From 2b4f438eb52f56c500bf3e901bd25aafe8a62f48 Mon Sep 17 00:00:00 2001
From: wbaopaul <yuw1@email.chop.edu>
Date: Tue, 16 Feb 2021 12:02:39 -0500
Subject: [PATCH] minor change

---
 README.md                     |  1 +
 scripts/split_bam2clusters.sh | 12 ++++++------
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index f83b3d1..6efaafa 100644
--- a/README.md
+++ b/README.md
@@ -81,6 +81,7 @@ Dependencies
 
 -   R (&gt;=3.6.1)
 -   Python (&gt;=3.6.0)
+-   Perl
 
 ### Software packages required
 
diff --git a/scripts/split_bam2clusters.sh b/scripts/split_bam2clusters.sh
index 3dc45f3..579db2c 100755
--- a/scripts/split_bam2clusters.sh
+++ b/scripts/split_bam2clusters.sh
@@ -33,17 +33,17 @@ do
     ${SAMTOOLS_PATH}/samtools index -@ $ncore $file0
     ${DEEPTOOLS_PATH}/bamCoverage --numberOfProcessors max --normalizeUsing BPM \
          --bam $file0 --binSize 100 --skipNonCoveredRegions \
-         --outFileName $fname_bw  &
+         --outFileName $fname_bw  
     fname_bedgraph=${file0/.bam/.bedgraph}
-    ${DEEPTOOLS_PATH}/bamCoverage --numberOfProcessors max --normalizeUsing BPM \
-         --outFileFormat bedgraph --bam $file0 --binSize 100 --skipNonCoveredRegions \
-         --outFileName $fname_bedgraph &
-    wait
+    #${DEEPTOOLS_PATH}/bamCoverage --numberOfProcessors max --normalizeUsing BPM \
+    #     --outFileFormat bedgraph --bam $file0 --binSize 100 --skipNonCoveredRegions \
+    #     --outFileName $fname_bedgraph 
+    #wait
 done
 
 ## move signal to output/signal
 mv ${output_dir}/*bw ${OUTPUT_DIR}/signal/
-mv ${output_dir}/*bedgraph ${OUTPUT_DIR}/signal/
+#mv ${output_dir}/*bedgraph ${OUTPUT_DIR}/signal/
 
 echo "The bam file was split into different clusters!"