bam2intron

#!/bin/bash


# specify input data in order and output settings
bam=$1
intronbed=$2
output=$3
purename=$4
MAPQ=$5
threads=$6
mem=$7


# prepare out directory
if [ ! -d $output ];then 
	mkdir -p $output 
fi


#filename=$(echo ${bam} | awk 'BEGIN {FS="/"}  {print $NF}')
#purename=$(echo ${filename} | awk  'BEGIN {FS=".bam"} {print $1}')

prefix="$output"/"$purename" 

umapbam="${prefix}""_umap.bam"
bambed="${prefix}""_bambed.bed"
overlap="${prefix}""_overlap_initial.bed"



# index bam file
bai="$bam".bai
if [ ! -e "$bai" ]; then
	echo "BAM index does not exist. Create using Samtools."
	samtools index $bam
fi 

# pre-filter bam using intron bed files
samtools view -b -q $MAPQ -@ $threads  -L $intronbed $bam > $umapbam

# covert to bed format
#echo '--->   Converting bam to bed file'
bam2bed —input bam -r tmp  -m $mem < "${umapbam}" |bedscore > $bambed

# get intron-spanning reads
bedmap --bp-ovr 1  --skip-unmapped --echo --sum --echo-overlap-size --echo-map-id-uniq  $intronbed $bambed > $overlap


rm "${umapbam}"