Wrong Output when using granges filter #13
Description
Hi Vince,
Thanks for this great library, which has a fantastic speed-up. Although only intended for benchmarking, I used ranges filter (via the command line) with a small dataset with partial overlaps. Haven't tested in using the lib. I want to filter out the intervals in left with no overlaps in right (e.g., filter --genome --left --right)
genome
chr14 251744
chrX 221185
chr18 138573
chr8 101337
chr1 60131
left:
chr1 3278 12709 intvl_83
chr1 13542 16554 intvl_88
chr1 19473 20158 intvl_89
chr1 24738 33373 intvl_94
chr1 37806 41968 intvl_95
chr1 42231 49198 intvl_96
chr1 50917 59900 intvl_98
chr14 4612 5516 intvl_1
chr14 6298 14399 intvl_2
chr14 17468 24457 intvl_3
chr14 25850 32491 intvl_4
chr14 35745 37396 intvl_5
chr14 40978 42521 intvl_6
chr14 44301 47325 intvl_7
chr14 48365 52757 intvl_8
chr14 56885 60612 intvl_9
chr14 64799 70360 intvl_10
chr14 72108 72921 intvl_11
chr14 74661 76902 intvl_14
chr14 81518 86267 intvl_19
chr14 86401 93780 intvl_20
chr14 94121 96687 intvl_21
chr14 98862 107238 intvl_28
chr14 111403 112345 intvl_30
chr14 112992 115624 intvl_33
chr14 120325 128338 intvl_41
chr14 133162 139280 intvl_42
chr14 141008 146707 intvl_43
chr14 149356 155488 intvl_45
chr14 156661 156786 intvl_47
chr14 161666 171494 intvl_48
chr14 175297 176195 intvl_51
chr14 177963 186769 intvl_54
chr14 191180 195284 intvl_66
chr14 196416 202921 intvl_72
chr14 206110 209561 intvl_74
chr14 213977 216445 intvl_76
chr14 218178 224565 intvl_80
chr14 228828 230125 intvl_84
chr14 233387 239248 intvl_85
chr14 240765 249646 intvl_97
chr18 620 3295 intvl_26
chr18 8118 17043 intvl_29
chr18 19129 25587 intvl_31
chr18 28462 36626 intvl_34
chr18 39621 48986 intvl_35
chr18 52910 61822 intvl_39
chr18 65902 74865 intvl_40
chr18 78965 81118 intvl_44
chr18 84550 88421 intvl_46
chr18 89154 96102 intvl_49
chr18 100024 100512 intvl_53
chr18 101234 103890 intvl_55
chr18 107168 114098 intvl_64
chr18 115888 118232 intvl_65
chr18 122338 130188 intvl_71
chr18 131354 133998 intvl_100
chr8 893 1504 intvl_50
chr8 4341 8598 intvl_52
chr8 9181 15018 intvl_56
chr8 19370 28461 intvl_57
chr8 32532 40382 intvl_58
chr8 42610 51910 intvl_68
chr8 56251 60320 intvl_69
chr8 61523 64226 intvl_77
chr8 65064 66768 intvl_78
chr8 67229 70104 intvl_79
chr8 72048 78333 intvl_81
chr8 83261 87591 intvl_87
chr8 89168 93727 intvl_91
chr8 97701 100625 intvl_99
chrX 314 930 intvl_12
chrX 4499 13333 intvl_13
chrX 16055 17261 intvl_15
chrX 18347 25316 intvl_16
chrX 29831 34220 intvl_17
chrX 34414 40682 intvl_18
chrX 40817 46927 intvl_22
chrX 50663 54980 intvl_23
chrX 56366 64902 intvl_24
chrX 65203 69929 intvl_25
chrX 70667 78223 intvl_27
chrX 80105 87922 intvl_32
chrX 88320 97866 intvl_36
chrX 99354 102559 intvl_37
chrX 107355 108213 intvl_38
chrX 109079 113346 intvl_59
chrX 116030 121324 intvl_60
chrX 124967 125450 intvl_61
chrX 126947 133101 intvl_62
chrX 137438 145668 intvl_63
chrX 150354 158187 intvl_67
chrX 161569 170514 intvl_70
chrX 171434 174005 intvl_73
chrX 174498 180190 intvl_75
chrX 180586 185816 intvl_82
chrX 186729 191388 intvl_86
chrX 194540 194872 intvl_90
chrX 197199 205217 intvl_92
chrX 209095 217194 intvl_93
right
chr1 2436 6078 intvl_83_5p
chr1 13340 14735 intvl_88_5p
chr1 18834 19488 intvl_89_5p
chr1 23054 25682 intvl_94_5p
chr1 37741 38490 intvl_95_5p
chr1 42152 45215 intvl_96_5p
chr1 50723 53317 intvl_98_5p
chr14 2322 4948 intvl_1_5p
chr14 6067 8118 intvl_2_5p
chr14 17092 19682 intvl_3_5p
chr14 25535 27832 intvl_4_5p
chr14 34991 36420 intvl_5_5p
chr14 39999 41072 intvl_6_5p
chr14 43737 45540 intvl_7_5p
chr14 48336 50393 intvl_8_5p
chr14 54896 58167 intvl_9_5p
chr14 63414 66466 intvl_10_5p
chr14 71847 72392 intvl_11_5p
chr14 74408 75291 intvl_14_5p
chr14 81107 81735 intvl_19_5p
chr14 86347 88149 intvl_20_5p
chr14 94018 94875 intvl_21_5p
chr14 98294 101816 intvl_28_5p
chr14 110496 111723 intvl_30_5p
chr14 112974 114126 intvl_33_5p
chr14 118947 124165 intvl_41_5p
chr14 130860 134109 intvl_42_5p
chr14 140864 143439 intvl_43_5p
chr14 148052 150350 intvl_45_5p
chr14 156332 156667 intvl_47_5p
chr14 159564 162410 intvl_48_5p
chr14 174008 175662 intvl_51_5p
chr14 177106 178883 intvl_54_5p
chr14 189029 193217 intvl_66_5p
chr14 196371 197736 intvl_72_5p
chr14 205758 207288 intvl_74_5p
chr14 211975 214379 intvl_76_5p
chr14 217617 220748 intvl_80_5p
chr14 228508 229099 intvl_84_5p
chr14 233352 236207 intvl_85_5p
chr14 240397 245173 intvl_97_5p
chr18 530 1736 intvl_26_5p
chr18 7474 9208 intvl_29_5p
chr18 18374 20070 intvl_31_5p
chr18 27338 32333 intvl_34_5p
chr18 39399 41016 intvl_35_5p
chr18 52594 54804 intvl_39_5p
chr18 64876 69784 intvl_40_5p
chr18 78154 79036 intvl_44_5p
chr18 84026 85118 intvl_46_5p
chr18 89103 92191 intvl_49_5p
chr18 98471 100107 intvl_53_5p
chr18 101082 101641 intvl_55_5p
chr18 106442 108286 intvl_64_5p
chr18 115654 115997 intvl_65_5p
chr18 121798 125531 intvl_71_5p
chr18 131233 132134 intvl_100_5p
chr8 782 1024 intvl_50_5p
chr8 3329 5049 intvl_52_5p
chr8 8927 10882 intvl_56_5p
chr8 19114 21355 intvl_57_5p
chr8 30793 35885 intvl_58_5p
chr8 42306 45662 intvl_68_5p
chr8 55850 57123 intvl_69_5p
chr8 60997 62392 intvl_77_5p
chr8 64932 65706 intvl_78_5p
chr8 67102 67470 intvl_79_5p
chr8 71951 74878 intvl_81_5p
chr8 81274 83810 intvl_87_5p
chr8 88704 90285 intvl_91_5p
chr8 96087 97831 intvl_99_5p
chrX 252 534 intvl_12_5p
chrX 4293 8440 intvl_13_5p
chrX 15331 16066 intvl_15_5p
chrX 18289 18949 intvl_16_5p
chrX 29178 30174 intvl_17_5p
chrX 34324 36497 intvl_18_5p
chrX 40775 41962 intvl_22_5p
chrX 49765 52739 intvl_23_5p
chrX 56052 56921 intvl_24_5p
chrX 65199 65384 intvl_25_5p
chrX 70478 73534 intvl_27_5p
chrX 80073 82712 intvl_32_5p
chrX 88284 90735 intvl_36_5p
chrX 99342 100325 intvl_37_5p
chrX 105339 107384 intvl_38_5p
chrX 108727 110915 intvl_59_5p
chrX 115785 117445 intvl_60_5p
chrX 124573 125121 intvl_61_5p
chrX 126822 128647 intvl_62_5p
chrX 135597 137569 intvl_63_5p
chrX 150302 153749 intvl_67_5p
chrX 161267 162707 intvl_70_5p
chrX 171367 171541 intvl_73_5p
chrX 174427 175390 intvl_75_5p
chrX 180533 183172 intvl_82_5p
chrX 186408 188128 intvl_86_5p
chrX 193490 194699 intvl_90_5p
chrX 196241 198546 intvl_92_5p
chrX 208358 210859 intvl_93_5p
However, this gives me:
chr1 3278 12709 intvl_2
chr1 19473 20158 intvl_3
chr1 24738 33373 intvl_4
chr1 37806 41968 intvl_6
chr1 42231 49198 intvl_8
chr1 50917 59900 intvl_10
chr8 4341 8598 intvl_13
chr8 32532 40382 intvl_16
chr8 42610 51910 intvl_18
chr8 56251 60320 intvl_19
chr8 65064 66768 intvl_20
chr8 72048 78333 intvl_22
chr8 89168 93727 intvl_23
chr8 97701 100625 intvl_26
chr14 6298 14399 intvl_28
chr14 17468 24457 intvl_29
chr14 25850 32491 intvl_31
chr14 40978 42521 intvl_34
chr14 48365 52757 intvl_35
chr14 64799 70360 intvl_39
chr14 81518 86267 intvl_40
chr14 86401 93780 intvl_41
chr14 98862 107238 intvl_49
chr14 120325 128338 intvl_52
chr18 620 3295 intvl_58
chr18 8118 17043 intvl_68
chr18 19129 25587 intvl_69
chr18 28462 36626 intvl_78
chr18 39621 48986 intvl_81
chr18 52910 61822 intvl_83
chr18 65902 74865 intvl_89
chr18 89154 96102 intvl_91
chrX 4499 13333 intvl_94
chrX 18347 25316 intvl_95
chrX 34414 40682 intvl_96
chrX 40817 46927 intvl_98
chrX 50663 54980 intvl_99
Reports only a fraction of the overlaps, and the naming in the name column is wrong. For example, 'intvl83becomesintvl2`.
What am I missing?