# Put this file in the configuration directory for alignment.
# The configuration directory is the directory where a setting file for alignment
# (e.g., "settingfile_alignment") exists.
# The following setting  files required for each step of alignment will be
# automatically generated in the configuration directory if these files are absent.
# - files_match.txt
# - files_match1.txt
# - files_match2.txt
# - files_match3.txt
# - files_msn.txt

# Lines start with "#" are ignored.

# Set the directory path for the PowerGetBatch results.

dir = /dir/path/for/powergetbatch/results

# Set the data to be aligned in the format below.
# Label <tab> s/m (sample or mock) <tab> h/l (high or low resolution data) <tab> directory name

S1_HR	s	h	DirNameOfSample1_HR
S2_HR	s	h	DirNameOfSample2_HR
S1_LR	s	l	DirNameOfSample1_LR
S2_LR	s	l	DirNameOfSample2_LR

# You can change the dir path by inserting a line starts with "dir = "
# The following

dir = /dir/path/for/powergetbatch/results2

S1_HR2	s	h	DirNameOfSample1_HR_retry
S2_HR2	s	h	DirNameOfSample2_HR_retry

Mock1	m	h	DirNameOfMock1
Mock1	m	h	DirNameOfMock2
