar); n = split(cigar,vals,"[A-Z]"); s = 0; for (i=1;i<=n;i++) s=s+vals[i]; seqlen=length($10) ; if (s!=seqlen) print $1"\t" ; }'""",
"sort",
--
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