diff -r 85c57cc9b558 -r 82fb5e3bb93e test-data/gdout.txt
--- 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
diff -r 85c57cc9b558 -r 82fb5e3bb93e test-data/lambda.short_sequence_repeats.fastq.gz
Binary file test-data/lambda.short_sequence_repeats.fastq.gz has changed
diff -r 85c57cc9b558 -r 82fb5e3bb93e test-data/log.txt
--- a/test-data/log.txt Mon Dec 02 04:51:27 2019 -0500
+++ b/test-data/log.txt Wed Apr 07 12:17:45 2021 +0000
@@ -1,4 +1,4 @@
-Thu Oct 17 16:09:32 2019
+Wed Apr 7 12:46:45 2021
-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
+breseq --num-processors 1 -o results --reference /tmp/tmpld3eebea/files/3/b/d/dataset_3bd49447-677c-47c9-af83-1faa6f250e8b.dat /tmp/tmpld3eebea/files/e/5/8/dataset_e5864299-c116-4b7a-99b8-a39bd2f2c727.dat --name smallest
diff -r 85c57cc9b558 -r 82fb5e3bb93e test-data/report.html
--- a/test-data/report.html Mon Dec 02 04:51:27 2019 -0500
+++ b/test-data/report.html Wed Apr 07 12:17:45 2021 +0000
@@ -55,7 +55,7 @@
 |
-breseq version 0.34.0
+breseq version 0.35.5
mutation predictions |
marginal predictions |
summary statistics |
|