# HG changeset patch # User artbio # Date 1554080301 14400 # Node ID e75a10eba0a60b076b8d54da261bf5f645c74dfa # Parent 3ca8113cc7580462715276ff055476f0201fa844 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 0293b0f9b07302ba0b71e7877be1ea7a7ed04718 diff -r 3ca8113cc758 -r e75a10eba0a6 small_rna_maps.py --- a/small_rna_maps.py Tue Dec 25 06:02:08 2018 -0500 +++ b/small_rna_maps.py Sun Mar 31 20:58:21 2019 -0400 @@ -146,15 +146,33 @@ accumulator = [] for coor in F_clust_dic[centcoor]: accumulator.extend(map_dic[(chrom, coor, 'F')]) + ''' + compute the offset of the cluster due to + size of reads + ''' + last = sorted(F_clust_dic[centcoor])[-1] + try: + margin = max(map_dic[(chrom, last, 'F')]) - 1 + except ValueError: + margin = 0 clustered_dic[(chrom, centcoor, 'F')] = [len(accumulator), [ F_clust_dic[centcoor][0], - F_clust_dic[centcoor][-1]]] + F_clust_dic[centcoor][-1] + margin]] for centcoor in R_clust_dic: accumulator = [] for coor in R_clust_dic[centcoor]: accumulator.extend(map_dic[(chrom, coor, 'R')]) + ''' + compute the offset of the cluster due to + size of reads + ''' + first = sorted(R_clust_dic[centcoor])[0] + try: + margin = max(map_dic[(chrom, first, 'R')]) - 1 + except ValueError: + margin = 0 clustered_dic[(chrom, centcoor, 'R')] = [len(accumulator), [ - R_clust_dic[centcoor][0], + R_clust_dic[centcoor][0] - margin, R_clust_dic[centcoor][-1]]] return clustered_dic diff -r 3ca8113cc758 -r e75a10eba0a6 small_rna_maps.xml --- a/small_rna_maps.xml Tue Dec 25 06:02:08 2018 -0500 +++ b/small_rna_maps.xml Sun Mar 31 20:58:21 2019 -0400 @@ -1,4 +1,4 @@ - + numpy @@ -19,7 +19,6 @@ sambamba view -t \${GALAXY_SLOTS} -F "not unmapped and sequence_length >= ${minsize} and sequence_length <= ${maxsize}" -f bam '$file' -o '$file.element_identifier' && samtools index '$file.element_identifier' && #end for - ls -la ./ && python '$__tool_directory__'/small_rna_maps.py --inputs ${ ' '.join(['"%s"' % x.element_identifier for x in $inputs]) } #set $labels = list() diff -r 3ca8113cc758 -r e75a10eba0a6 test-data/bed1.bed --- a/test-data/bed1.bed Tue Dec 25 06:02:08 2018 -0500 +++ b/test-data/bed1.bed Sun Mar 31 20:58:21 2019 -0400 @@ -1,84 +1,84 @@ -FBtr0070001 0 1 cluster_1 1 + 1.0 -FBtr0070001 6 18 cluster_2 14 + 1.16666666667 -FBtr0070001 26 34 cluster_3 42 + 5.25 -FBtr0070533 0 1 cluster_4 1 + 1.0 -FBtr0070533 11 38 cluster_5 23 + 0.851851851852 -FBtr0070603 0 42 cluster_6 68 + 1.61904761905 -FBtr0070603 50 56 cluster_7 2 + 0.333333333333 -FBtr0070604 0 1 cluster_8 1 + 1.0 -FBtr0070604 17 22 cluster_9 2 + 0.4 -FBtr0070604 29 32 cluster_10 36 + 12.0 -FBtr0070604 56 57 cluster_11 1 + 1.0 -FBtr0070911 14 15 cluster_12 1 + 1.0 -FBtr0070911 37 38 cluster_13 1 + 1.0 -FBtr0078490 12 18 cluster_14 4 + 0.666666666667 -FBtr0078490 24 28 cluster_15 3 + 0.75 -FBtr0078490 37 38 cluster_16 1 + 1.0 -FBtr0078580 0 31 cluster_17 1102 + 35.5483870968 -FBtr0078580 51 52 cluster_18 2 + 2.0 -FBtr0078790 0 1 cluster_19 1 + 1.0 -FBtr0078790 16 17 cluster_20 2 + 2.0 -FBtr0078790 32 33 cluster_21 1 + 1.0 -FBtr0078790 41 52 cluster_22 9 + 0.818181818182 -FBtr0078790 68 69 cluster_23 1 - 1.0 -FBtr0079064 0 3 cluster_24 2 + 0.666666666667 -FBtr0079064 32 33 cluster_25 1 + 1.0 -FBtr0079064 51 52 cluster_26 1 + 1.0 -FBtr0079090 0 1 cluster_27 2 + 2.0 -FBtr0079090 25 26 cluster_28 1 + 1.0 -FBtr0079090 32 33 cluster_29 1 + 1.0 -FBtr0079090 52 53 cluster_30 1 + 1.0 -FBtr0079090 55 56 cluster_31 1 - 1.0 -FBtr0079338 11 17 cluster_32 5 + 0.833333333333 -FBtr0079338 24 25 cluster_33 1 + 1.0 -FBtr0079338 41 46 cluster_34 10 + 2.0 -FBtr0079528 0 18 cluster_35 97 + 5.38888888889 -FBtr0079528 27 28 cluster_36 1 + 1.0 -FBtr0079528 34 37 cluster_37 3 + 1.0 -FBtr0079528 50 51 cluster_38 5 + 5.0 -FBtr0079596 0 19 cluster_39 148 + 7.78947368421 -FBtr0079596 52 54 cluster_40 4 + 2.0 -FBtr0079677 0 5 cluster_41 2 + 0.4 -FBtr0079677 51 53 cluster_42 2 + 1.0 -FBtr0079690 0 1 cluster_43 1 + 1.0 -FBtr0079690 21 27 cluster_44 2 + 0.333333333333 -FBtr0079690 32 33 cluster_45 2 + 2.0 -FBtr0079692 0 1 cluster_46 3 + 3.0 -FBtr0079692 17 18 cluster_47 1 + 1.0 -FBtr0079692 24 25 cluster_48 1 + 1.0 -FBtr0079692 31 32 cluster_49 1 + 1.0 -FBtr0079693 0 1 cluster_50 5 + 5.0 -FBtr0079693 24 25 cluster_51 1 + 1.0 -FBtr0079694 0 1 cluster_52 5 + 5.0 -FBtr0079694 17 18 cluster_53 1 + 1.0 -FBtr0079694 51 52 cluster_54 1 + 1.0 -FBtr0079702 0 1 cluster_55 1 + 1.0 -FBtr0079702 18 19 cluster_56 2 + 2.0 -FBtr0079702 55 56 cluster_57 1 + 1.0 -FBtr0079728 0 1 cluster_58 2 + 2.0 -FBtr0079728 7 8 cluster_59 1 + 1.0 -FBtr0079728 18 19 cluster_60 1 + 1.0 -FBtr0079728 32 33 cluster_61 3 + 3.0 -FBtr0079728 55 56 cluster_62 1 + 1.0 -FBtr0079729 0 1 cluster_63 1 + 1.0 -FBtr0079729 12 13 cluster_64 1 + 1.0 -FBtr0079729 51 57 cluster_65 2 + 0.333333333333 -FBtr0079752 0 1 cluster_66 2 + 2.0 -FBtr0079752 6 12 cluster_67 2 + 0.333333333333 -FBtr0079752 32 33 cluster_68 2 + 2.0 -FBtr0079752 51 52 cluster_69 2 + 2.0 -FBtr0079820 44 56 cluster_70 13 + 1.08333333333 -FBtr0080609 0 20 cluster_71 60 + 3.0 -FBtr0080609 41 42 cluster_72 1 + 1.0 -FBtr0080609 50 52 cluster_73 2 + 1.0 -FBtr0080644 0 12 cluster_74 6 + 0.5 -FBtr0080646 0 7 cluster_75 3 + 0.428571428571 -FBtr0080647 0 12 cluster_76 10 + 0.833333333333 -FBtr0080660 0 7 cluster_77 7 + 1.0 -FBtr0080663 0 17 cluster_78 102 + 6.0 -FBtr0080663 25 26 cluster_79 1 + 1.0 -FBtr0080663 31 32 cluster_80 2 + 2.0 -FBtr0080663 49 51 cluster_81 10 + 5.0 -FBtr0080664 0 21 cluster_82 108 + 5.14285714286 -FBtr0080664 27 38 cluster_83 9 + 0.818181818182 -FBtr0080664 49 56 cluster_84 11 + 1.57142857143 +FBtr0070001 0 17 cluster_1 1 + 0.0588235294118 +FBtr0070001 6 33 cluster_2 14 + 0.518518518519 +FBtr0070001 26 53 cluster_3 42 + 1.55555555556 +FBtr0070533 0 15 cluster_4 1 + 0.0666666666667 +FBtr0070533 11 55 cluster_5 23 + 0.522727272727 +FBtr0070603 0 62 cluster_6 68 + 1.09677419355 +FBtr0070603 50 71 cluster_7 2 + 0.0952380952381 +FBtr0070604 0 15 cluster_8 1 + 0.0666666666667 +FBtr0070604 17 40 cluster_9 2 + 0.0869565217391 +FBtr0070604 29 53 cluster_10 36 + 1.5 +FBtr0070604 56 71 cluster_11 1 + 0.0666666666667 +FBtr0070911 14 35 cluster_12 1 + 0.047619047619 +FBtr0070911 37 52 cluster_13 1 + 0.0666666666667 +FBtr0078490 12 32 cluster_14 4 + 0.2 +FBtr0078490 24 50 cluster_15 3 + 0.115384615385 +FBtr0078490 37 55 cluster_16 1 + 0.0555555555556 +FBtr0078580 0 47 cluster_17 1102 + 23.4468085106 +FBtr0078580 51 68 cluster_18 2 + 0.117647058824 +FBtr0078790 0 19 cluster_19 1 + 0.0526315789474 +FBtr0078790 16 32 cluster_20 2 + 0.125 +FBtr0078790 32 55 cluster_21 1 + 0.0434782608696 +FBtr0078790 41 71 cluster_22 9 + 0.3 +FBtr0078790 54 69 cluster_23 1 - 0.0666666666667 +FBtr0079064 0 23 cluster_24 2 + 0.0869565217391 +FBtr0079064 32 47 cluster_25 1 + 0.0666666666667 +FBtr0079064 51 68 cluster_26 1 + 0.0588235294118 +FBtr0079090 0 28 cluster_27 2 + 0.0714285714286 +FBtr0079090 25 49 cluster_28 1 + 0.0416666666667 +FBtr0079090 32 48 cluster_29 1 + 0.0625 +FBtr0079090 52 70 cluster_30 1 + 0.0555555555556 +FBtr0079090 35 56 cluster_31 1 - 0.047619047619 +FBtr0079338 11 31 cluster_32 5 + 0.25 +FBtr0079338 24 40 cluster_33 1 + 0.0625 +FBtr0079338 41 63 cluster_34 10 + 0.454545454545 +FBtr0079528 0 38 cluster_35 97 + 2.55263157895 +FBtr0079528 27 43 cluster_36 1 + 0.0625 +FBtr0079528 34 54 cluster_37 3 + 0.15 +FBtr0079528 50 65 cluster_38 5 + 0.333333333333 +FBtr0079596 0 33 cluster_39 148 + 4.48484848485 +FBtr0079596 52 73 cluster_40 4 + 0.190476190476 +FBtr0079677 0 23 cluster_41 2 + 0.0869565217391 +FBtr0079677 51 70 cluster_42 2 + 0.105263157895 +FBtr0079690 0 15 cluster_43 1 + 0.0666666666667 +FBtr0079690 21 51 cluster_44 2 + 0.0666666666667 +FBtr0079690 32 49 cluster_45 2 + 0.117647058824 +FBtr0079692 0 23 cluster_46 3 + 0.130434782609 +FBtr0079692 17 35 cluster_47 1 + 0.0555555555556 +FBtr0079692 24 41 cluster_48 1 + 0.0588235294118 +FBtr0079692 31 51 cluster_49 1 + 0.05 +FBtr0079693 0 24 cluster_50 5 + 0.208333333333 +FBtr0079693 24 47 cluster_51 1 + 0.0434782608696 +FBtr0079694 0 25 cluster_52 5 + 0.2 +FBtr0079694 17 36 cluster_53 1 + 0.0526315789474 +FBtr0079694 51 68 cluster_54 1 + 0.0588235294118 +FBtr0079702 0 15 cluster_55 1 + 0.0666666666667 +FBtr0079702 18 36 cluster_56 2 + 0.111111111111 +FBtr0079702 55 70 cluster_57 1 + 0.0666666666667 +FBtr0079728 0 17 cluster_58 2 + 0.117647058824 +FBtr0079728 7 27 cluster_59 1 + 0.05 +FBtr0079728 18 42 cluster_60 1 + 0.0416666666667 +FBtr0079728 32 49 cluster_61 3 + 0.176470588235 +FBtr0079728 55 70 cluster_62 1 + 0.0666666666667 +FBtr0079729 0 15 cluster_63 1 + 0.0666666666667 +FBtr0079729 12 34 cluster_64 1 + 0.0454545454545 +FBtr0079729 51 72 cluster_65 2 + 0.0952380952381 +FBtr0079752 0 24 cluster_66 2 + 0.0833333333333 +FBtr0079752 6 27 cluster_67 2 + 0.0952380952381 +FBtr0079752 32 49 cluster_68 2 + 0.117647058824 +FBtr0079752 51 71 cluster_69 2 + 0.1 +FBtr0079820 44 74 cluster_70 13 + 0.433333333333 +FBtr0080609 0 44 cluster_71 60 + 1.36363636364 +FBtr0080609 41 62 cluster_72 1 + 0.047619047619 +FBtr0080609 50 66 cluster_73 2 + 0.125 +FBtr0080644 0 27 cluster_74 6 + 0.222222222222 +FBtr0080646 0 27 cluster_75 3 + 0.111111111111 +FBtr0080647 0 27 cluster_76 10 + 0.37037037037 +FBtr0080660 0 27 cluster_77 7 + 0.259259259259 +FBtr0080663 0 34 cluster_78 102 + 3.0 +FBtr0080663 25 43 cluster_79 1 + 0.0555555555556 +FBtr0080663 31 47 cluster_80 2 + 0.125 +FBtr0080663 49 70 cluster_81 10 + 0.47619047619 +FBtr0080664 0 35 cluster_82 108 + 3.08571428571 +FBtr0080664 27 52 cluster_83 9 + 0.36 +FBtr0080664 49 71 cluster_84 11 + 0.5 diff -r 3ca8113cc758 -r e75a10eba0a6 test-data/bed2.bed --- a/test-data/bed2.bed Tue Dec 25 06:02:08 2018 -0500 +++ b/test-data/bed2.bed Sun Mar 31 20:58:21 2019 -0400 @@ -1,83 +1,83 @@ -FBtr0070001 0 1 cluster_1 1 . 1.0 -FBtr0070001 6 18 cluster_2 14 . 1.16666666667 -FBtr0070001 26 34 cluster_3 42 . 5.25 -FBtr0070533 0 1 cluster_4 1 . 1.0 -FBtr0070533 11 38 cluster_5 23 . 0.851851851852 -FBtr0070603 0 42 cluster_6 68 . 1.61904761905 -FBtr0070603 50 56 cluster_7 2 . 0.333333333333 -FBtr0070604 0 1 cluster_8 1 . 1.0 -FBtr0070604 17 22 cluster_9 2 . 0.4 -FBtr0070604 29 32 cluster_10 36 . 12.0 -FBtr0070604 56 57 cluster_11 1 . 1.0 -FBtr0070911 14 15 cluster_12 1 . 1.0 -FBtr0070911 37 38 cluster_13 1 . 1.0 -FBtr0078490 12 18 cluster_14 4 . 0.666666666667 -FBtr0078490 24 28 cluster_15 3 . 0.75 -FBtr0078490 37 38 cluster_16 1 . 1.0 -FBtr0078580 0 31 cluster_17 1102 . 35.5483870968 -FBtr0078580 51 52 cluster_18 2 . 2.0 -FBtr0078790 0 1 cluster_19 1 . 1.0 -FBtr0078790 16 17 cluster_20 2 . 2.0 -FBtr0078790 32 33 cluster_21 1 . 1.0 -FBtr0078790 41 52 cluster_22 9 . 0.818181818182 +FBtr0070001 0 17 cluster_1 1 . 0.0588235294118 +FBtr0070001 6 33 cluster_2 14 . 0.518518518519 +FBtr0070001 26 53 cluster_3 42 . 1.55555555556 +FBtr0070533 0 15 cluster_4 1 . 0.0666666666667 +FBtr0070533 11 55 cluster_5 23 . 0.522727272727 +FBtr0070603 0 62 cluster_6 68 . 1.09677419355 +FBtr0070603 50 71 cluster_7 2 . 0.0952380952381 +FBtr0070604 0 15 cluster_8 1 . 0.0666666666667 +FBtr0070604 17 40 cluster_9 2 . 0.0869565217391 +FBtr0070604 29 53 cluster_10 36 . 1.5 +FBtr0070604 56 71 cluster_11 1 . 0.0666666666667 +FBtr0070911 14 35 cluster_12 1 . 0.047619047619 +FBtr0070911 37 52 cluster_13 1 . 0.0666666666667 +FBtr0078490 12 32 cluster_14 4 . 0.2 +FBtr0078490 24 50 cluster_15 3 . 0.115384615385 +FBtr0078490 37 55 cluster_16 1 . 0.0555555555556 +FBtr0078580 0 47 cluster_17 1102 . 23.4468085106 +FBtr0078580 51 68 cluster_18 2 . 0.117647058824 +FBtr0078790 0 19 cluster_19 1 . 0.0526315789474 +FBtr0078790 16 32 cluster_20 2 . 0.125 +FBtr0078790 32 55 cluster_21 1 . 0.0434782608696 +FBtr0078790 41 71 cluster_22 9 . 0.3 FBtr0078790 68 73 cluster_23 1 . 0.2 -FBtr0079064 0 3 cluster_24 2 . 0.666666666667 -FBtr0079064 32 33 cluster_25 1 . 1.0 -FBtr0079064 51 52 cluster_26 1 . 1.0 -FBtr0079090 0 1 cluster_27 2 . 2.0 -FBtr0079090 25 26 cluster_28 1 . 1.0 -FBtr0079090 32 33 cluster_29 1 . 1.0 -FBtr0079090 52 56 cluster_30 2 . 0.5 -FBtr0079338 11 17 cluster_31 5 . 0.833333333333 -FBtr0079338 24 25 cluster_32 1 . 1.0 -FBtr0079338 41 46 cluster_33 10 . 2.0 -FBtr0079528 0 18 cluster_34 97 . 5.38888888889 -FBtr0079528 27 28 cluster_35 1 . 1.0 -FBtr0079528 34 37 cluster_36 3 . 1.0 -FBtr0079528 50 51 cluster_37 5 . 5.0 -FBtr0079596 0 19 cluster_38 148 . 7.78947368421 -FBtr0079596 52 54 cluster_39 4 . 2.0 -FBtr0079677 0 5 cluster_40 2 . 0.4 -FBtr0079677 51 53 cluster_41 2 . 1.0 -FBtr0079690 0 1 cluster_42 1 . 1.0 -FBtr0079690 21 27 cluster_43 2 . 0.333333333333 -FBtr0079690 32 33 cluster_44 2 . 2.0 -FBtr0079692 0 1 cluster_45 3 . 3.0 -FBtr0079692 17 18 cluster_46 1 . 1.0 -FBtr0079692 24 25 cluster_47 1 . 1.0 -FBtr0079692 31 32 cluster_48 1 . 1.0 -FBtr0079693 0 1 cluster_49 5 . 5.0 -FBtr0079693 24 25 cluster_50 1 . 1.0 -FBtr0079694 0 1 cluster_51 5 . 5.0 -FBtr0079694 17 18 cluster_52 1 . 1.0 -FBtr0079694 51 52 cluster_53 1 . 1.0 -FBtr0079702 0 1 cluster_54 1 . 1.0 -FBtr0079702 18 19 cluster_55 2 . 2.0 -FBtr0079702 55 56 cluster_56 1 . 1.0 -FBtr0079728 0 1 cluster_57 2 . 2.0 -FBtr0079728 7 8 cluster_58 1 . 1.0 -FBtr0079728 18 19 cluster_59 1 . 1.0 -FBtr0079728 32 33 cluster_60 3 . 3.0 -FBtr0079728 55 56 cluster_61 1 . 1.0 -FBtr0079729 0 1 cluster_62 1 . 1.0 -FBtr0079729 12 13 cluster_63 1 . 1.0 -FBtr0079729 51 57 cluster_64 2 . 0.333333333333 -FBtr0079752 0 1 cluster_65 2 . 2.0 -FBtr0079752 6 12 cluster_66 2 . 0.333333333333 -FBtr0079752 32 33 cluster_67 2 . 2.0 -FBtr0079752 51 52 cluster_68 2 . 2.0 -FBtr0079820 44 56 cluster_69 13 . 1.08333333333 -FBtr0080609 0 20 cluster_70 60 . 3.0 -FBtr0080609 41 42 cluster_71 1 . 1.0 -FBtr0080609 50 52 cluster_72 2 . 1.0 -FBtr0080644 0 12 cluster_73 6 . 0.5 -FBtr0080646 0 7 cluster_74 3 . 0.428571428571 -FBtr0080647 0 12 cluster_75 10 . 0.833333333333 -FBtr0080660 0 7 cluster_76 7 . 1.0 -FBtr0080663 0 17 cluster_77 102 . 6.0 -FBtr0080663 25 26 cluster_78 1 . 1.0 -FBtr0080663 31 32 cluster_79 2 . 2.0 -FBtr0080663 49 51 cluster_80 10 . 5.0 -FBtr0080664 0 21 cluster_81 108 . 5.14285714286 -FBtr0080664 27 38 cluster_82 9 . 0.818181818182 -FBtr0080664 49 56 cluster_83 11 . 1.57142857143 +FBtr0079064 0 23 cluster_24 2 . 0.0869565217391 +FBtr0079064 32 47 cluster_25 1 . 0.0666666666667 +FBtr0079064 51 68 cluster_26 1 . 0.0588235294118 +FBtr0079090 0 28 cluster_27 2 . 0.0714285714286 +FBtr0079090 25 49 cluster_28 1 . 0.0416666666667 +FBtr0079090 32 48 cluster_29 1 . 0.0625 +FBtr0079090 52 76 cluster_30 2 . 0.0833333333333 +FBtr0079338 11 31 cluster_31 5 . 0.25 +FBtr0079338 24 40 cluster_32 1 . 0.0625 +FBtr0079338 41 63 cluster_33 10 . 0.454545454545 +FBtr0079528 0 38 cluster_34 97 . 2.55263157895 +FBtr0079528 27 43 cluster_35 1 . 0.0625 +FBtr0079528 34 54 cluster_36 3 . 0.15 +FBtr0079528 50 65 cluster_37 5 . 0.333333333333 +FBtr0079596 0 33 cluster_38 148 . 4.48484848485 +FBtr0079596 52 73 cluster_39 4 . 0.190476190476 +FBtr0079677 0 23 cluster_40 2 . 0.0869565217391 +FBtr0079677 51 70 cluster_41 2 . 0.105263157895 +FBtr0079690 0 15 cluster_42 1 . 0.0666666666667 +FBtr0079690 21 51 cluster_43 2 . 0.0666666666667 +FBtr0079690 32 49 cluster_44 2 . 0.117647058824 +FBtr0079692 0 23 cluster_45 3 . 0.130434782609 +FBtr0079692 17 35 cluster_46 1 . 0.0555555555556 +FBtr0079692 24 41 cluster_47 1 . 0.0588235294118 +FBtr0079692 31 51 cluster_48 1 . 0.05 +FBtr0079693 0 24 cluster_49 5 . 0.208333333333 +FBtr0079693 24 47 cluster_50 1 . 0.0434782608696 +FBtr0079694 0 25 cluster_51 5 . 0.2 +FBtr0079694 17 36 cluster_52 1 . 0.0526315789474 +FBtr0079694 51 68 cluster_53 1 . 0.0588235294118 +FBtr0079702 0 15 cluster_54 1 . 0.0666666666667 +FBtr0079702 18 36 cluster_55 2 . 0.111111111111 +FBtr0079702 55 70 cluster_56 1 . 0.0666666666667 +FBtr0079728 0 17 cluster_57 2 . 0.117647058824 +FBtr0079728 7 27 cluster_58 1 . 0.05 +FBtr0079728 18 42 cluster_59 1 . 0.0416666666667 +FBtr0079728 32 49 cluster_60 3 . 0.176470588235 +FBtr0079728 55 70 cluster_61 1 . 0.0666666666667 +FBtr0079729 0 15 cluster_62 1 . 0.0666666666667 +FBtr0079729 12 34 cluster_63 1 . 0.0454545454545 +FBtr0079729 51 72 cluster_64 2 . 0.0952380952381 +FBtr0079752 0 24 cluster_65 2 . 0.0833333333333 +FBtr0079752 6 27 cluster_66 2 . 0.0952380952381 +FBtr0079752 32 49 cluster_67 2 . 0.117647058824 +FBtr0079752 51 71 cluster_68 2 . 0.1 +FBtr0079820 44 74 cluster_69 13 . 0.433333333333 +FBtr0080609 0 44 cluster_70 60 . 1.36363636364 +FBtr0080609 41 62 cluster_71 1 . 0.047619047619 +FBtr0080609 50 66 cluster_72 2 . 0.125 +FBtr0080644 0 27 cluster_73 6 . 0.222222222222 +FBtr0080646 0 27 cluster_74 3 . 0.111111111111 +FBtr0080647 0 27 cluster_75 10 . 0.37037037037 +FBtr0080660 0 27 cluster_76 7 . 0.259259259259 +FBtr0080663 0 34 cluster_77 102 . 3.0 +FBtr0080663 25 43 cluster_78 1 . 0.0555555555556 +FBtr0080663 31 47 cluster_79 2 . 0.125 +FBtr0080663 49 70 cluster_80 10 . 0.47619047619 +FBtr0080664 0 35 cluster_81 108 . 3.08571428571 +FBtr0080664 27 52 cluster_82 9 . 0.36 +FBtr0080664 49 71 cluster_83 11 . 0.5 diff -r 3ca8113cc758 -r e75a10eba0a6 test-data/bed3.bed --- a/test-data/bed3.bed Tue Dec 25 06:02:08 2018 -0500 +++ b/test-data/bed3.bed Sun Mar 31 20:58:21 2019 -0400 @@ -1,35 +1,84 @@ -FBtr0070001 6 18 cluster_1 14 + 1.16666666667 -FBtr0070001 26 34 cluster_2 42 + 5.25 -FBtr0070533 11 38 cluster_3 23 + 0.851851851852 -FBtr0070603 0 42 cluster_4 68 + 1.61904761905 -FBtr0070603 50 56 cluster_5 2 + 0.333333333333 -FBtr0070604 17 22 cluster_6 2 + 0.4 -FBtr0070604 29 32 cluster_7 36 + 12.0 -FBtr0078490 12 18 cluster_8 4 + 0.666666666667 -FBtr0078490 24 28 cluster_9 3 + 0.75 -FBtr0078580 0 31 cluster_10 1102 + 35.5483870968 -FBtr0078790 41 52 cluster_11 9 + 0.818181818182 -FBtr0079064 0 3 cluster_12 2 + 0.666666666667 -FBtr0079338 11 17 cluster_13 5 + 0.833333333333 -FBtr0079338 41 46 cluster_14 10 + 2.0 -FBtr0079528 0 18 cluster_15 97 + 5.38888888889 -FBtr0079528 34 37 cluster_16 3 + 1.0 -FBtr0079596 0 19 cluster_17 148 + 7.78947368421 -FBtr0079596 52 54 cluster_18 4 + 2.0 -FBtr0079677 0 5 cluster_19 2 + 0.4 -FBtr0079677 51 53 cluster_20 2 + 1.0 -FBtr0079690 21 27 cluster_21 2 + 0.333333333333 -FBtr0079729 51 57 cluster_22 2 + 0.333333333333 -FBtr0079752 6 12 cluster_23 2 + 0.333333333333 -FBtr0079820 44 56 cluster_24 13 + 1.08333333333 -FBtr0080609 0 20 cluster_25 60 + 3.0 -FBtr0080609 50 52 cluster_26 2 + 1.0 -FBtr0080644 0 12 cluster_27 6 + 0.5 -FBtr0080646 0 7 cluster_28 3 + 0.428571428571 -FBtr0080647 0 12 cluster_29 10 + 0.833333333333 -FBtr0080660 0 7 cluster_30 7 + 1.0 -FBtr0080663 0 17 cluster_31 102 + 6.0 -FBtr0080663 49 51 cluster_32 10 + 5.0 -FBtr0080664 0 21 cluster_33 108 + 5.14285714286 -FBtr0080664 27 38 cluster_34 9 + 0.818181818182 -FBtr0080664 49 56 cluster_35 11 + 1.57142857143 +FBtr0070001 0 17 cluster_1 1 + 0.0588235294118 +FBtr0070001 6 33 cluster_2 14 + 0.518518518519 +FBtr0070001 26 53 cluster_3 42 + 1.55555555556 +FBtr0070533 0 15 cluster_4 1 + 0.0666666666667 +FBtr0070533 11 55 cluster_5 23 + 0.522727272727 +FBtr0070603 0 62 cluster_6 68 + 1.09677419355 +FBtr0070603 50 71 cluster_7 2 + 0.0952380952381 +FBtr0070604 0 15 cluster_8 1 + 0.0666666666667 +FBtr0070604 17 40 cluster_9 2 + 0.0869565217391 +FBtr0070604 29 53 cluster_10 36 + 1.5 +FBtr0070604 56 71 cluster_11 1 + 0.0666666666667 +FBtr0070911 14 35 cluster_12 1 + 0.047619047619 +FBtr0070911 37 52 cluster_13 1 + 0.0666666666667 +FBtr0078490 12 32 cluster_14 4 + 0.2 +FBtr0078490 24 50 cluster_15 3 + 0.115384615385 +FBtr0078490 37 55 cluster_16 1 + 0.0555555555556 +FBtr0078580 0 47 cluster_17 1102 + 23.4468085106 +FBtr0078580 51 68 cluster_18 2 + 0.117647058824 +FBtr0078790 0 19 cluster_19 1 + 0.0526315789474 +FBtr0078790 16 32 cluster_20 2 + 0.125 +FBtr0078790 32 55 cluster_21 1 + 0.0434782608696 +FBtr0078790 41 71 cluster_22 9 + 0.3 +FBtr0078790 54 69 cluster_23 1 - 0.0666666666667 +FBtr0079064 0 23 cluster_24 2 + 0.0869565217391 +FBtr0079064 32 47 cluster_25 1 + 0.0666666666667 +FBtr0079064 51 68 cluster_26 1 + 0.0588235294118 +FBtr0079090 0 28 cluster_27 2 + 0.0714285714286 +FBtr0079090 25 49 cluster_28 1 + 0.0416666666667 +FBtr0079090 32 48 cluster_29 1 + 0.0625 +FBtr0079090 52 70 cluster_30 1 + 0.0555555555556 +FBtr0079090 35 56 cluster_31 1 - 0.047619047619 +FBtr0079338 11 31 cluster_32 5 + 0.25 +FBtr0079338 24 40 cluster_33 1 + 0.0625 +FBtr0079338 41 63 cluster_34 10 + 0.454545454545 +FBtr0079528 0 38 cluster_35 97 + 2.55263157895 +FBtr0079528 27 43 cluster_36 1 + 0.0625 +FBtr0079528 34 54 cluster_37 3 + 0.15 +FBtr0079528 50 65 cluster_38 5 + 0.333333333333 +FBtr0079596 0 33 cluster_39 148 + 4.48484848485 +FBtr0079596 52 73 cluster_40 4 + 0.190476190476 +FBtr0079677 0 23 cluster_41 2 + 0.0869565217391 +FBtr0079677 51 70 cluster_42 2 + 0.105263157895 +FBtr0079690 0 15 cluster_43 1 + 0.0666666666667 +FBtr0079690 21 51 cluster_44 2 + 0.0666666666667 +FBtr0079690 32 49 cluster_45 2 + 0.117647058824 +FBtr0079692 0 23 cluster_46 3 + 0.130434782609 +FBtr0079692 17 35 cluster_47 1 + 0.0555555555556 +FBtr0079692 24 41 cluster_48 1 + 0.0588235294118 +FBtr0079692 31 51 cluster_49 1 + 0.05 +FBtr0079693 0 24 cluster_50 5 + 0.208333333333 +FBtr0079693 24 47 cluster_51 1 + 0.0434782608696 +FBtr0079694 0 25 cluster_52 5 + 0.2 +FBtr0079694 17 36 cluster_53 1 + 0.0526315789474 +FBtr0079694 51 68 cluster_54 1 + 0.0588235294118 +FBtr0079702 0 15 cluster_55 1 + 0.0666666666667 +FBtr0079702 18 36 cluster_56 2 + 0.111111111111 +FBtr0079702 55 70 cluster_57 1 + 0.0666666666667 +FBtr0079728 0 17 cluster_58 2 + 0.117647058824 +FBtr0079728 7 27 cluster_59 1 + 0.05 +FBtr0079728 18 42 cluster_60 1 + 0.0416666666667 +FBtr0079728 32 49 cluster_61 3 + 0.176470588235 +FBtr0079728 55 70 cluster_62 1 + 0.0666666666667 +FBtr0079729 0 15 cluster_63 1 + 0.0666666666667 +FBtr0079729 12 34 cluster_64 1 + 0.0454545454545 +FBtr0079729 51 72 cluster_65 2 + 0.0952380952381 +FBtr0079752 0 24 cluster_66 2 + 0.0833333333333 +FBtr0079752 6 27 cluster_67 2 + 0.0952380952381 +FBtr0079752 32 49 cluster_68 2 + 0.117647058824 +FBtr0079752 51 71 cluster_69 2 + 0.1 +FBtr0079820 44 74 cluster_70 13 + 0.433333333333 +FBtr0080609 0 44 cluster_71 60 + 1.36363636364 +FBtr0080609 41 62 cluster_72 1 + 0.047619047619 +FBtr0080609 50 66 cluster_73 2 + 0.125 +FBtr0080644 0 27 cluster_74 6 + 0.222222222222 +FBtr0080646 0 27 cluster_75 3 + 0.111111111111 +FBtr0080647 0 27 cluster_76 10 + 0.37037037037 +FBtr0080660 0 27 cluster_77 7 + 0.259259259259 +FBtr0080663 0 34 cluster_78 102 + 3.0 +FBtr0080663 25 43 cluster_79 1 + 0.0555555555556 +FBtr0080663 31 47 cluster_80 2 + 0.125 +FBtr0080663 49 70 cluster_81 10 + 0.47619047619 +FBtr0080664 0 35 cluster_82 108 + 3.08571428571 +FBtr0080664 27 52 cluster_83 9 + 0.36 +FBtr0080664 49 71 cluster_84 11 + 0.5 diff -r 3ca8113cc758 -r e75a10eba0a6 test-data/bed4.bed --- a/test-data/bed4.bed Tue Dec 25 06:02:08 2018 -0500 +++ b/test-data/bed4.bed Sun Mar 31 20:58:21 2019 -0400 @@ -1,15 +1,9 @@ -FBtr0070001 6 18 cluster_1 14 + 1.16666666667 -FBtr0070001 26 34 cluster_2 42 + 5.25 -FBtr0070603 0 42 cluster_3 68 + 1.61904761905 -FBtr0070604 29 32 cluster_4 36 + 12.0 -FBtr0078580 0 31 cluster_5 1102 + 35.5483870968 -FBtr0079338 41 46 cluster_6 10 + 2.0 -FBtr0079528 0 18 cluster_7 97 + 5.38888888889 -FBtr0079596 0 19 cluster_8 148 + 7.78947368421 -FBtr0079596 52 54 cluster_9 4 + 2.0 -FBtr0079820 44 56 cluster_10 13 + 1.08333333333 -FBtr0080609 0 20 cluster_11 60 + 3.0 -FBtr0080663 0 17 cluster_12 102 + 6.0 -FBtr0080663 49 51 cluster_13 10 + 5.0 -FBtr0080664 0 21 cluster_14 108 + 5.14285714286 -FBtr0080664 49 56 cluster_15 11 + 1.57142857143 +FBtr0070001 26 53 cluster_1 42 + 1.55555555556 +FBtr0070603 0 62 cluster_2 68 + 1.09677419355 +FBtr0070604 29 53 cluster_3 36 + 1.5 +FBtr0078580 0 47 cluster_4 1102 + 23.4468085106 +FBtr0079528 0 38 cluster_5 97 + 2.55263157895 +FBtr0079596 0 33 cluster_6 148 + 4.48484848485 +FBtr0080609 0 44 cluster_7 60 + 1.36363636364 +FBtr0080663 0 34 cluster_8 102 + 3.0 +FBtr0080664 0 35 cluster_9 108 + 3.08571428571 diff -r 3ca8113cc758 -r e75a10eba0a6 test-data/bed5.bed --- a/test-data/bed5.bed Tue Dec 25 06:02:08 2018 -0500 +++ b/test-data/bed5.bed Sun Mar 31 20:58:21 2019 -0400 @@ -1,30 +1,15 @@ -FBtr0070001 6 18 cluster_1 14 . 1.16666666667 -FBtr0070001 26 34 cluster_2 42 . 5.25 -FBtr0070533 11 38 cluster_3 23 . 0.851851851852 -FBtr0070603 0 42 cluster_4 68 . 1.61904761905 -FBtr0070604 29 32 cluster_5 36 . 12.0 -FBtr0078490 12 18 cluster_6 4 . 0.666666666667 -FBtr0078490 24 28 cluster_7 3 . 0.75 -FBtr0078580 0 31 cluster_8 1102 . 35.5483870968 -FBtr0078790 41 52 cluster_9 9 . 0.818181818182 -FBtr0079064 0 3 cluster_10 2 . 0.666666666667 -FBtr0079090 52 56 cluster_11 2 . 0.5 -FBtr0079338 11 17 cluster_12 5 . 0.833333333333 -FBtr0079338 41 46 cluster_13 10 . 2.0 -FBtr0079528 0 18 cluster_14 97 . 5.38888888889 -FBtr0079528 34 37 cluster_15 3 . 1.0 -FBtr0079596 0 19 cluster_16 148 . 7.78947368421 -FBtr0079596 52 54 cluster_17 4 . 2.0 -FBtr0079677 51 53 cluster_18 2 . 1.0 -FBtr0079820 44 56 cluster_19 13 . 1.08333333333 -FBtr0080609 0 20 cluster_20 60 . 3.0 -FBtr0080609 50 52 cluster_21 2 . 1.0 -FBtr0080644 0 12 cluster_22 6 . 0.5 -FBtr0080646 0 7 cluster_23 3 . 0.428571428571 -FBtr0080647 0 12 cluster_24 10 . 0.833333333333 -FBtr0080660 0 7 cluster_25 7 . 1.0 -FBtr0080663 0 17 cluster_26 102 . 6.0 -FBtr0080663 49 51 cluster_27 10 . 5.0 -FBtr0080664 0 21 cluster_28 108 . 5.14285714286 -FBtr0080664 27 38 cluster_29 9 . 0.818181818182 -FBtr0080664 49 56 cluster_30 11 . 1.57142857143 +FBtr0070001 6 33 cluster_1 14 . 0.518518518519 +FBtr0070001 26 53 cluster_2 42 . 1.55555555556 +FBtr0070533 11 55 cluster_3 23 . 0.522727272727 +FBtr0070603 0 62 cluster_4 68 . 1.09677419355 +FBtr0070604 29 53 cluster_5 36 . 1.5 +FBtr0078580 0 47 cluster_6 1102 . 23.4468085106 +FBtr0079338 41 63 cluster_7 10 . 0.454545454545 +FBtr0079528 0 38 cluster_8 97 . 2.55263157895 +FBtr0079596 0 33 cluster_9 148 . 4.48484848485 +FBtr0079820 44 74 cluster_10 13 . 0.433333333333 +FBtr0080609 0 44 cluster_11 60 . 1.36363636364 +FBtr0080663 0 34 cluster_12 102 . 3.0 +FBtr0080663 49 70 cluster_13 10 . 0.47619047619 +FBtr0080664 0 35 cluster_14 108 . 3.08571428571 +FBtr0080664 49 71 cluster_15 11 . 0.5 diff -r 3ca8113cc758 -r e75a10eba0a6 test-data/clustering.pdf Binary file test-data/clustering.pdf has changed diff -r 3ca8113cc758 -r e75a10eba0a6 test-data/clustering.tab --- a/test-data/clustering.tab Tue Dec 25 06:02:08 2018 -0500 +++ b/test-data/clustering.tab Sun Mar 31 20:58:21 2019 -0400 @@ -1,119 +1,119 @@ Dataset Chromosome Chrom_length Coordinate Polarity Counts Start-End Cluster Size density -input1.bam FBtr0070001 72 1 F 1 1-1 1 1.0 -input1.bam FBtr0070001 72 12 F 14 7-18 12 1.16666666667 -input1.bam FBtr0070001 72 30 F 42 27-34 8 5.25 +input1.bam FBtr0070001 72 1 F 1 1-17 17 0.0588235294118 +input1.bam FBtr0070001 72 12 F 14 7-33 27 0.518518518519 +input1.bam FBtr0070001 72 30 F 42 27-53 27 1.55555555556 input1.bam FBtr0070001 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0070533 72 1 F 1 1-1 1 1.0 -input1.bam FBtr0070533 72 25 F 23 12-38 27 0.851851851852 +input1.bam FBtr0070533 72 1 F 1 1-15 15 0.0666666666667 +input1.bam FBtr0070533 72 25 F 23 12-55 44 0.522727272727 input1.bam FBtr0070533 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0070603 72 21 F 68 1-42 42 1.61904761905 -input1.bam FBtr0070603 72 53 F 2 51-56 6 0.333333333333 +input1.bam FBtr0070603 72 21 F 68 1-62 62 1.09677419355 +input1.bam FBtr0070603 72 53 F 2 51-71 21 0.0952380952381 input1.bam FBtr0070603 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0070604 72 1 F 1 1-1 1 1.0 -input1.bam FBtr0070604 72 20 F 2 18-22 5 0.4 -input1.bam FBtr0070604 72 31 F 36 30-32 3 12.0 -input1.bam FBtr0070604 72 57 F 1 57-57 1 1.0 +input1.bam FBtr0070604 72 1 F 1 1-15 15 0.0666666666667 +input1.bam FBtr0070604 72 20 F 2 18-40 23 0.0869565217391 +input1.bam FBtr0070604 72 31 F 36 30-53 24 1.5 +input1.bam FBtr0070604 72 57 F 1 57-71 15 0.0666666666667 input1.bam FBtr0070604 72 72 F 0 72-72 1 0.0 input1.bam FBtr0070911 73 1 F 0 1-1 1 0.0 -input1.bam FBtr0070911 73 15 F 1 15-15 1 1.0 -input1.bam FBtr0070911 73 38 F 1 38-38 1 1.0 +input1.bam FBtr0070911 73 15 F 1 15-35 21 0.047619047619 +input1.bam FBtr0070911 73 38 F 1 38-52 15 0.0666666666667 input1.bam FBtr0070911 73 73 F 0 73-73 1 0.0 input1.bam FBtr0078490 72 1 F 0 1-1 1 0.0 -input1.bam FBtr0078490 72 15 F 4 13-18 6 0.666666666667 -input1.bam FBtr0078490 72 26 F 3 25-28 4 0.75 -input1.bam FBtr0078490 72 38 F 1 38-38 1 1.0 +input1.bam FBtr0078490 72 15 F 4 13-32 20 0.2 +input1.bam FBtr0078490 72 26 F 3 25-50 26 0.115384615385 +input1.bam FBtr0078490 72 38 F 1 38-55 18 0.0555555555556 input1.bam FBtr0078490 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0078580 72 16 F 1102 1-31 31 35.5483870968 -input1.bam FBtr0078580 72 52 F 2 52-52 1 2.0 +input1.bam FBtr0078580 72 16 F 1102 1-47 47 23.4468085106 +input1.bam FBtr0078580 72 52 F 2 52-68 17 0.117647058824 input1.bam FBtr0078580 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0078790 73 1 F 1 1-1 1 1.0 -input1.bam FBtr0078790 73 17 F 2 17-17 1 2.0 -input1.bam FBtr0078790 73 33 F 1 33-33 1 1.0 -input1.bam FBtr0078790 73 47 F 9 42-52 11 0.818181818182 -input1.bam FBtr0078790 73 69 R 1 69-69 1 1.0 +input1.bam FBtr0078790 73 1 F 1 1-19 19 0.0526315789474 +input1.bam FBtr0078790 73 17 F 2 17-32 16 0.125 +input1.bam FBtr0078790 73 33 F 1 33-55 23 0.0434782608696 +input1.bam FBtr0078790 73 47 F 9 42-71 30 0.3 +input1.bam FBtr0078790 73 69 R 1 55-69 15 0.0666666666667 input1.bam FBtr0078790 73 73 F 0 73-73 1 0.0 -input1.bam FBtr0079064 72 2 F 2 1-3 3 0.666666666667 -input1.bam FBtr0079064 72 33 F 1 33-33 1 1.0 -input1.bam FBtr0079064 72 52 F 1 52-52 1 1.0 +input1.bam FBtr0079064 72 2 F 2 1-23 23 0.0869565217391 +input1.bam FBtr0079064 72 33 F 1 33-47 15 0.0666666666667 +input1.bam FBtr0079064 72 52 F 1 52-68 17 0.0588235294118 input1.bam FBtr0079064 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079090 72 1 F 2 1-1 1 2.0 -input1.bam FBtr0079090 72 26 F 1 26-26 1 1.0 -input1.bam FBtr0079090 72 33 F 1 33-33 1 1.0 -input1.bam FBtr0079090 72 53 F 1 53-53 1 1.0 -input1.bam FBtr0079090 72 56 R 1 56-56 1 1.0 +input1.bam FBtr0079090 72 1 F 2 1-28 28 0.0714285714286 +input1.bam FBtr0079090 72 26 F 1 26-49 24 0.0416666666667 +input1.bam FBtr0079090 72 33 F 1 33-48 16 0.0625 +input1.bam FBtr0079090 72 53 F 1 53-70 18 0.0555555555556 +input1.bam FBtr0079090 72 56 R 1 36-56 21 0.047619047619 input1.bam FBtr0079090 72 72 F 0 72-72 1 0.0 input1.bam FBtr0079338 73 1 F 0 1-1 1 0.0 -input1.bam FBtr0079338 73 14 F 5 12-17 6 0.833333333333 -input1.bam FBtr0079338 73 25 F 1 25-25 1 1.0 -input1.bam FBtr0079338 73 44 F 10 42-46 5 2.0 +input1.bam FBtr0079338 73 14 F 5 12-31 20 0.25 +input1.bam FBtr0079338 73 25 F 1 25-40 16 0.0625 +input1.bam FBtr0079338 73 44 F 10 42-63 22 0.454545454545 input1.bam FBtr0079338 73 73 F 0 73-73 1 0.0 -input1.bam FBtr0079528 71 9 F 97 1-18 18 5.38888888889 -input1.bam FBtr0079528 71 28 F 1 28-28 1 1.0 -input1.bam FBtr0079528 71 36 F 3 35-37 3 1.0 -input1.bam FBtr0079528 71 51 F 5 51-51 1 5.0 +input1.bam FBtr0079528 71 9 F 97 1-38 38 2.55263157895 +input1.bam FBtr0079528 71 28 F 1 28-43 16 0.0625 +input1.bam FBtr0079528 71 36 F 3 35-54 20 0.15 +input1.bam FBtr0079528 71 51 F 5 51-65 15 0.333333333333 input1.bam FBtr0079528 71 71 F 0 71-71 1 0.0 -input1.bam FBtr0079596 73 10 F 148 1-19 19 7.78947368421 -input1.bam FBtr0079596 73 53 F 4 53-54 2 2.0 +input1.bam FBtr0079596 73 10 F 148 1-33 33 4.48484848485 +input1.bam FBtr0079596 73 53 F 4 53-73 21 0.190476190476 input1.bam FBtr0079596 73 73 F 0 73-73 1 0.0 -input1.bam FBtr0079677 72 3 F 2 1-5 5 0.4 -input1.bam FBtr0079677 72 52 F 2 52-53 2 1.0 +input1.bam FBtr0079677 72 3 F 2 1-23 23 0.0869565217391 +input1.bam FBtr0079677 72 52 F 2 52-70 19 0.105263157895 input1.bam FBtr0079677 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079690 72 1 F 1 1-1 1 1.0 -input1.bam FBtr0079690 72 24 F 2 22-27 6 0.333333333333 -input1.bam FBtr0079690 72 33 F 2 33-33 1 2.0 +input1.bam FBtr0079690 72 1 F 1 1-15 15 0.0666666666667 +input1.bam FBtr0079690 72 24 F 2 22-51 30 0.0666666666667 +input1.bam FBtr0079690 72 33 F 2 33-49 17 0.117647058824 input1.bam FBtr0079690 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079692 73 1 F 3 1-1 1 3.0 -input1.bam FBtr0079692 73 18 F 1 18-18 1 1.0 -input1.bam FBtr0079692 73 25 F 1 25-25 1 1.0 -input1.bam FBtr0079692 73 32 F 1 32-32 1 1.0 +input1.bam FBtr0079692 73 1 F 3 1-23 23 0.130434782609 +input1.bam FBtr0079692 73 18 F 1 18-35 18 0.0555555555556 +input1.bam FBtr0079692 73 25 F 1 25-41 17 0.0588235294118 +input1.bam FBtr0079692 73 32 F 1 32-51 20 0.05 input1.bam FBtr0079692 73 73 F 0 73-73 1 0.0 -input1.bam FBtr0079693 72 1 F 5 1-1 1 5.0 -input1.bam FBtr0079693 72 25 F 1 25-25 1 1.0 +input1.bam FBtr0079693 72 1 F 5 1-24 24 0.208333333333 +input1.bam FBtr0079693 72 25 F 1 25-47 23 0.0434782608696 input1.bam FBtr0079693 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079694 72 1 F 5 1-1 1 5.0 -input1.bam FBtr0079694 72 18 F 1 18-18 1 1.0 -input1.bam FBtr0079694 72 52 F 1 52-52 1 1.0 +input1.bam FBtr0079694 72 1 F 5 1-25 25 0.2 +input1.bam FBtr0079694 72 18 F 1 18-36 19 0.0526315789474 +input1.bam FBtr0079694 72 52 F 1 52-68 17 0.0588235294118 input1.bam FBtr0079694 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079702 72 1 F 1 1-1 1 1.0 -input1.bam FBtr0079702 72 19 F 2 19-19 1 2.0 -input1.bam FBtr0079702 72 56 F 1 56-56 1 1.0 +input1.bam FBtr0079702 72 1 F 1 1-15 15 0.0666666666667 +input1.bam FBtr0079702 72 19 F 2 19-36 18 0.111111111111 +input1.bam FBtr0079702 72 56 F 1 56-70 15 0.0666666666667 input1.bam FBtr0079702 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079728 72 1 F 2 1-1 1 2.0 -input1.bam FBtr0079728 72 8 F 1 8-8 1 1.0 -input1.bam FBtr0079728 72 19 F 1 19-19 1 1.0 -input1.bam FBtr0079728 72 33 F 3 33-33 1 3.0 -input1.bam FBtr0079728 72 56 F 1 56-56 1 1.0 +input1.bam FBtr0079728 72 1 F 2 1-17 17 0.117647058824 +input1.bam FBtr0079728 72 8 F 1 8-27 20 0.05 +input1.bam FBtr0079728 72 19 F 1 19-42 24 0.0416666666667 +input1.bam FBtr0079728 72 33 F 3 33-49 17 0.176470588235 +input1.bam FBtr0079728 72 56 F 1 56-70 15 0.0666666666667 input1.bam FBtr0079728 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079729 72 1 F 1 1-1 1 1.0 -input1.bam FBtr0079729 72 13 F 1 13-13 1 1.0 -input1.bam FBtr0079729 72 54 F 2 52-57 6 0.333333333333 +input1.bam FBtr0079729 72 1 F 1 1-15 15 0.0666666666667 +input1.bam FBtr0079729 72 13 F 1 13-34 22 0.0454545454545 +input1.bam FBtr0079729 72 54 F 2 52-72 21 0.0952380952381 input1.bam FBtr0079729 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079752 72 1 F 2 1-1 1 2.0 -input1.bam FBtr0079752 72 9 F 2 7-12 6 0.333333333333 -input1.bam FBtr0079752 72 33 F 2 33-33 1 2.0 -input1.bam FBtr0079752 72 52 F 2 52-52 1 2.0 +input1.bam FBtr0079752 72 1 F 2 1-24 24 0.0833333333333 +input1.bam FBtr0079752 72 9 F 2 7-27 21 0.0952380952381 +input1.bam FBtr0079752 72 33 F 2 33-49 17 0.117647058824 +input1.bam FBtr0079752 72 52 F 2 52-71 20 0.1 input1.bam FBtr0079752 72 72 F 0 72-72 1 0.0 input1.bam FBtr0079820 74 1 F 0 1-1 1 0.0 -input1.bam FBtr0079820 74 50 F 13 45-56 12 1.08333333333 +input1.bam FBtr0079820 74 50 F 13 45-74 30 0.433333333333 input1.bam FBtr0079820 74 74 F 0 74-74 1 0.0 -input1.bam FBtr0080609 72 10 F 60 1-20 20 3.0 -input1.bam FBtr0080609 72 42 F 1 42-42 1 1.0 -input1.bam FBtr0080609 72 51 F 2 51-52 2 1.0 +input1.bam FBtr0080609 72 10 F 60 1-44 44 1.36363636364 +input1.bam FBtr0080609 72 42 F 1 42-62 21 0.047619047619 +input1.bam FBtr0080609 72 51 F 2 51-66 16 0.125 input1.bam FBtr0080609 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0080644 72 6 F 6 1-12 12 0.5 +input1.bam FBtr0080644 72 6 F 6 1-27 27 0.222222222222 input1.bam FBtr0080644 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0080646 72 4 F 3 1-7 7 0.428571428571 +input1.bam FBtr0080646 72 4 F 3 1-27 27 0.111111111111 input1.bam FBtr0080646 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0080647 72 6 F 10 1-12 12 0.833333333333 +input1.bam FBtr0080647 72 6 F 10 1-27 27 0.37037037037 input1.bam FBtr0080647 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0080660 72 4 F 7 1-7 7 1.0 +input1.bam FBtr0080660 72 4 F 7 1-27 27 0.259259259259 input1.bam FBtr0080660 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0080663 71 9 F 102 1-17 17 6.0 -input1.bam FBtr0080663 71 26 F 1 26-26 1 1.0 -input1.bam FBtr0080663 71 32 F 2 32-32 1 2.0 -input1.bam FBtr0080663 71 50 F 10 50-51 2 5.0 +input1.bam FBtr0080663 71 9 F 102 1-34 34 3.0 +input1.bam FBtr0080663 71 26 F 1 26-43 18 0.0555555555556 +input1.bam FBtr0080663 71 32 F 2 32-47 16 0.125 +input1.bam FBtr0080663 71 50 F 10 50-70 21 0.47619047619 input1.bam FBtr0080663 71 71 F 0 71-71 1 0.0 -input1.bam FBtr0080664 71 11 F 108 1-21 21 5.14285714286 -input1.bam FBtr0080664 71 33 F 9 28-38 11 0.818181818182 -input1.bam FBtr0080664 71 53 F 11 50-56 7 1.57142857143 +input1.bam FBtr0080664 71 11 F 108 1-35 35 3.08571428571 +input1.bam FBtr0080664 71 33 F 9 28-52 25 0.36 +input1.bam FBtr0080664 71 53 F 11 50-71 22 0.5 input1.bam FBtr0080664 71 71 F 0 71-71 1 0.0 diff -r 3ca8113cc758 -r e75a10eba0a6 test-data/clustering_unstranded.pdf Binary file test-data/clustering_unstranded.pdf has changed diff -r 3ca8113cc758 -r e75a10eba0a6 test-data/clustering_unstranded.tab --- a/test-data/clustering_unstranded.tab Tue Dec 25 06:02:08 2018 -0500 +++ b/test-data/clustering_unstranded.tab Sun Mar 31 20:58:21 2019 -0400 @@ -1,117 +1,117 @@ Dataset Chromosome Chrom_length Coordinate Polarity Counts Start-End Cluster Size density -input1.bam FBtr0070001 72 1 F 1 1-1 1 1.0 -input1.bam FBtr0070001 72 12 F 14 7-18 12 1.16666666667 -input1.bam FBtr0070001 72 30 F 42 27-34 8 5.25 +input1.bam FBtr0070001 72 1 F 1 1-17 17 0.0588235294118 +input1.bam FBtr0070001 72 12 F 14 7-33 27 0.518518518519 +input1.bam FBtr0070001 72 30 F 42 27-53 27 1.55555555556 input1.bam FBtr0070001 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0070533 72 1 F 1 1-1 1 1.0 -input1.bam FBtr0070533 72 25 F 23 12-38 27 0.851851851852 +input1.bam FBtr0070533 72 1 F 1 1-15 15 0.0666666666667 +input1.bam FBtr0070533 72 25 F 23 12-55 44 0.522727272727 input1.bam FBtr0070533 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0070603 72 21 F 68 1-42 42 1.61904761905 -input1.bam FBtr0070603 72 53 F 2 51-56 6 0.333333333333 +input1.bam FBtr0070603 72 21 F 68 1-62 62 1.09677419355 +input1.bam FBtr0070603 72 53 F 2 51-71 21 0.0952380952381 input1.bam FBtr0070603 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0070604 72 1 F 1 1-1 1 1.0 -input1.bam FBtr0070604 72 20 F 2 18-22 5 0.4 -input1.bam FBtr0070604 72 31 F 36 30-32 3 12.0 -input1.bam FBtr0070604 72 57 F 1 57-57 1 1.0 +input1.bam FBtr0070604 72 1 F 1 1-15 15 0.0666666666667 +input1.bam FBtr0070604 72 20 F 2 18-40 23 0.0869565217391 +input1.bam FBtr0070604 72 31 F 36 30-53 24 1.5 +input1.bam FBtr0070604 72 57 F 1 57-71 15 0.0666666666667 input1.bam FBtr0070604 72 72 F 0 72-72 1 0.0 input1.bam FBtr0070911 73 1 F 0 1-1 1 0.0 -input1.bam FBtr0070911 73 15 F 1 15-15 1 1.0 -input1.bam FBtr0070911 73 38 F 1 38-38 1 1.0 +input1.bam FBtr0070911 73 15 F 1 15-35 21 0.047619047619 +input1.bam FBtr0070911 73 38 F 1 38-52 15 0.0666666666667 input1.bam FBtr0070911 73 73 F 0 73-73 1 0.0 input1.bam FBtr0078490 72 1 F 0 1-1 1 0.0 -input1.bam FBtr0078490 72 15 F 4 13-18 6 0.666666666667 -input1.bam FBtr0078490 72 26 F 3 25-28 4 0.75 -input1.bam FBtr0078490 72 38 F 1 38-38 1 1.0 +input1.bam FBtr0078490 72 15 F 4 13-32 20 0.2 +input1.bam FBtr0078490 72 26 F 3 25-50 26 0.115384615385 +input1.bam FBtr0078490 72 38 F 1 38-55 18 0.0555555555556 input1.bam FBtr0078490 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0078580 72 16 F 1102 1-31 31 35.5483870968 -input1.bam FBtr0078580 72 52 F 2 52-52 1 2.0 +input1.bam FBtr0078580 72 16 F 1102 1-47 47 23.4468085106 +input1.bam FBtr0078580 72 52 F 2 52-68 17 0.117647058824 input1.bam FBtr0078580 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0078790 73 1 F 1 1-1 1 1.0 -input1.bam FBtr0078790 73 17 F 2 17-17 1 2.0 -input1.bam FBtr0078790 73 33 F 1 33-33 1 1.0 -input1.bam FBtr0078790 73 47 F 9 42-52 11 0.818181818182 +input1.bam FBtr0078790 73 1 F 1 1-19 19 0.0526315789474 +input1.bam FBtr0078790 73 17 F 2 17-32 16 0.125 +input1.bam FBtr0078790 73 33 F 1 33-55 23 0.0434782608696 +input1.bam FBtr0078790 73 47 F 9 42-71 30 0.3 input1.bam FBtr0078790 73 71 F 1 69-73 5 0.2 -input1.bam FBtr0079064 72 2 F 2 1-3 3 0.666666666667 -input1.bam FBtr0079064 72 33 F 1 33-33 1 1.0 -input1.bam FBtr0079064 72 52 F 1 52-52 1 1.0 +input1.bam FBtr0079064 72 2 F 2 1-23 23 0.0869565217391 +input1.bam FBtr0079064 72 33 F 1 33-47 15 0.0666666666667 +input1.bam FBtr0079064 72 52 F 1 52-68 17 0.0588235294118 input1.bam FBtr0079064 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079090 72 1 F 2 1-1 1 2.0 -input1.bam FBtr0079090 72 26 F 1 26-26 1 1.0 -input1.bam FBtr0079090 72 33 F 1 33-33 1 1.0 -input1.bam FBtr0079090 72 54 F 2 53-56 4 0.5 +input1.bam FBtr0079090 72 1 F 2 1-28 28 0.0714285714286 +input1.bam FBtr0079090 72 26 F 1 26-49 24 0.0416666666667 +input1.bam FBtr0079090 72 33 F 1 33-48 16 0.0625 +input1.bam FBtr0079090 72 54 F 2 53-76 24 0.0833333333333 input1.bam FBtr0079090 72 72 F 0 72-72 1 0.0 input1.bam FBtr0079338 73 1 F 0 1-1 1 0.0 -input1.bam FBtr0079338 73 14 F 5 12-17 6 0.833333333333 -input1.bam FBtr0079338 73 25 F 1 25-25 1 1.0 -input1.bam FBtr0079338 73 44 F 10 42-46 5 2.0 +input1.bam FBtr0079338 73 14 F 5 12-31 20 0.25 +input1.bam FBtr0079338 73 25 F 1 25-40 16 0.0625 +input1.bam FBtr0079338 73 44 F 10 42-63 22 0.454545454545 input1.bam FBtr0079338 73 73 F 0 73-73 1 0.0 -input1.bam FBtr0079528 71 9 F 97 1-18 18 5.38888888889 -input1.bam FBtr0079528 71 28 F 1 28-28 1 1.0 -input1.bam FBtr0079528 71 36 F 3 35-37 3 1.0 -input1.bam FBtr0079528 71 51 F 5 51-51 1 5.0 +input1.bam FBtr0079528 71 9 F 97 1-38 38 2.55263157895 +input1.bam FBtr0079528 71 28 F 1 28-43 16 0.0625 +input1.bam FBtr0079528 71 36 F 3 35-54 20 0.15 +input1.bam FBtr0079528 71 51 F 5 51-65 15 0.333333333333 input1.bam FBtr0079528 71 71 F 0 71-71 1 0.0 -input1.bam FBtr0079596 73 10 F 148 1-19 19 7.78947368421 -input1.bam FBtr0079596 73 53 F 4 53-54 2 2.0 +input1.bam FBtr0079596 73 10 F 148 1-33 33 4.48484848485 +input1.bam FBtr0079596 73 53 F 4 53-73 21 0.190476190476 input1.bam FBtr0079596 73 73 F 0 73-73 1 0.0 -input1.bam FBtr0079677 72 3 F 2 1-5 5 0.4 -input1.bam FBtr0079677 72 52 F 2 52-53 2 1.0 +input1.bam FBtr0079677 72 3 F 2 1-23 23 0.0869565217391 +input1.bam FBtr0079677 72 52 F 2 52-70 19 0.105263157895 input1.bam FBtr0079677 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079690 72 1 F 1 1-1 1 1.0 -input1.bam FBtr0079690 72 24 F 2 22-27 6 0.333333333333 -input1.bam FBtr0079690 72 33 F 2 33-33 1 2.0 +input1.bam FBtr0079690 72 1 F 1 1-15 15 0.0666666666667 +input1.bam FBtr0079690 72 24 F 2 22-51 30 0.0666666666667 +input1.bam FBtr0079690 72 33 F 2 33-49 17 0.117647058824 input1.bam FBtr0079690 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079692 73 1 F 3 1-1 1 3.0 -input1.bam FBtr0079692 73 18 F 1 18-18 1 1.0 -input1.bam FBtr0079692 73 25 F 1 25-25 1 1.0 -input1.bam FBtr0079692 73 32 F 1 32-32 1 1.0 +input1.bam FBtr0079692 73 1 F 3 1-23 23 0.130434782609 +input1.bam FBtr0079692 73 18 F 1 18-35 18 0.0555555555556 +input1.bam FBtr0079692 73 25 F 1 25-41 17 0.0588235294118 +input1.bam FBtr0079692 73 32 F 1 32-51 20 0.05 input1.bam FBtr0079692 73 73 F 0 73-73 1 0.0 -input1.bam FBtr0079693 72 1 F 5 1-1 1 5.0 -input1.bam FBtr0079693 72 25 F 1 25-25 1 1.0 +input1.bam FBtr0079693 72 1 F 5 1-24 24 0.208333333333 +input1.bam FBtr0079693 72 25 F 1 25-47 23 0.0434782608696 input1.bam FBtr0079693 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079694 72 1 F 5 1-1 1 5.0 -input1.bam FBtr0079694 72 18 F 1 18-18 1 1.0 -input1.bam FBtr0079694 72 52 F 1 52-52 1 1.0 +input1.bam FBtr0079694 72 1 F 5 1-25 25 0.2 +input1.bam FBtr0079694 72 18 F 1 18-36 19 0.0526315789474 +input1.bam FBtr0079694 72 52 F 1 52-68 17 0.0588235294118 input1.bam FBtr0079694 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079702 72 1 F 1 1-1 1 1.0 -input1.bam FBtr0079702 72 19 F 2 19-19 1 2.0 -input1.bam FBtr0079702 72 56 F 1 56-56 1 1.0 +input1.bam FBtr0079702 72 1 F 1 1-15 15 0.0666666666667 +input1.bam FBtr0079702 72 19 F 2 19-36 18 0.111111111111 +input1.bam FBtr0079702 72 56 F 1 56-70 15 0.0666666666667 input1.bam FBtr0079702 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079728 72 1 F 2 1-1 1 2.0 -input1.bam FBtr0079728 72 8 F 1 8-8 1 1.0 -input1.bam FBtr0079728 72 19 F 1 19-19 1 1.0 -input1.bam FBtr0079728 72 33 F 3 33-33 1 3.0 -input1.bam FBtr0079728 72 56 F 1 56-56 1 1.0 +input1.bam FBtr0079728 72 1 F 2 1-17 17 0.117647058824 +input1.bam FBtr0079728 72 8 F 1 8-27 20 0.05 +input1.bam FBtr0079728 72 19 F 1 19-42 24 0.0416666666667 +input1.bam FBtr0079728 72 33 F 3 33-49 17 0.176470588235 +input1.bam FBtr0079728 72 56 F 1 56-70 15 0.0666666666667 input1.bam FBtr0079728 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079729 72 1 F 1 1-1 1 1.0 -input1.bam FBtr0079729 72 13 F 1 13-13 1 1.0 -input1.bam FBtr0079729 72 54 F 2 52-57 6 0.333333333333 +input1.bam FBtr0079729 72 1 F 1 1-15 15 0.0666666666667 +input1.bam FBtr0079729 72 13 F 1 13-34 22 0.0454545454545 +input1.bam FBtr0079729 72 54 F 2 52-72 21 0.0952380952381 input1.bam FBtr0079729 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079752 72 1 F 2 1-1 1 2.0 -input1.bam FBtr0079752 72 9 F 2 7-12 6 0.333333333333 -input1.bam FBtr0079752 72 33 F 2 33-33 1 2.0 -input1.bam FBtr0079752 72 52 F 2 52-52 1 2.0 +input1.bam FBtr0079752 72 1 F 2 1-24 24 0.0833333333333 +input1.bam FBtr0079752 72 9 F 2 7-27 21 0.0952380952381 +input1.bam FBtr0079752 72 33 F 2 33-49 17 0.117647058824 +input1.bam FBtr0079752 72 52 F 2 52-71 20 0.1 input1.bam FBtr0079752 72 72 F 0 72-72 1 0.0 input1.bam FBtr0079820 74 1 F 0 1-1 1 0.0 -input1.bam FBtr0079820 74 50 F 13 45-56 12 1.08333333333 +input1.bam FBtr0079820 74 50 F 13 45-74 30 0.433333333333 input1.bam FBtr0079820 74 74 F 0 74-74 1 0.0 -input1.bam FBtr0080609 72 10 F 60 1-20 20 3.0 -input1.bam FBtr0080609 72 42 F 1 42-42 1 1.0 -input1.bam FBtr0080609 72 51 F 2 51-52 2 1.0 +input1.bam FBtr0080609 72 10 F 60 1-44 44 1.36363636364 +input1.bam FBtr0080609 72 42 F 1 42-62 21 0.047619047619 +input1.bam FBtr0080609 72 51 F 2 51-66 16 0.125 input1.bam FBtr0080609 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0080644 72 6 F 6 1-12 12 0.5 +input1.bam FBtr0080644 72 6 F 6 1-27 27 0.222222222222 input1.bam FBtr0080644 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0080646 72 4 F 3 1-7 7 0.428571428571 +input1.bam FBtr0080646 72 4 F 3 1-27 27 0.111111111111 input1.bam FBtr0080646 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0080647 72 6 F 10 1-12 12 0.833333333333 +input1.bam FBtr0080647 72 6 F 10 1-27 27 0.37037037037 input1.bam FBtr0080647 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0080660 72 4 F 7 1-7 7 1.0 +input1.bam FBtr0080660 72 4 F 7 1-27 27 0.259259259259 input1.bam FBtr0080660 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0080663 71 9 F 102 1-17 17 6.0 -input1.bam FBtr0080663 71 26 F 1 26-26 1 1.0 -input1.bam FBtr0080663 71 32 F 2 32-32 1 2.0 -input1.bam FBtr0080663 71 50 F 10 50-51 2 5.0 +input1.bam FBtr0080663 71 9 F 102 1-34 34 3.0 +input1.bam FBtr0080663 71 26 F 1 26-43 18 0.0555555555556 +input1.bam FBtr0080663 71 32 F 2 32-47 16 0.125 +input1.bam FBtr0080663 71 50 F 10 50-70 21 0.47619047619 input1.bam FBtr0080663 71 71 F 0 71-71 1 0.0 -input1.bam FBtr0080664 71 11 F 108 1-21 21 5.14285714286 -input1.bam FBtr0080664 71 33 F 9 28-38 11 0.818181818182 -input1.bam FBtr0080664 71 53 F 11 50-56 7 1.57142857143 +input1.bam FBtr0080664 71 11 F 108 1-35 35 3.08571428571 +input1.bam FBtr0080664 71 33 F 9 28-52 25 0.36 +input1.bam FBtr0080664 71 53 F 11 50-71 22 0.5 input1.bam FBtr0080664 71 71 F 0 71-71 1 0.0