#!/bin/bash
input_sample="leaf_bams.txt"
input_proms="promoter_list.txt"

while IFS= read -r file
do
echo "Getting region list for $file" 

export= frag1=" "
export= frag2="proms"

    while  IFS= read -r prom
    do
    export= frag1="$frag1 \"$prom\" "
    done < "$input_proms"

echo "Extracting regions"
CMD="samtools view -b $file.bam $frag1 -h > $file.$frag2.bam"
echo $CMD
eval $CMD

#CMD="samtools  sort   $file.$frag2.bam  >  $file.$frag2.sorted.bam"
#echo $CMD
#eval $CMD

#CMD="time samtools mpileup  $file.$frag2.sorted.bam | python /home/hansvgdub/bin/bam_coveragev2.py > $file.$frag2.tsv"
#eval $CMD

done < "$input_sample"

#CMD="paste  *$frag2.tsv  |head -2  |cut -f1,2,3,4,6,7,8,10,11,12,14,15,16,18,19,20,22,23,24,26,27,28,30,31,32,34,35,36,38,39,40,42,43,44,46,47,48,50,51,52,54,55,56,58,59,60,62,63,64,66,67,68,70,71,72,74,75,76,78,79,80,82,83,84,86,87,88,90,91,92,94,95,96,98,99,100,102,103,104,106,107,108,110,111,112,114,115,116,118,119,120,122,123,124,126,127,128,130,131,132,134,135,136,138,139,140,142,143,144,146,147,148,150,151,152,154,155,156,158,159,160,162,163,164,166,167,168,170,171,172,174,175,176"
#eval $CMD