RonaldFindling

#!/bin/bash

##############################
#set the following variables
##############################

#use the bamfile without .bam
myfile="alignment"
#the chromosome to filter for
mychrom="chr1"

RonaldFindling

# Created by https://www.gitignore.io/api/linux

### Linux ###
*~

# KDE directory preferences
.directory

# Linux trash folder which might appear on any partition or disk

RonaldFindling

# Created by https://www.gitignore.io/api/linux

### Linux ###
*~

# KDE directory preferences
.directory

# Linux trash folder which might appear on any partition or disk

RonaldFindling

#get hash-values for all unreachable files sorted by timestamps by Mark Longair http://stackoverflow.com/questions/7374069/undo-git-reset-hard-with-uncommitted-files-in-the-staging-area
find .git/objects/ -type f -printf '%TY-%Tm-%Td %TT %p\n' | sort | cut -d " " -f 3 | sed "s/\.git\/objects\/\(.*\)\/\(.*\)/\\1\\2/" > file_hashes_to_recover.txt

#create git restore commands
# awk '{FS="\t"} {print "git show "$1" > recovered"FNR".pdf"}' file_hashes_to_recover.txt > file_recovery_commands.txt
awk '{FS="\t"} {print "git show "$1" > recovered"FNR}' file_hashes_to_recover.txt > file_recovery_commands.txt

#run the restoration commands
bash file_recovery_commands.txt