Commit 8c41cdc0 authored by Neva C. Durand's avatar Neva C. Durand
Browse files

Merge branch 'encode' of https://github.com/aidenlab/juicer into encode

parents 6bbcdd26 fce5b1f3

CPU/common/sam_to_mnd.sh

+2 −1
Changes for CPU/common/sam_to_mnd.sh: 2 added lines, 1 removed line.
Original line number Diff line number Diff line 
# How to create old style merged_nodups.txt for 3D-DNA

# File should be dedupped SAM

saamtools view -O SAM -F 1024 $1 | awk -v mnd=1 -f sam_to_pre.awk 
# NB: you should likely put the directory in from of the sam_to_pre.awk file

samtools view -O SAM -F 1024 $1 | awk -v mnd=1 -f sam_to_pre.awk

SLURM/scripts/juicer.sh

+1 −2
Changes for SLURM/scripts/juicer.sh: 1 added line, 2 removed lines.
Original line number Diff line number Diff line
@@ -264,7 +264,6 @@ while getopts "d:g:a:hq:s:p:l:y:z:S:C:D:Q:L:b:A:i:t:jfuec-:T:w:k:" opt; do 
	e) earlyexit=1 ;;

	T) threadsHic=$OPTARG ;;

	i) sampleName=$OPTARG ;;

	k) libraryNamee=$OPTARG ;;

	u) singleend=1 ;;

	w) wobbleDist=$OPTARG ;;

	k) libraryName=$OPTARG ;;
@@ -1030,7 +1029,7 @@ EOF` 
fi



# Remove the duplicates from the big sorted file

if [ -z $final ] && [ -z $postproc ] && [ -z $dedup ]

if [ -z $final ] && [ -z $postproc ] && [ -z $afterdedup ]

then

    if [ -z $dedup ]

    then

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