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#!/bin/bash
if [ -z $6 ]
then
echo "$0 <min_mapping_threshold> <back_distance> <tt> <read len> <pe bam> <sr bam> "
exit
fi
MIN_MAP_T=$1
BACK=$2
TT=$3
READ_LENGTH=$4
PE_BAM=$5
SR_BAM=$6
Z=4
WEIGHT=4
OUT_FILE=`basename $PE_BAM .bam`
MEAN_STDEV=`samtools view $PE_BAM \
| ../../scripts/pairend_distro.py \
-r $READ_LENGTH \
-X $Z \
-N 10000 \
-o $OUT_FILE.histo`
MEAN=`echo $MEAN_STDEV | cut -d " " -f1 | cut -d ":" -f2`
STDEV=`echo $MEAN_STDEV | cut -d " " -f2 | cut -d ":" -f2`
../../bin/lumpy \
-b \
-mw $WEIGHT \
-tt $TT \
-sr \
bam_file:$SR_BAM,back_distance:$2,weight:1,id:1,min_mapping_threshold:$MIN_MAP_T \
-pe \
bam_file:$PE_BAM,histo_file:$OUT_FILE.histo,mean:$MEAN,stdev:$STDEV,read_length:$READ_LENGTH,min_non_overlap:$READ_LENGTH,discordant_z:4,back_distance:$BACK,weight:1,id:1,min_mapping_threshold:$MIN_MAP_T
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