### Bits for script

#FILEA="General ROH file"
#FILEB="Inbred ROH file"

# 1 - Split ${FILEA} and ${FILEB} per chromosome

for chr in {1..22}; 
do 
grep -w "^${chr}" ${FILEA} > ${FILEA%.*}-${chr}.txt; grep "^${chr}" ${FILEB} > ${FILEB%.*}-${chr}.txt; 
done

awk -v var="${chr}" {'if ($2==var) print $0'} 

# 2 - search each RHO from ${FILEB} against each RHO from ${FILEA}
# 2.1. Extract positions ${C} and ${D} from ${FILEB} and positions ${A} and ${B} from ${FILEB}

# save it on one script named - e.g. COMPARE-ROHs.sh

#CHR_TO_PROCESS="$(seq 1 22) X Y"
#THREADS=12
#parallel -j ${THREADS} A=${FILEA%.*}-{}.txt B=${FILEB%.*}-{}.txt  .\COMPARE-ROHS.sh  ::: ${CHR_TO_PROCESS}

##!/bin/bash
# Usage   ${FILEA} ${FILEB} ./COMPARE-ROHS.sh

FILEA="${A}"
FILEB="${B}"
OUTFILE="outfile.${A}.txt" ## Output file

while read -r ROHA;
do

A=`echo ${ROHA} | cut -d " " -f 8`; ## ROH Start
B=`echo ${ROHA} | cut -d " " -f 9`; ## ROH End

while read -r ROHB;
do

C=`echo ${ROH} | cut -d " " -f 8`; ## ROH Start
D=`echo ${ROHB} | cut -d " " -f 9 `; ## ROH End

# option1 
if [[(${C} -lt ${A}) && (${D} -gt ${A}) && (${D} -lt ${B})]]; then echo -e "${RHOB} DOWSNTREAM-intercal ${RHOA}" >> ${OUTFILE}
elif [[(${C} -gt ${A}) && (${C} -lt ${B}) && (${D} -gt ${B})]]; then echo -e "${RHOB} UPSTREAM-intercal $ {RHOA}" >> ${OUTFILE}

# option2
elif [[(${C} -eq ${A}) && (${D} -lt ${B})]]; then echo -e "${RHOB} DOWNSTREAM-anchor-inside ${RHOA}" >> ${OUTFILE}
elif [[(${C} -gt ${A}) && (${D} -eq ${B})]]; then echo -e "${RHOB} UPSTREAM-anchor-inside ${RHOA}" >> ${OUTFILE}

# option3 
elif [[(${D} -eq ${A}) ]]; then echo -e "${RHOB} DOWNSTREAM-anchor-out ${RHOA}" >> ${OUTFILE}
elif [[(${C} -eq ${B}) ]]; then echo -e "${RHOB} UPSTREAM-anchor-out ${RHOA}" >> ${OUTFILE}

# option4 
elif [[(${C} -gt ${A}) && (${D} -lt ${B})]]; then echo -e "${RHOB} INTERIOR ${RHOA}" >> ${OUTFILE}
elif [[(${C} -lt ${A}) && (${D} -gt ${B})]]; then echo -e "${RHOB} LARGER ${RHOA}" >> ${OUTFILE}

#option5
elif [[(${C} -eq ${A}) && (${D} -eq ${B})]]; then echo -e "${RHOB} EQUAL ${RHOA}" >> ${OUTFILE}

#option6
elif [[(${C} -lt ${A}) && (${D} -eq ${B})]]; then echo -e "${RHOB} LARGER-anchor-down ${RHOA}" >> ${OUTFILE}

# option7
elif [[(${C} -eq ${A}) && (${D} -gt ${B})]]; then echo -e "${RHOB} LARGER-anchor-up ${RHOA}" >> ${OUTFILE}
#       else echo "this is not a match" >> ${OUTFILE}
fi
done< ${FILEB}
done< ${FILEA}