11-25-2016
Are you trying to rename *.bam and *.vcf files? Or, only *.bam files? There is nothing in your current script that does anything with *.vcf files, is there?
Do you only want to rename the files in the directory /home/cmccabe/Desktop/index/R_2016_09_21_14_01_15_user_S5-00580-9-Medexome? Or do you want to rename the files in all of the directories in /home/cmccabe/Desktop/index/ that are named in your input file?
Do you need to look at the directory name to determine which name change needs to occur, or will the "unique identifiers" found in your input file be unique across all directories?
This User Gave Thanks to Don Cragun For This Post:
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LEARN ABOUT CENTOS
git-mv
GIT-MV(1) Git Manual GIT-MV(1)
NAME
git-mv - Move or rename a file, a directory, or a symlink
SYNOPSIS
git mv <options>... <args>...
DESCRIPTION
This script is used to move or rename a file, directory or symlink.
git mv [-v] [-f] [-n] [-k] <source> <destination>
git mv [-v] [-f] [-n] [-k] <source> ... <destination directory>
In the first form, it renames <source>, which must exist and be either a file, symlink or directory, to <destination>. In the second form,
the last argument has to be an existing directory; the given sources will be moved into this directory.
The index is updated after successful completion, but the change must still be committed.
OPTIONS
-f, --force
Force renaming or moving of a file even if the target exists
-k
Skip move or rename actions which would lead to an error condition. An error happens when a source is neither existing nor controlled
by Git, or when it would overwrite an existing file unless -f is given.
-n, --dry-run
Do nothing; only show what would happen
-v, --verbose
Report the names of files as they are moved.
GIT
Part of the git(1) suite
Git 1.8.3.1 06/10/2014 GIT-MV(1)