--- a/albacore_1D.py	Fri Sep 08 10:14:40 2017 -0400
+++ b/albacore_1D.py	Tue Oct 03 20:12:09 2017 -0400
@@ -7,7 +7,6 @@
 import shutil
 import h5py
 import numpy as np
-import tarfile
 from distutils.util import strtobool
 
 def main():
@@ -93,8 +92,15 @@
         if not os.path.exists(in_dir):
             os.makedirs(in_dir)
 
-        tar = tarfile.open(fn, mode='r')
-        tar.extractall(path=in_dir)
+        # python's tarfile interface does not sanitize file paths within
+        # tarballs, which can be a big security risk. GNU tar does sanitize by
+        # default, so it's easier/safer here just to call the system tar
+        subprocess.call([
+            "tar",
+            "-xf",
+            fn,
+            "-C",
+            in_dir])
 
         files = glob.glob(
             os.path.join(in_dir, "**", "*.fast5"),

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--- a/out_dir/configuration.cfg	Fri Sep 08 10:14:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-[pipeline]
-basecall_type = linear
-log_summaries = false
-log_all_intermodule_messages = false
-desc_file = /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned/layout_basecall_barcode_1d.jsn
-
-[data_trimmer]
-ev_window = 20
-ev_threshold = 5
-min_events = 3
-delta = 2
-
-[event_detector]
-window1 = 4
-window2 = 8
-threshold1 = 1.5
-threshold2 = 9.0
-peak_height = 0.2
-min_events = 1000
-trim_front = 0
-
-[basecaller]
-model = template_r9.5_450bps_5mer.jsn
-min_events = 100
-max_events = 1000
-overlap = 50
-min_quality = -100.0
-min_prob = 1e-5
-simple_decoding = 1
-model_path = /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned
-
-[call_handler]
-record_base = read
-qscore_adjuster_intercept = -4.5
-qscore_adjuster_slope = 3.0
-
-[barcode_detector]
-arrangements_files = barcode_arrs_pcr96.cfg barcode_arrs_nb.cfg barcode_arrs_rbk.cfg barcode_arrs_lwb.cfg barcode_arrs_rlb.cfg barcode_arrs_rab.cfg
-score_matrix = 4x4_mismatch_matrix.txt
-start_gap1 = 40
-end_gap1 = 40
-open_gap1 = 40
-extend_gap1 = 40
-start_gap2 = 40
-end_gap2 = 40
-open_gap2 = 160
-extend_gap2 = 160
-min_score = 60.0
-front_window_size = 150
-rear_window_size = 150
-
-[fastq]
-header = {read_id} runid={run_id} read={read_number} ch={channel_id} start_time={start_time_utc}
-header_with_barcoding = {read_id} runid={run_id} read={read_number} ch={channel_id} start_time={start_time_utc} barcode={barcode_id}
-batch_file_name = fastq_runid_{run_id}_{batch_counter}.fastq
-single_file_name = {read_id}.fastq
-

--- a/out_dir/pipeline.log	Fri Sep 08 10:14:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-2017-09-08 09:12:50,286 ONT Albacore Sequencing Pipeline Software (version 1.2.6)
-2017-09-08 09:12:50,286 Debug level is 0
-2017-09-08 09:12:50,292 Selected config file /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned/r95_450bps_linear.cfg to match flowcell FLO-MIN107 and kit SQK-LSK108
-2017-09-08 09:12:50,292 Loaded barcoding config from /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned/barcoding.cfg
-2017-09-08 09:12:51,304 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12068_ch_399_strand.fast5".
-2017-09-08 09:12:51,456 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12091_ch_399_strand.fast5".
-2017-09-08 09:12:51,550 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12068_ch_399_strand.fast5".
-2017-09-08 09:12:51,644 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12153_ch_399_strand.fast5".
-2017-09-08 09:12:51,671 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12091_ch_399_strand.fast5".
-2017-09-08 09:12:51,786 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12175_ch_399_strand.fast5".
-2017-09-08 09:12:51,840 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12153_ch_399_strand.fast5".
-2017-09-08 09:12:52,070 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12081_ch_399_strand.fast5".
-2017-09-08 09:12:52,124 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12175_ch_399_strand.fast5".
-2017-09-08 09:12:52,395 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12113_ch_399_strand.fast5".
-2017-09-08 09:12:52,450 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12081_ch_399_strand.fast5".
-2017-09-08 09:12:52,656 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12085_ch_399_strand.fast5".
-2017-09-08 09:12:52,681 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12113_ch_399_strand.fast5".
-2017-09-08 09:12:52,819 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12103_ch_399_strand.fast5".
-2017-09-08 09:12:52,873 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12085_ch_399_strand.fast5".
-2017-09-08 09:12:53,126 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12103_ch_399_strand.fast5".
-2017-09-08 09:12:53,128 Done.

--- a/out_dir/sequencing_summary.txt	Fri Sep 08 10:14:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-filename	read_id	run_id	channel	start_time	duration	num_events	template_start	num_events_template	template_duration	num_called_template	sequence_length_template	mean_qscore_template	strand_score_template	barcode_arrangement	barcode_score	barcode_full_arrangement	front_score	rear_score	front_begin_index	front_foundseq_length	rear_end_index	rear_foundseq_length	kit	variant
-macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12068_ch_399_strand.fast5	3030a28d-1f16-4086-9ba1-ff31a97f434d	d28f9f1c34b8f7416c367df1e0c4a864ba830c9c	1	5196.22842	1.10525	861	0.05129	861	1.05395	861	441	6.087	-0.0015	unclassified	37.230770111083984	NB09_var1	-inf	-inf	-1	0	-1	0	n/a	n/a
-macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12091_ch_399_strand.fast5	86fd3e14-b5ee-4453-98fa-084d75821456	d28f9f1c34b8f7416c367df1e0c4a864ba830c9c	1	5208.88562	1.84645	1417	0.09329	1417	1.75315	1417	793	6.096	-0.0017	unclassified	39.43589782714844	NB09_var2	-inf	-inf	-1	0	-1	0	n/a	n/a
-macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12153_ch_399_strand.fast5	2dd21811-c9af-4c4a-aaa0-4fd1f605abf8	d28f9f1c34b8f7416c367df1e0c4a864ba830c9c	1	5224.53552	1.14675	910	0.04997	910	1.09678	910	512	6.447	-0.0013	unclassified	33.28205108642578	NB08_var1	-inf	-inf	-1	0	-1	0	n/a	n/a
-macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12175_ch_399_strand.fast5	28daae22-d0dc-4fee-8453-3a2178b331c8	d28f9f1c34b8f7416c367df1e0c4a864ba830c9c	1	5230.13961	2.28967	1728	0.11604	1728	2.17364	1728	964	6.992	-0.001	unclassified	34.377357482910156	LWB09_var2	-inf	-inf	-1	0	-1	0	n/a	n/a
-macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12081_ch_399_strand.fast5	15bdfe23-0646-4c89-b523-185bc14c3a2a	d28f9f1c34b8f7416c367df1e0c4a864ba830c9c	1	5202.95983	2.90405	2423	0.01726	2423	2.88679	2423	1276	5.486	-0.0018	unclassified	35.8983039855957	BC24_var2	-inf	-inf	-1	0	-1	0	n/a	n/a
-macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12113_ch_399_strand.fast5	310f7b48-a3e0-4cdc-b396-09f4b86081dd	d28f9f1c34b8f7416c367df1e0c4a864ba830c9c	1	5216.31192	1.84894	1486	0.0	1486	1.84894	1486	821	6.153	-0.0018	unclassified	35.66101837158203	BC15_var1	-inf	-inf	-1	0	-1	0	n/a	n/a
-macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12085_ch_399_strand.fast5	921ea44a-1215-4f98-9f38-bf36b1bdf69c	d28f9f1c34b8f7416c367df1e0c4a864ba830c9c	1	5206.51394	1.57155	1271	0.0	1271	1.57155	1271	634	6.138	-0.0011	unclassified	29.743589401245117	NB04_var1	-inf	-inf	-1	0	-1	0	n/a	n/a
-macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12103_ch_399_strand.fast5	aabaf035-7aa8-439b-8773-523c69a350ca	d28f9f1c34b8f7416c367df1e0c4a864ba830c9c	1	5212.72327	1.70734	1427	0.0	1427	1.70734	1427	824	5.971	-0.0014	unclassified	33.01960754394531	RLB05	-inf	-inf	-1	0	-1	0	n/a	n/a

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