diff test-data/gdout.txt @ 2:82fb5e3bb93e draft

"planemo upload commit 9f3f6fbbe2653d4c42818a89d6897ddaef6706b1"

--- a/test-data/gdout.txt	Mon Dec 02 04:51:27 2019 -0500
+++ b/test-data/gdout.txt	Wed Apr 07 12:17:45 2021 +0000
@@ -1,29 +1,29 @@
 #=GENOME_DIFF	1.0
 #=TITLE	smallest
-#=CREATED	16:09:36 17 Oct 2019
-#=PROGRAM	breseq 0.34.0 
-#=COMMAND	breseq --num-processors 1 -o results --reference /private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpYSLdP2/files/000/dataset_3.dat /private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpYSLdP2/files/000/dataset_1.dat --name smallest
-#=REFSEQ	/private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpYSLdP2/files/000/dataset_3.dat
-#=READSEQ	/private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpYSLdP2/files/000/dataset_1.dat
+#=CREATED	12:47:14 07 Apr 2021
+#=PROGRAM	breseq 0.35.5 
+#=COMMAND	breseq --num-processors 1 -o results --reference /home/berntm/.planemo/planemo_tmp_c9ga3mbq/test-data/lambda.gbk /tmp/tmpld3eebea/files/8/e/1/dataset_8e1ab48f-6786-4ed7-bf44-beec17749bb3.dat --name smallest
+#=REFSEQ	/home/berntm/.planemo/planemo_tmp_c9ga3mbq/test-data/lambda.gbk
+#=READSEQ	/tmp/tmpld3eebea/files/8/e/1/dataset_8e1ab48f-6786-4ed7-bf44-beec17749bb3.dat
 #=CONVERTED-BASES	250000
 #=CONVERTED-READS	5000
 #=INPUT-BASES	250000
 #=INPUT-READS	5000
-#=MAPPED-BASES	243031
-#=MAPPED-READS	4872
+#=MAPPED-BASES	242755
+#=MAPPED-READS	4870
 INS	1	11	NC_001416	41405	GCGGCGGCG	repeat_length=3	repeat_new_copies=5	repeat_ref_copies=2	repeat_seq=GCG
 DEL	2	8,12	NC_001416	41601	3	repeat_length=3	repeat_new_copies=1	repeat_ref_copies=2	repeat_seq=AAC
 INS	3	13	NC_001416	41716	TTTT	repeat_length=1	repeat_new_copies=9	repeat_ref_copies=5	repeat_seq=T
 DEL	4	9,14	NC_001416	44075	4	repeat_length=4	repeat_new_copies=1	repeat_ref_copies=2	repeat_seq=CAAA
 SNP	5	6	NC_001416	47317	T
-RA	6	.	NC_001416	47317	0	N	T	consensus_score=103.5	frequency=1	major_base=T	major_cov=17/17	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=17/17	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=17/17
+RA	6	.	NC_001416	47317	0	N	T	consensus_score=105.6	frequency=1	major_base=T	major_cov=17/17	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=17/17	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=17/17
 MC	7	.	NC_001416	1	38810	0	0	left_inside_cov=0	left_outside_cov=NA	right_inside_cov=10	right_outside_cov=13
 MC	8	.	NC_001416	41601	41603	0	0	left_inside_cov=0	left_outside_cov=29	right_inside_cov=0	right_outside_cov=28
 MC	9	.	NC_001416	44075	44078	0	0	left_inside_cov=0	left_outside_cov=28	right_inside_cov=0	right_outside_cov=27
 MC	10	.	NC_001416	48475	48502	0	0	left_inside_cov=10	left_outside_cov=12	right_inside_cov=0	right_outside_cov=NA
-JC	11	.	NC_001416	41398	1	NC_001416	41405	-1	-1	alignment_overlap=-1	coverage_minus=6	coverage_plus=18	flanking_left=50	flanking_right=50	frequency=1	junction_possible_overlap_registers=48	key=NC_001416__41398__1__NC_001416__41405__-1__-1__C__50__50__0__0	max_left=44	max_left_minus=39	max_left_plus=44	max_min_left=24	max_min_left_minus=23	max_min_left_plus=24	max_min_right=23	max_min_right_minus=11	max_min_right_plus=23	max_pos_hash_score=96	max_right=47	max_right_minus=34	max_right_plus=47	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.10	new_junction_read_count=27	polymorphism_frequency=9.168e-01	pos_hash_score=22	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.04	side_1_overlap=0	side_1_possible_overlap_registers=49	side_1_read_count=1	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.16	side_2_overlap=0	side_2_possible_overlap_registers=49	side_2_read_count=4	side_2_redundant=0	total_non_overlap_reads=24	unique_read_sequence=C
+JC	11	.	NC_001416	41398	1	NC_001416	41405	-1	-1	alignment_overlap=-1	coverage_minus=5	coverage_plus=18	flanking_left=50	flanking_right=50	frequency=1	junction_possible_overlap_registers=48	key=NC_001416__41398__1__NC_001416__41405__-1__-1__C__50__50__0__0	max_left=44	max_left_minus=38	max_left_plus=44	max_min_left=24	max_min_left_minus=23	max_min_left_plus=24	max_min_right=23	max_min_right_minus=11	max_min_right_plus=23	max_pos_hash_score=96	max_right=47	max_right_minus=34	max_right_plus=47	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.10	new_junction_read_count=27	polymorphism_frequency=9.168e-01	pos_hash_score=21	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.04	side_1_overlap=0	side_1_possible_overlap_registers=49	side_1_read_count=1	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.16	side_2_overlap=0	side_2_possible_overlap_registers=49	side_2_read_count=4	side_2_redundant=0	total_non_overlap_reads=23	unique_read_sequence=C
 JC	12	.	NC_001416	41600	-1	NC_001416	41604	1	0	alignment_overlap=4	coverage_minus=14	coverage_plus=8	flanking_left=50	flanking_right=50	frequency=1	junction_possible_overlap_registers=45	key=NC_001416__41600__-1__NC_001416__41600__1__4____50__50__0__0	max_left=42	max_left_minus=42	max_left_plus=38	max_min_left=22	max_min_left_minus=20	max_min_left_plus=22	max_min_right=20	max_min_right_minus=12	max_min_right_plus=20	max_pos_hash_score=90	max_right=44	max_right_minus=44	max_right_plus=37	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.00	new_junction_read_count=23	polymorphism_frequency=1.000e+00	pos_hash_score=19	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=4	side_1_possible_overlap_registers=49	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=45	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=22
-JC	13	.	NC_001416	41711	-1	NC_001416	41712	1	-4	alignment_overlap=-4	coverage_minus=10	coverage_plus=11	flanking_left=50	flanking_right=50	frequency=1	junction_possible_overlap_registers=45	key=NC_001416__41711__-1__NC_001416__41712__1__-4__TTTT__50__50__0__0	max_left=42	max_left_minus=42	max_left_plus=30	max_min_left=19	max_min_left_minus=19	max_min_left_plus=19	max_min_right=22	max_min_right_minus=19	max_min_right_plus=22	max_pos_hash_score=80	max_right=40	max_right_minus=37	max_right_plus=40	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.30	new_junction_read_count=30	polymorphism_frequency=1.000e+00	pos_hash_score=20	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=5	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=44	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=49	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=21	unique_read_sequence=TTTT
+JC	13	.	NC_001416	41712	1	NC_001416	41715	-1	0	alignment_overlap=1	coverage_minus=11	coverage_plus=11	flanking_left=50	flanking_right=50	frequency=1	junction_possible_overlap_registers=48	key=NC_001416__41712__1__NC_001416__41716__-1__1____50__50__0__0	max_left=48	max_left_minus=39	max_left_plus=48	max_min_left=21	max_min_left_minus=21	max_min_left_plus=18	max_min_right=23	max_min_right_minus=23	max_min_right_plus=23	max_pos_hash_score=96	max_right=46	max_right_minus=34	max_right_plus=46	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.06	new_junction_read_count=26	polymorphism_frequency=8.826e-01	pos_hash_score=21	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.16	side_1_overlap=1	side_1_possible_overlap_registers=49	side_1_read_count=4	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.12	side_2_overlap=0	side_2_possible_overlap_registers=48	side_2_read_count=3	side_2_redundant=0	total_non_overlap_reads=22
 JC	14	.	NC_001416	44074	-1	NC_001416	44079	1	0	alignment_overlap=5	coverage_minus=19	coverage_plus=5	flanking_left=50	flanking_right=50	frequency=1	junction_possible_overlap_registers=44	key=NC_001416__44074__-1__NC_001416__44074__1__5____50__50__0__0	max_left=44	max_left_minus=43	max_left_plus=44	max_min_left=21	max_min_left_minus=21	max_min_left_plus=18	max_min_right=22	max_min_right_minus=22	max_min_right_plus=12	max_pos_hash_score=88	max_right=43	max_right_minus=43	max_right_plus=27	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.11	new_junction_read_count=25	polymorphism_frequency=1.000e+00	pos_hash_score=20	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=5	side_1_possible_overlap_registers=49	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=44	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=24
 UN	15	.	NC_001416	1	38807
 UN	16	.	NC_001416	41601	41603