#!/bin/bash

# gunzip files
logfile=/home/cmccabe/Desktop/NGS/test/process.log
for f in /home/cmccabe/Desktop/NGS/test/*.vcf ; do
     echo "Start vcf.gz creation: $(date) - file: $f"
     bname=`basename $f`
     gzip $f
     echo "End vcf.gz creation: $(date) - file: $f"
done >> "$logfile"

# find undefined annotations
logfile=/home/cmccabe/Desktop/NGS/test/process.log
for f in /home/cmccabe/Desktop/NGS/test/*.vcf.gz ; do
     echo "Start vcf missing header creation: $(date) - file: $f"
     bname=`basename $f`
     pref=${bname%%.vcf.gz}
    bcftools view -h $f > /home/cmccabe/Desktop/NGS/test/${pref}_header.txt
     echo "End missing header creation: $(date) - file: $f"
done >> "$logfile"

# match files
IAm=${0##*/}

InDir1='/home/cmccabe/Desktop/NGS/test'
InDir2='/home/cmccabe/Desktop/NGS/test'
OutDir='/home/cmccabe/Desktop/NGS/test'

cd "$InDir1"
for file1 in *.txt
do	# Grab file prefix.
	p=${file1%%_*}

	# Find matching file2.
	file2=$(printf '%s' "$InDir2/$p"_*.vcf)
	if [ ! -f "$file2" ]
	then	printf '%s: No single file matching %s found.\n' "$IAm" \
		    "$file1" >&2
		continue
	fi
# store matches
    out=${file1##*/} && ${file2##*/}

# edit the header
logfile=/home/cmccabe/Desktop/NGS/test/process.log
for f in /home/cmccabe/Desktop/NGS/test/*.vcf.gz ; do
     echo "Start vcf edit header creation: $(date) - file: $f"
     bname=`basename $f`
     pref=${bname%%.vcf.gz}
      bcftools reheader -h $file1 $file2 > ${pref}_fixed.vcf.gz
     echo "End edit header creation: $(date) - file: $f"
done >> "$logfile"

file1_header.txt is stored as $file1 matched with file1.vcf.gz stored as $file2
file2_header.txt is stored as $file1 matched with file2.vcf.gz stored as $file2f
file3_header.txt is stored as $file1 matched with file3.vcf.gz stored as $file2

$file1
$file2

bcftools reheader -h $file1 $file2 > ${pref}_fixed.vcf.gz

ls -l
total 12288
-rwxrwx---+ 1 cmccabe Domain Users 2031823 Jan 31 11:07 file1.vcf.gz
-rwxrwx---+ 1 cmccabe Domain Users    9312 Feb  2 13:17 file1_header.txt
-rwxrwx---+ 1 cmccabe Domain Users 2361873 Jan 31 11:07 file2.vcf.gz
-rwxrwx---+ 1 cmccabe Domain Users    9315 Feb  2 13:17 file2_header.txt
-rwxrwx---+ 1 cmccabe Domain Users 1816662 Jan 31 11:07 file3.vcf.gz
-rwxrwx---+ 1 cmccabe Domain Users    9313 Feb  2 13:17 file3_header.txt
-rwxrwx---+ 1 cmccabe Domain Users    1356 Feb  2 13:22 process.log
-rwxrwx---+ 1 cmccabe Domain Users    1278 Feb  2 13:17 process.log~