Shell Programming and Scripting

if(low[i] <= $2 && $2 <= high[i]) {
            # Match found, add field and break out of loop.
            $(NF + 1) = "low"
            Else
[I]if(low[i] != $2 && $2 != high) {
            # No match found, add field and break out of loop.
            $(NF+1) = "no low"
            fi
            break

line1     Not low
line2     Not low
line3     Low
line4     Not low

Match:
chr15    68521889    C    T    exonic    CLN6    GOOD    50    het    4
chr7    147183143    A    G    intronic    CNTNAP2    GOOD    382    het    22
Missing in Reference but found in IDP:
chr2    51666313    T    C    intergenic    NRXN1,NONE    GOOD    108    het    7
chr2    166903445    T    C    exonic    SCN1A    GOOD    400    het    28
Missing in IDP but found in Reference:
2    166210776    C    T    exonic    SCN2A    c.[2994C>T]+[=]    3095    23.1    24.56
7    148106478    -    GT    intronic    CNTNAP2    c.3716-5_3716-4insGT    4168    28.6    51.01

chr2    50573818    50574097    NRXN1
chr7    148106400    148106550    CNTNAP2

Match:
chr15    68521889    C    T    exonic    CLN6    GOOD    50    het    4
chr7    147183143    A    G    intronic    CNTNAP2    GOOD    382    het    22
Missing in Reference but found in IDP:
chr2    51666313    T    C    intergenic    NRXN1,NONE    GOOD    108    het    7
chr2    166903445    T    C    exonic    SCN1A    GOOD    400    het    28
Missing in IDP but found in Reference:
2    166210776    C    T    exonic    SCN2A    c.[2994C>T]+[=]    3095    23.1    24.56     Not Low
7    148106478    -    GT    intronic    CNTNAP2    c.3716-5_3716-4insGT    4168    28.6    51.01     Low

#!/bin/bash

for file in /home/cmccabe/Desktop/concordance/comparison/update/*.txt ; do
    file1=${file##*/}    # Strip off directory
    getprefix=${file1%%_*.txt}
    file1=$(printf '%s\n' "/home/cmccabe/Desktop/concordance/low/${file1%%_*.txt}_"*.txt) # look for matching file
    if [[ -f "$file1" ]]
    then
TmpFile=${0##*/}.$$
awk '
BEGIN {    # Set input and output field separators...
    OFS = "\t"
}
NR == FNR {
    # Grab low and high ends of ranges from the 1st input file...
    low[++c] = $2
    high[c] = $3
    next
}
sect == 3 {
    # We are in the 3rd section of the 2nd input file (after the section
    # header line)...
    # Look for a range of vaues from a line in the 1st file that includes
    # the 2nd field in this file...
    for(i = 1; i <= c; i++)
        if(low[i] <= $2 && $2 <= high[i]) {
            # Match found, add field and break out of loop.
            $(NF + 1) = "low"
            Else
            if(low[i] = $2 && $2 = high[i]) {
            # No match found, add field and break out of loop.
            $(NF+1) = "no low"
            fi
            break
        }
}
/:$/ {    # Increment the 2nd input file section number when we find a colon at
    # the end of a line...
    sect++
}
1    # print the current contents of the 2nd file input line.
' $file1 $file > "$TmpFile" &&    # End awk script, specifying input files and
                # redirect the output to a temp file...
    cp "$TmpFile" $file &&     # If the awk script was successful, copy the
                    # temp file back to the 2nd input file...
    rm "$TmpFile"        # and, if that was also successful, remove the
                    # temp file.
fi
done

    # Look for a range of vaues from a line in the 1st file that includes
    # the 2nd field in this file...
    for(i = 1; i <= c; i++)
        if(low[i] <= $2 && $2 <= high[i]) {
            # Match found, add field and break out of loop.
            $(NF + 1) = "low"
            Else
            if(low[i] = $2 && $2 = high[i]) {
            # No match found, add field and break out of loop.
            $(NF+1) = "no low"
            fi
            break
        }

    # Add new field with default value.
    $(NF + 1) = "Not low"
    # Look for a range of vaues from a line in the 1st file that includes
    # the 2nd field in this file...
    for(i = 1; i <= c; i++)
        if(low[i] <= $2 && $2 <= high[i]) {
            # Match found, update the added field and break out of loop.
            $NF = "low"
            break
        }