From 04ab908841a54bafe18e51e9e4541bab268698bf Mon Sep 17 00:00:00 2001
From: Don Armstrong <don@donarmstrong.com>
Date: Tue, 26 May 2015 10:29:13 -0700
Subject: [PATCH] use - for stdin

---
 fpkm_from_srr | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fpkm_from_srr b/fpkm_from_srr
index 27cad20..7de768a 100755
--- a/fpkm_from_srr
+++ b/fpkm_from_srr
@@ -12,7 +12,7 @@ function actually_run_the_alignment {
     module load samtools/1.0;
     (cd $FROM_SRR_SRR;
      fastq-dump --gzip ${FROM_SRR_SRR}.sra;
-     bwa mem -t ${CORES} $FROM_SRR_REF ${FROM_SRR_SRR}.fastq.gz | samtools view -b -o ${FROM_SRR_SRR}.bam;
+     bwa mem -t ${CORES} $FROM_SRR_REF ${FROM_SRR_SRR}.fastq.gz | samtools view -b -o ${FROM_SRR_SRR}.bam -;
      samtools sort ${FROM_SRR_SRR}.bam -o ${FROM_SRR_SRR}.sorted.bam -T temp
      cufflinks -p ${MAX_MEM} -G $FROM_SRR_GTF ${FROM_SRR_SRR}.sorted.bam;
      rm -f ${FROM_SRR_SRR}.fastq.gz ${FROM_SRR_SRR}.bam
-- 
2.39.2