# HG changeset patch # User iuc # Date 1556800222 14400 # Node ID c4b926c9831c911e26f857393086cf5218b1aa9c # Parent 71188f3f4b7667acd5dd4e114f722e61613da342 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit ca66053a0d915edba3d7f1d4ce014718e7f4f0f2 diff -r 71188f3f4b76 -r c4b926c9831c cwpair2.py --- a/cwpair2.py Mon Nov 06 23:19:50 2017 -0500 +++ b/cwpair2.py Thu May 02 08:30:22 2019 -0400 @@ -62,7 +62,7 @@ by_file[path].append(stats) # Write tabular statistics file. keys = ['fname', 'final_mode', 'preview_mode', 'perc95', 'paired', 'orphans'] - statistics_out = csv.writer(open(args.statistics_output, 'wt'), delimiter='\t') + statistics_out = csv.writer(open(args.statistics_output, 'wt'), delimiter='\t', lineterminator="\n") statistics_out.writerow(keys) for file_path, statistics in by_file.items(): for stats in statistics: diff -r 71188f3f4b76 -r c4b926c9831c cwpair2.xml --- a/cwpair2.xml Mon Nov 06 23:19:50 2017 -0500 +++ b/cwpair2.xml Thu May 02 08:30:22 2019 -0400 @@ -1,5 +1,5 @@ - + find matched pairs and unmatched orphans cwpair2_macros.xml @@ -83,9 +83,9 @@ - - - + + + @@ -106,19 +106,19 @@ - - - + + + - - - + + + - - - + + + diff -r 71188f3f4b76 -r c4b926c9831c cwpair2_macros.xml --- a/cwpair2_macros.xml Mon Nov 06 23:19:50 2017 -0500 +++ b/cwpair2_macros.xml Thu May 02 08:30:22 2019 -0400 @@ -1,9 +1,8 @@ - 1.1 - matplotlib + matplotlib @@ -14,7 +13,7 @@ title = {None}, year = {None}, eprint = {None}, - url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation} + url = {http://www.cegr.psu.edu/} } diff -r 71188f3f4b76 -r c4b926c9831c cwpair2_util.py --- a/cwpair2_util.py Mon Nov 06 23:19:50 2017 -0500 +++ b/cwpair2_util.py Thu May 02 08:30:22 2019 -0400 @@ -15,7 +15,7 @@ # Data output formats GFF_EXT = 'gff' TABULAR_EXT = 'tabular' -# Statistics historgrams output directory. +# Statistics histograms output directory. HISTOGRAM = 'H' # Statistics outputs FINAL_PLOTS = 'F' @@ -46,7 +46,7 @@ def get_bin(self, x): """ - Returns the bin in which a data point falls + Returns the centre of the bin in which a data point falls """ return self.start + (x - self.start) // self.binsize * self.binsize + self.binsize / 2.0 @@ -64,7 +64,12 @@ return x, y def mode(self): - return max(self.dist.items(), key=lambda data: data[1])[0] + # There could be more than one mode for a frequency distribution, + # return the median of the modes to be consistent + max_frequency = max(self.dist.values()) + modes = sorted(_[0] for _ in self.dist.items() if _[1] == max_frequency) + median_index = len(modes) // 2 + return modes[median_index] def size(self): return sum(self.dist.values()) @@ -76,7 +81,7 @@ def distance(peak1, peak2): - return (peak2[1] + peak2[2]) / 2 - (peak1[1] + peak1[2]) / 2 + return (peak2[1] + peak2[2]) / 2.0 - (peak1[1] + peak1[2]) / 2.0 def gff_row(cname, start, end, score, source, type='.', strand='.', phase='.', attrs={}): @@ -92,9 +97,11 @@ def parse_chromosomes(reader): # This version of cwpair2 accepts only gff format as input. chromosomes = {} - next(reader) for line in reader: - cname, junk, junk, start, end, value, strand, junk, junk = line + line = line.rstrip("\r\n") + if not line or line.startswith('#'): + continue + cname, _, _, start, end, value, strand, _, _ = line.split("\t") start = int(start) end = int(end) value = float(value) @@ -118,7 +125,7 @@ return values[int(len(values) * 0.95)] -def filter(chromosomes, threshold=0.05): +def peak_filter(chromosomes, threshold): """ Filters the peaks to those above a threshold. Threshold < 1.0 is interpreted as a proportion of the maximum, >=1.0 as an absolute value. @@ -139,7 +146,7 @@ def all_pair_distribution(chromosomes, up_distance, down_distance, binsize): dist = FrequencyDistribution(-up_distance, down_distance, binsize=binsize) - for cname, data in chromosomes.items(): + for data in chromosomes.values(): watson, crick = split_strands(data) crick.sort(key=lambda data: float(data[1])) keys = make_keys(crick) @@ -256,7 +263,6 @@ output_orphans = output_files in ["all", "matched_pair_orphan", "matched_pair_orphan_detail"] # Keep track of statistics for the output file statistics = {} - input = csv.reader(open(dataset_path, 'rt'), delimiter='\t') fpath, fname = os.path.split(dataset_path) statistics['fname'] = '%s: data %s' % (method, str(galaxy_hid)) statistics['dir'] = fpath @@ -276,12 +282,13 @@ def td_writer(output_type, extension, fname): # Returns a tab-delimited writer for a specified output. output_file_path = make_path(output_type, extension, fname) - return csv.writer(open(output_file_path, 'wt'), delimiter='\t') + return csv.writer(open(output_file_path, 'wt'), delimiter='\t', lineterminator="\n") - try: - chromosomes = parse_chromosomes(input) - except Exception: - stop_err('Unable to parse file "%s".\n%s' % (dataset_path, traceback.format_exc())) + with open(dataset_path, 'rt') as input: + try: + chromosomes = parse_chromosomes(input) + except Exception: + stop_err('Unable to parse file "%s".\n%s' % (dataset_path, traceback.format_exc())) if output_details: # Details detailed_output = td_writer('data_%s' % DETAILS, TABULAR_EXT, fname) @@ -303,8 +310,8 @@ statistics['graph_path'] = make_histogram_path(STATS_GRAPH, fname) statistics['perc95'] = perc95(chromosomes) if threshold > 0: - # Apply filter - filter(chromosomes, threshold) + # Apply peak_filter + peak_filter(chromosomes, threshold) if method == 'mode': freq = all_pair_distribution(chromosomes, up_distance, down_distance, binsize) mode = freq.mode() diff -r 71188f3f4b76 -r c4b926c9831c test-data/closest_d_output2.tabular --- a/test-data/closest_d_output2.tabular Mon Nov 06 23:19:50 2017 -0500 +++ b/test-data/closest_d_output2.tabular Thu May 02 08:30:22 2019 -0400 @@ -1,66 +1,67 @@ -chrom start end value strand chrom start end value strand midpoint c-w reads sum c-w distance (bp) -chr1 87147 87167 3492.0 + chr1 87158 87178 2039.0 - 87162 5531.0 11 -chr1 87 107 3211.0 + chr1 139 159 993.0 - 123 4204.0 52 -chr1 48 68 2842.0 + chr1 50 70 39.0 - 59 2881.0 2 -chr1 255 275 2810.0 + chr1 261 281 1278.0 - 268 4088.0 6 -chr1 117 137 2163.0 + chr1 176 196 14.0 - 156 2177.0 59 -chr1 86954 86974 1948.0 + chr1 86991 87011 65.0 - 86982 2013.0 37 -chr1 169107 169127 1811.0 + chr1 169064 169084 76.0 - 169095 1887.0 -43 -chr1 87171 87191 1436.0 + chr1 87198 87218 2207.0 - 87194 3643.0 27 -chr1 201 221 1411.0 + chr1 215 235 2611.0 - 218 4022.0 14 -chr1 229741 229761 1380.0 + chr1 229757 229777 3151.0 - 229759 4531.0 16 -chr1 185076 185096 1309.0 + chr1 185122 185142 62.0 - 185109 1371.0 46 -chr1 39081 39101 1268.0 + chr1 39052 39072 82.0 - 39076 1350.0 -29 -chr1 92411 92431 1252.0 + chr1 92411 92431 136.0 - 92421 1388.0 0 -chr1 203872 203892 1234.0 + chr1 203835 203855 242.0 - 203863 1476.0 -37 -chr1 70776 70796 1148.0 + chr1 70788 70808 998.0 - 70792 2146.0 12 -chr1 231 251 1146.0 + chr1 279 299 1328.0 - 265 2474.0 48 -chr1 87098 87118 1125.0 + chr1 87101 87121 1134.0 - 87109 2259.0 3 -chr1 6163 6183 1049.0 + chr1 6254 6274 1076.0 - 6218 2125.0 91 -chr1 25246 25266 995.0 + chr1 25345 25365 188.0 - 25305 1183.0 99 -chr1 101411 101431 973.0 + chr1 101367 101387 1388.0 - 101399 2361.0 -44 -chr1 139213 139233 965.0 + chr1 139228 139248 214.0 - 139230 1179.0 15 -chr1 87019 87039 769.0 + chr1 87049 87069 422.0 - 87044 1191.0 30 -chr1 124318 124338 749.0 + chr1 124275 124295 12.0 - 124306 761.0 -43 -chr1 348 368 699.0 + chr1 373 393 200.0 - 370 899.0 25 -chr1 92543 92563 699.0 + chr1 92571 92591 90.0 - 92567 789.0 28 -chr1 138868 138888 698.0 + chr1 138864 138884 13.0 - 138876 711.0 -4 -chr1 307 327 685.0 + chr1 323 343 486.0 - 325 1171.0 16 -chr1 6413 6433 682.0 + chr1 6476 6496 567.0 - 6454 1249.0 63 -chr1 72781 72801 657.0 + chr1 72810 72830 212.0 - 72805 869.0 29 -chr1 22571 22591 609.0 + chr1 22569 22589 254.0 - 22580 863.0 -2 -chr1 65152 65172 575.0 + chr1 65148 65168 43.0 - 65160 618.0 -4 -chr1 106034 106054 558.0 + chr1 106041 106061 14.0 - 106047 572.0 7 -chr1 155028 155048 522.0 + chr1 155111 155131 1051.0 - 155079 1573.0 83 -chr1 32449 32469 476.0 + chr1 32497 32517 2.0 - 32483 478.0 48 -chr1 6706 6726 431.0 + chr1 6702 6722 2.0 - 6714 433.0 -4 -chr1 113782 113802 420.0 + chr1 113762 113782 296.0 - 113782 716.0 -20 -chr1 228633 228653 371.0 + chr1 228691 228711 255.0 - 228672 626.0 58 -chr1 438 458 334.0 + chr1 446 466 170.0 - 452 504.0 8 -chr1 72671 72691 304.0 + chr1 72771 72791 406.0 - 72731 710.0 100 -chr1 170119 170139 284.0 + chr1 170129 170149 373.0 - 170134 657.0 10 -chr1 92631 92651 260.0 + chr1 92639 92659 2137.0 - 92645 2397.0 8 -chr1 136366 136386 248.0 + chr1 136352 136372 117.0 - 136369 365.0 -14 -chr1 108624 108644 206.0 + chr1 108579 108599 367.0 - 108611 573.0 -45 -chr1 45678 45698 198.0 + chr1 45643 45663 295.0 - 45670 493.0 -35 -chr1 368 388 192.0 + chr1 388 408 167.0 - 388 359.0 20 -chr1 682 702 168.0 + chr1 634 654 151.0 - 668 319.0 -48 -chr1 59190 59210 168.0 + chr1 59246 59266 397.0 - 59228 565.0 56 -chr1 134170 134190 151.0 + chr1 134270 134290 508.0 - 134230 659.0 100 -chr1 55495 55515 125.0 + chr1 55581 55601 831.0 - 55548 956.0 86 -chr1 512 532 101.0 + chr1 468 488 468.0 - 500 569.0 -44 -chr1 39197 39217 101.0 + chr1 39258 39278 261.0 - 39237 362.0 61 -chr1 229721 229741 84.0 + chr1 229784 229804 615.0 - 229762 699.0 63 -chr1 116660 116680 74.0 + chr1 116619 116639 699.0 - 116649 773.0 -41 -chr1 19216 19236 42.0 + chr1 19191 19211 736.0 - 19213 778.0 -25 -chr1 230110 230130 42.0 + chr1 230120 230140 2.0 - 230125 44.0 10 -chr1 31627 31647 40.0 + chr1 31693 31713 450.0 - 31670 490.0 66 -chr1 180280 180300 38.0 + chr1 180362 180382 59.0 - 180331 97.0 82 -chr1 98528 98548 34.0 + chr1 98555 98575 88.0 - 98551 122.0 27 -chr1 230163 230183 23.0 + chr1 230173 230193 33.0 - 230178 56.0 10 -chr1 173262 173282 11.0 + chr1 173270 173290 535.0 - 173276 546.0 8 -chr1 230145 230165 8.0 + chr1 230150 230170 7.0 - 230157 15.0 5 -chr1 95920 95940 5.0 + chr1 95971 95991 684.0 - 95955 689.0 51 -chr1 199418 199438 5.0 + chr1 199388 199408 805.0 - 199413 810.0 -30 -chr1 197489 197509 3.0 + chr1 197562 197582 2.0 - 197535 5.0 73 -chr1 96908 96928 2.0 + chr1 96911 96931 10.0 - 96919 12.0 3 +chrom start end value strand chrom start end value strand midpoint c-w reads sum c-w distance (bp) +chr1 87147 87167 3492.0 + chr1 87158 87178 2039.0 - 87162 5531.0 11.0 +chr1 87 107 3211.0 + chr1 139 159 993.0 - 123 4204.0 52.0 +chr1 48 68 2842.0 + chr1 50 70 39.0 - 59 2881.0 2.0 +chr1 255 275 2810.0 + chr1 261 281 1278.0 - 268 4088.0 6.0 +chr1 117 137 2163.0 + chr1 176 196 14.0 - 156 2177.0 59.0 +chr1 86954 86974 1948.0 + chr1 86991 87011 65.0 - 86982 2013.0 37.0 +chr1 169107 169127 1811.0 + chr1 169064 169084 76.0 - 169095 1887.0 -43.0 +chr1 87171 87191 1436.0 + chr1 87198 87218 2207.0 - 87194 3643.0 27.0 +chr1 201 221 1411.0 + chr1 215 235 2611.0 - 218 4022.0 14.0 +chr1 229741 229761 1380.0 + chr1 229757 229777 3151.0 - 229759 4531.0 16.0 +chr1 185076 185096 1309.0 + chr1 185122 185142 62.0 - 185109 1371.0 46.0 +chr1 39081 39101 1268.0 + chr1 39052 39072 82.0 - 39076 1350.0 -29.0 +chr1 92411 92431 1252.0 + chr1 92411 92431 136.0 - 92421 1388.0 0.0 +chr1 203872 203892 1234.0 + chr1 203835 203855 242.0 - 203863 1476.0 -37.0 +chr1 70776 70796 1148.0 + chr1 70788 70808 998.0 - 70792 2146.0 12.0 +chr1 231 251 1146.0 + chr1 279 299 1328.0 - 265 2474.0 48.0 +chr1 87098 87118 1125.0 + chr1 87101 87121 1134.0 - 87109 2259.0 3.0 +chr1 6163 6183 1049.0 + chr1 6254 6274 1076.0 - 6218 2125.0 91.0 +chr1 25246 25266 995.0 + chr1 25345 25365 188.0 - 25305 1183.0 99.0 +chr1 101411 101431 973.0 + chr1 101367 101387 1388.0 - 101399 2361.0 -44.0 +chr1 139213 139233 965.0 + chr1 139228 139248 214.0 - 139230 1179.0 15.0 +chr1 87019 87039 769.0 + chr1 87049 87069 422.0 - 87044 1191.0 30.0 +chr1 124318 124338 749.0 + chr1 124275 124295 12.0 - 124306 761.0 -43.0 +chr1 348 368 699.0 + chr1 373 393 200.0 - 370 899.0 25.0 +chr1 92543 92563 699.0 + chr1 92571 92591 90.0 - 92567 789.0 28.0 +chr1 138868 138888 698.0 + chr1 138864 138884 13.0 - 138876 711.0 -4.0 +chr1 307 327 685.0 + chr1 323 343 486.0 - 325 1171.0 16.0 +chr1 6413 6433 682.0 + chr1 6476 6496 567.0 - 6454 1249.0 63.0 +chr1 72781 72801 657.0 + chr1 72810 72830 212.0 - 72805 869.0 29.0 +chr1 22571 22591 609.0 + chr1 22569 22589 254.0 - 22580 863.0 -2.0 +chr1 65152 65172 575.0 + chr1 65148 65168 43.0 - 65160 618.0 -4.0 +chr1 106034 106054 558.0 + chr1 106041 106061 14.0 - 106047 572.0 7.0 +chr1 155028 155048 522.0 + chr1 155111 155131 1051.0 - 155079 1573.0 83.0 +chr1 32449 32469 476.0 + chr1 32497 32517 2.0 - 32483 478.0 48.0 +chr1 6706 6726 431.0 + chr1 6702 6722 2.0 - 6714 433.0 -4.0 +chr1 113782 113802 420.0 + chr1 113762 113782 296.0 - 113782 716.0 -20.0 +chr1 228633 228653 371.0 + chr1 228691 228711 255.0 - 228672 626.0 58.0 +chr1 438 458 334.0 + chr1 446 466 170.0 - 452 504.0 8.0 +chr1 72671 72691 304.0 + chr1 72771 72791 406.0 - 72731 710.0 100.0 +chr1 170119 170139 284.0 + chr1 170129 170149 373.0 - 170134 657.0 10.0 +chr1 92631 92651 260.0 + chr1 92639 92659 2137.0 - 92645 2397.0 8.0 +chr1 136366 136386 248.0 + chr1 136352 136372 117.0 - 136369 365.0 -14.0 +chr1 108624 108644 206.0 + chr1 108579 108599 367.0 - 108611 573.0 -45.0 +chr1 45678 45698 198.0 + chr1 45643 45663 295.0 - 45670 493.0 -35.0 +chr1 368 388 192.0 + chr1 388 408 167.0 - 388 359.0 20.0 +chr1 682 702 168.0 + chr1 634 654 151.0 - 668 319.0 -48.0 +chr1 59190 59210 168.0 + chr1 59246 59266 397.0 - 59228 565.0 56.0 +chr1 134170 134190 151.0 + chr1 134270 134290 508.0 - 134230 659.0 100.0 +chr1 55495 55515 125.0 + chr1 55581 55601 831.0 - 55548 956.0 86.0 +chr1 512 532 101.0 + chr1 468 488 468.0 - 500 569.0 -44.0 +chr1 39197 39217 101.0 + chr1 39258 39278 261.0 - 39237 362.0 61.0 +chr1 229721 229741 84.0 + chr1 229784 229804 615.0 - 229762 699.0 63.0 +chr1 116660 116680 74.0 + chr1 116619 116639 699.0 - 116649 773.0 -41.0 +chr1 19216 19236 42.0 + chr1 19191 19211 736.0 - 19213 778.0 -25.0 +chr1 230110 230130 42.0 + chr1 230120 230140 2.0 - 230125 44.0 10.0 +chr1 31627 31647 40.0 + chr1 31693 31713 450.0 - 31670 490.0 66.0 +chr1 180280 180300 38.0 + chr1 180362 180382 59.0 - 180331 97.0 82.0 +chr1 98528 98548 34.0 + chr1 98555 98575 88.0 - 98551 122.0 27.0 +chr1 230163 230183 23.0 + chr1 230173 230193 33.0 - 230178 56.0 10.0 +chr1 173262 173282 11.0 + chr1 173270 173290 535.0 - 173276 546.0 8.0 +chr1 230145 230165 8.0 + chr1 230150 230170 7.0 - 230157 15.0 5.0 +chr1 95920 95940 5.0 + chr1 95971 95991 684.0 - 95955 689.0 51.0 +chr1 199418 199438 5.0 + chr1 199388 199408 805.0 - 199413 810.0 -30.0 +chr1 197489 197509 3.0 + chr1 197562 197582 2.0 - 197535 5.0 73.0 +chr1 96908 96928 2.0 + chr1 96911 96931 10.0 - 96919 12.0 3.0 +chr1 151369 151389 2.0 + chr1 151341 151361 593.0 - 151365 595.0 -28.0 diff -r 71188f3f4b76 -r c4b926c9831c test-data/closest_mp_output1.gff --- a/test-data/closest_mp_output1.gff Mon Nov 06 23:19:50 2017 -0500 +++ b/test-data/closest_mp_output1.gff Thu May 02 08:30:22 2019 -0400 @@ -1,55 +1,56 @@ -chr1 cwpair . 87162 87163 5531.0 . . cw_distance=11 -chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16 -chr1 cwpair . 123 124 4204.0 . . cw_distance=52 -chr1 cwpair . 268 269 4088.0 . . cw_distance=6 -chr1 cwpair . 218 219 4022.0 . . cw_distance=14 -chr1 cwpair . 87194 87195 3643.0 . . cw_distance=27 -chr1 cwpair . 59 60 2881.0 . . cw_distance=2 -chr1 cwpair . 265 266 2474.0 . . cw_distance=48 -chr1 cwpair . 92645 92646 2397.0 . . cw_distance=8 -chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3 -chr1 cwpair . 156 157 2177.0 . . cw_distance=59 -chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 -chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 -chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37 -chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 -chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 -chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 -chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 -chr1 cwpair . 87044 87045 1191.0 . . cw_distance=30 -chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 -chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 -chr1 cwpair . 325 326 1171.0 . . cw_distance=16 -chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 -chr1 cwpair . 370 371 899.0 . . cw_distance=25 -chr1 cwpair . 72805 72806 869.0 . . cw_distance=29 -chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 -chr1 cwpair . 92567 92568 789.0 . . cw_distance=28 -chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 -chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 -chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 -chr1 cwpair . 72731 72732 710.0 . . cw_distance=100 -chr1 cwpair . 229762 229763 699.0 . . cw_distance=63 -chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 -chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 -chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 -chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 -chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 -chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 -chr1 cwpair . 477 478 566.0 . . cw_distance=1 -chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 -chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 -chr1 cwpair . 452 453 504.0 . . cw_distance=8 -chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 -chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 -chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 -chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 -chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 -chr1 cwpair . 388 389 359.0 . . cw_distance=20 -chr1 cwpair . 627 628 247.0 . . cw_distance=33 -chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 -chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 -chr1 cwpair . 230178 230179 56.0 . . cw_distance=10 -chr1 cwpair . 230125 230126 44.0 . . cw_distance=10 -chr1 cwpair . 230157 230158 15.0 . . cw_distance=5 -chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 +chr1 cwpair . 87162 87163 5531.0 . . cw_distance=11.0 +chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16.0 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52.0 +chr1 cwpair . 268 269 4088.0 . . cw_distance=6.0 +chr1 cwpair . 218 219 4022.0 . . cw_distance=14.0 +chr1 cwpair . 87194 87195 3643.0 . . cw_distance=27.0 +chr1 cwpair . 59 60 2881.0 . . cw_distance=2.0 +chr1 cwpair . 265 266 2474.0 . . cw_distance=48.0 +chr1 cwpair . 92645 92646 2397.0 . . cw_distance=8.0 +chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3.0 +chr1 cwpair . 156 157 2177.0 . . cw_distance=59.0 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12.0 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91.0 +chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37.0 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83.0 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0.0 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46.0 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63.0 +chr1 cwpair . 87044 87045 1191.0 . . cw_distance=30.0 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99.0 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15.0 +chr1 cwpair . 325 326 1171.0 . . cw_distance=16.0 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86.0 +chr1 cwpair . 370 371 899.0 . . cw_distance=25.0 +chr1 cwpair . 72805 72806 869.0 . . cw_distance=29.0 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2.0 +chr1 cwpair . 92567 92568 789.0 . . cw_distance=28.0 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25.0 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20.0 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4.0 +chr1 cwpair . 72731 72732 710.0 . . cw_distance=100.0 +chr1 cwpair . 229762 229763 699.0 . . cw_distance=63.0 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51.0 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100.0 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10.0 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58.0 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4.0 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7.0 +chr1 cwpair . 477 478 566.0 . . cw_distance=1.0 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56.0 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8.0 +chr1 cwpair . 452 453 504.0 . . cw_distance=8.0 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66.0 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48.0 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4.0 +chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14.0 +chr1 cwpair . 39237 39238 362.0 . . cw_distance=61.0 +chr1 cwpair . 388 389 359.0 . . cw_distance=20.0 +chr1 cwpair . 627 628 247.0 . . cw_distance=33.0 +chr1 cwpair . 98551 98552 122.0 . . cw_distance=27.0 +chr1 cwpair . 180331 180332 97.0 . . cw_distance=82.0 +chr1 cwpair . 230178 230179 56.0 . . cw_distance=10.0 +chr1 cwpair . 230125 230126 44.0 . . cw_distance=10.0 +chr1 cwpair . 230157 230158 15.0 . . cw_distance=5.0 +chr1 cwpair . 96919 96920 12.0 . . cw_distance=3.0 +chr1 cwpair . 197535 197536 5.0 . . cw_distance=73.0 diff -r 71188f3f4b76 -r c4b926c9831c test-data/closest_mp_output2.gff --- a/test-data/closest_mp_output2.gff Mon Nov 06 23:19:50 2017 -0500 +++ b/test-data/closest_mp_output2.gff Thu May 02 08:30:22 2019 -0400 @@ -1,65 +1,66 @@ -chr1 cwpair . 87162 87163 5531.0 . . cw_distance=11 -chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16 -chr1 cwpair . 123 124 4204.0 . . cw_distance=52 -chr1 cwpair . 268 269 4088.0 . . cw_distance=6 -chr1 cwpair . 218 219 4022.0 . . cw_distance=14 -chr1 cwpair . 87194 87195 3643.0 . . cw_distance=27 -chr1 cwpair . 59 60 2881.0 . . cw_distance=2 -chr1 cwpair . 265 266 2474.0 . . cw_distance=48 -chr1 cwpair . 92645 92646 2397.0 . . cw_distance=8 -chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44 -chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3 -chr1 cwpair . 156 157 2177.0 . . cw_distance=59 -chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 -chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 -chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37 -chr1 cwpair . 169095 169096 1887.0 . . cw_distance=-43 -chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 -chr1 cwpair . 203863 203864 1476.0 . . cw_distance=-37 -chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 -chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 -chr1 cwpair . 39076 39077 1350.0 . . cw_distance=-29 -chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 -chr1 cwpair . 87044 87045 1191.0 . . cw_distance=30 -chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 -chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 -chr1 cwpair . 325 326 1171.0 . . cw_distance=16 -chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 -chr1 cwpair . 370 371 899.0 . . cw_distance=25 -chr1 cwpair . 72805 72806 869.0 . . cw_distance=29 -chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 -chr1 cwpair . 199413 199414 810.0 . . cw_distance=-30 -chr1 cwpair . 92567 92568 789.0 . . cw_distance=28 -chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 -chr1 cwpair . 116649 116650 773.0 . . cw_distance=-41 -chr1 cwpair . 124306 124307 761.0 . . cw_distance=-43 -chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 -chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 -chr1 cwpair . 72731 72732 710.0 . . cw_distance=100 -chr1 cwpair . 229762 229763 699.0 . . cw_distance=63 -chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 -chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 -chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 -chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 -chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 -chr1 cwpair . 151365 151366 595.0 . . cw_distance=-28 -chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45 -chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 -chr1 cwpair . 500 501 569.0 . . cw_distance=-44 -chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 -chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 -chr1 cwpair . 452 453 504.0 . . cw_distance=8 -chr1 cwpair . 45670 45671 493.0 . . cw_distance=-35 -chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 -chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 -chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 -chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 -chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 -chr1 cwpair . 388 389 359.0 . . cw_distance=20 -chr1 cwpair . 668 669 319.0 . . cw_distance=-48 -chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 -chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 -chr1 cwpair . 230178 230179 56.0 . . cw_distance=10 -chr1 cwpair . 230125 230126 44.0 . . cw_distance=10 -chr1 cwpair . 230157 230158 15.0 . . cw_distance=5 -chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 +chr1 cwpair . 87162 87163 5531.0 . . cw_distance=11.0 +chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16.0 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52.0 +chr1 cwpair . 268 269 4088.0 . . cw_distance=6.0 +chr1 cwpair . 218 219 4022.0 . . cw_distance=14.0 +chr1 cwpair . 87194 87195 3643.0 . . cw_distance=27.0 +chr1 cwpair . 59 60 2881.0 . . cw_distance=2.0 +chr1 cwpair . 265 266 2474.0 . . cw_distance=48.0 +chr1 cwpair . 92645 92646 2397.0 . . cw_distance=8.0 +chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44.0 +chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3.0 +chr1 cwpair . 156 157 2177.0 . . cw_distance=59.0 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12.0 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91.0 +chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37.0 +chr1 cwpair . 169095 169096 1887.0 . . cw_distance=-43.0 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83.0 +chr1 cwpair . 203863 203864 1476.0 . . cw_distance=-37.0 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0.0 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46.0 +chr1 cwpair . 39076 39077 1350.0 . . cw_distance=-29.0 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63.0 +chr1 cwpair . 87044 87045 1191.0 . . cw_distance=30.0 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99.0 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15.0 +chr1 cwpair . 325 326 1171.0 . . cw_distance=16.0 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86.0 +chr1 cwpair . 370 371 899.0 . . cw_distance=25.0 +chr1 cwpair . 72805 72806 869.0 . . cw_distance=29.0 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2.0 +chr1 cwpair . 199413 199414 810.0 . . cw_distance=-30.0 +chr1 cwpair . 92567 92568 789.0 . . cw_distance=28.0 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25.0 +chr1 cwpair . 116649 116650 773.0 . . cw_distance=-41.0 +chr1 cwpair . 124306 124307 761.0 . . cw_distance=-43.0 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20.0 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4.0 +chr1 cwpair . 72731 72732 710.0 . . cw_distance=100.0 +chr1 cwpair . 229762 229763 699.0 . . cw_distance=63.0 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51.0 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100.0 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10.0 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58.0 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4.0 +chr1 cwpair . 151365 151366 595.0 . . cw_distance=-28.0 +chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45.0 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7.0 +chr1 cwpair . 500 501 569.0 . . cw_distance=-44.0 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56.0 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8.0 +chr1 cwpair . 452 453 504.0 . . cw_distance=8.0 +chr1 cwpair . 45670 45671 493.0 . . cw_distance=-35.0 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66.0 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48.0 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4.0 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genetrack . 140857 140877 23 + . stddev=0.0 -chr1 genetrack . 142139 142159 43 + . stddev=0.0 -chr1 genetrack . 142905 142925 599 + . stddev=0.0 -chr1 genetrack . 142950 142970 12 + . stddev=0.0 -chr1 genetrack . 143657 143677 328 + . stddev=0.0 -chr1 genetrack . 145253 145273 1394 + . stddev=0.0 -chr1 genetrack . 146517 146537 69 + . stddev=0.0 -chr1 genetrack . 147211 147231 130 + . stddev=0.0 -chr1 genetrack . 147227 147247 101 + . stddev=0.0 -chr1 genetrack . 147322 147342 15 + . stddev=0.0 -chr1 genetrack . 149343 149363 159 + . stddev=0.0 -chr1 genetrack . 150449 150469 436 + . stddev=0.0 -chr1 genetrack . 151369 151389 2 + . stddev=0.0 -chr1 genetrack . 151431 151451 38 + . stddev=0.0 -chr1 genetrack . 152678 152698 135 + . stddev=0.0 -chr1 genetrack . 153095 153115 490 + . stddev=0.0 -chr1 genetrack . 153928 153948 768 + . stddev=0.0 -chr1 genetrack . 155028 155048 522 + . stddev=0.0 -chr1 genetrack . 156097 156117 2 + . stddev=0.0 -chr1 genetrack . 156252 156272 133 + . stddev=0.0 -chr1 genetrack . 158038 158058 2 + . stddev=0.0 -chr1 genetrack . 159372 159392 605 + . stddev=0.0 -chr1 genetrack . 165827 165847 1109 + . stddev=0.0 -chr1 genetrack . 166238 166258 21 + . stddev=0.0 -chr1 genetrack . 167443 167463 597 + . stddev=0.0 -chr1 genetrack . 167652 167672 5 + . stddev=0.0 -chr1 genetrack . 169107 169127 1811 + . stddev=0.0 -chr1 genetrack . 169159 169179 91 + . stddev=0.0 -chr1 genetrack . 169338 169358 2 + . stddev=0.0 -chr1 genetrack . 170119 170139 284 + . stddev=0.0 -chr1 genetrack . 172223 172243 338 + . stddev=0.0 -chr1 genetrack . 173262 173282 11 + . stddev=0.0 -chr1 genetrack . 175899 175919 2 + . stddev=0.0 -chr1 genetrack . 176858 176878 46 + . stddev=0.0 -chr1 genetrack . 177627 177647 51 + . stddev=0.0 -chr1 genetrack . 178117 178137 686 + . stddev=0.0 -chr1 genetrack . 179472 179492 696 + . stddev=0.0 -chr1 genetrack . 179554 179574 31 + . stddev=0.176684695969 -chr1 genetrack . 180280 180300 38 + . stddev=0.0 -chr1 genetrack . 180652 180672 154 + . stddev=0.0 -chr1 genetrack . 183610 183630 4 + . stddev=0.433012701892 -chr1 genetrack . 185076 185096 1309 + . stddev=0.0 -chr1 genetrack . 187009 187029 139 + . stddev=0.0 -chr1 genetrack . 187155 187175 455 + . stddev=0.0 -chr1 genetrack . 188920 188940 7 + . stddev=1.97948663722 -chr1 genetrack . 189494 189514 70 + . stddev=0.0 -chr1 genetrack . 191408 191428 50 + . stddev=0.0 -chr1 genetrack . 192271 192291 453 + . stddev=0.0 -chr1 genetrack . 192754 192774 668 + . stddev=0.0 -chr1 genetrack . 195756 195776 348 + . stddev=0.0 -chr1 genetrack . 197489 197509 3 + . stddev=0.0 -chr1 genetrack . 198594 198614 170 + . stddev=0.0 -chr1 genetrack . 199141 199161 2 + . stddev=0.0 -chr1 genetrack . 199418 199438 5 + . stddev=0.0 -chr1 genetrack . 199649 199669 264 + . stddev=0.0 -chr1 genetrack . 200580 200600 1298 + . stddev=0.0 -chr1 genetrack . 201841 201861 15 + . stddev=0.0 -chr1 genetrack . 203193 203213 789 + . stddev=0.0 -chr1 genetrack . 203872 203892 1234 + . stddev=0.0 -chr1 genetrack . 204126 204146 261 + . stddev=0.0 -chr1 genetrack . 204214 204234 36 + . stddev=0.0 -chr1 genetrack . 206684 206704 8 + . stddev=0.0 -chr1 genetrack . 210175 210195 62 + . stddev=0.0 -chr1 genetrack . 219301 219321 37 + . stddev=0.0 -chr1 genetrack . 227346 227366 114 + . stddev=0.0 -chr1 genetrack . 228150 228170 5 + . stddev=0.0 -chr1 genetrack . 228633 228653 371 + . stddev=0.0 -chr1 genetrack . 229721 229741 84 + . stddev=0.0 -chr1 genetrack . 229741 229761 1380 + . stddev=0.0 -chr1 genetrack . 229862 229882 110 + . stddev=0.0 -chr1 genetrack . 230110 230130 42 + . stddev=3.55113280767 -chr1 genetrack . 230145 230165 8 + . stddev=3.08220700148 -chr1 genetrack . 230163 230183 23 + . stddev=1.62796915016 -chr1 genetrack . 50 70 39 - . stddev=1.95948442816 -chr1 genetrack . 139 159 993 - . stddev=4.91699987402 -chr1 genetrack . 176 196 14 - . stddev=0.0 -chr1 genetrack . 215 235 2611 - . stddev=5.10619852562 -chr1 genetrack . 261 281 1278 - . stddev=3.36870454509 -chr1 genetrack . 279 299 1328 - . stddev=2.15740829792 -chr1 genetrack . 323 343 486 - . stddev=0.0453142295176 -chr1 genetrack . 373 393 200 - . stddev=0.551339278485 -chr1 genetrack . 388 408 167 - . stddev=0.0 -chr1 genetrack . 410 430 8 - . stddev=0.0 -chr1 genetrack . 446 466 170 - . stddev=0.748724405435 -chr1 genetrack . 468 488 468 - . stddev=0.0 -chr1 genetrack . 634 654 151 - . stddev=0.0 -chr1 genetrack . 1457 1477 111 - . stddev=0.0 -chr1 genetrack . 1970 1990 629 - . stddev=0.0 -chr1 genetrack . 3148 3168 1420 - . stddev=0.0265278988758 -chr1 genetrack . 4892 4912 272 - . stddev=0.0 -chr1 genetrack . 5546 5566 27 - . stddev=0.0 -chr1 genetrack . 6254 6274 1076 - . stddev=1.26363262979 -chr1 genetrack . 6476 6496 567 - . stddev=0.0 -chr1 genetrack . 6702 6722 2 - . stddev=0.0 -chr1 genetrack . 7659 7679 243 - . stddev=0.0 -chr1 genetrack . 8596 8616 114 - . stddev=0.0 -chr1 genetrack . 8904 8924 80 - . stddev=0.0 -chr1 genetrack . 9119 9139 22 - . stddev=0.0 -chr1 genetrack . 10107 10127 1622 - . stddev=0.0 -chr1 genetrack . 12157 12177 40 - . stddev=0.0 -chr1 genetrack . 13415 13435 634 - . stddev=0.0 -chr1 genetrack . 16739 16759 3 - . stddev=0.0 -chr1 genetrack . 19145 19165 618 - . stddev=0.0 -chr1 genetrack . 19191 19211 736 - . stddev=0.0 -chr1 genetrack . 20550 20570 865 - . stddev=0.0 -chr1 genetrack . 22383 22403 141 - . stddev=0.0 -chr1 genetrack . 22569 22589 254 - . stddev=0.0 -chr1 genetrack . 23046 23066 213 - . stddev=0.0 -chr1 genetrack . 25345 25365 188 - . stddev=0.0 -chr1 genetrack . 27517 27537 1459 - . stddev=0.0 -chr1 genetrack . 29325 29345 1074 - . stddev=0.0 -chr1 genetrack . 30046 30066 17 - . stddev=0.0 -chr1 genetrack . 31693 31713 450 - . stddev=0.0 -chr1 genetrack . 31876 31896 1344 - . stddev=0.0 -chr1 genetrack . 32497 32517 2 - . stddev=0.0 -chr1 genetrack . 37166 37186 1000 - . stddev=0.0 -chr1 genetrack . 38768 38788 1064 - . stddev=0.0 -chr1 genetrack . 38799 38819 9 - . stddev=0.0 -chr1 genetrack . 39000 39020 3 - . stddev=0.0 -chr1 genetrack . 39052 39072 82 - . stddev=0.0 -chr1 genetrack . 39258 39278 261 - . stddev=0.0 -chr1 genetrack . 39293 39313 2 - . stddev=0.0 -chr1 genetrack . 41867 41887 7 - . stddev=0.0 -chr1 genetrack . 45565 45585 246 - . stddev=1.46097357384 -chr1 genetrack . 45579 45599 78 - . stddev=0.0 -chr1 genetrack . 45643 45663 295 - . stddev=1.27157056343 -chr1 genetrack . 46616 46636 741 - . stddev=0.0 -chr1 genetrack . 49660 49680 6 - . stddev=0.0 -chr1 genetrack . 50091 50111 156 - . stddev=0.0 -chr1 genetrack . 51978 51998 633 - . stddev=0.0 -chr1 genetrack . 52308 52328 549 - . stddev=0.0 -chr1 genetrack . 53045 53065 31 - . stddev=0.0 -chr1 genetrack . 55581 55601 831 - . stddev=0.124372757427 -chr1 genetrack . 55616 55636 984 - . stddev=0.0 -chr1 genetrack . 56542 56562 606 - . stddev=0.0 -chr1 genetrack . 56664 56684 67 - . stddev=0.0 -chr1 genetrack . 56995 57015 1393 - . stddev=0.0 -chr1 genetrack . 57121 57141 4 - . stddev=0.0 -chr1 genetrack . 57212 57232 667 - . stddev=0.0 -chr1 genetrack . 57543 57563 2 - . stddev=0.0 -chr1 genetrack . 59157 59177 168 - . stddev=0.0 -chr1 genetrack . 59246 59266 397 - . stddev=0.0 -chr1 genetrack . 61877 61897 607 - . stddev=0.0 -chr1 genetrack . 65148 65168 43 - . stddev=0.0 -chr1 genetrack . 65687 65707 596 - . stddev=0.0 -chr1 genetrack . 66306 66326 2 - . stddev=0.0 -chr1 genetrack . 68423 68443 139 - . stddev=0.0 -chr1 genetrack . 70336 70356 652 - . stddev=0.0 -chr1 genetrack . 70788 70808 998 - . stddev=0.0 -chr1 genetrack . 72771 72791 406 - . stddev=0.0 -chr1 genetrack . 72810 72830 212 - . stddev=0.0 -chr1 genetrack . 74763 74783 430 - . stddev=0.0 -chr1 genetrack . 75897 75917 10 - . stddev=0.0 -chr1 genetrack . 77515 77535 797 - . stddev=0.0 -chr1 genetrack . 77530 77550 513 - . stddev=0.0 -chr1 genetrack . 78813 78833 113 - . stddev=0.0 -chr1 genetrack . 80958 80978 137 - . stddev=0.0 -chr1 genetrack . 81037 81057 4 - . stddev=0.0 -chr1 genetrack . 81972 81992 49 - 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genetrack . 92571 92591 90 - . stddev=0.0 -chr1 genetrack . 92639 92659 2137 - . stddev=3.28540359906 -chr1 genetrack . 92664 92684 187 - . stddev=0.390044546071 -chr1 genetrack . 94913 94933 1437 - . stddev=0.0 -chr1 genetrack . 95971 95991 684 - . stddev=0.0 -chr1 genetrack . 96278 96298 166 - . stddev=0.0 -chr1 genetrack . 96315 96335 2 - . stddev=0.0 -chr1 genetrack . 96566 96586 6 - . stddev=0.0 -chr1 genetrack . 96911 96931 10 - . stddev=0.0 -chr1 genetrack . 98555 98575 88 - . stddev=0.0 -chr1 genetrack . 101301 101321 48 - . stddev=0.0 -chr1 genetrack . 101367 101387 1388 - . stddev=0.0268317355181 -chr1 genetrack . 102072 102092 14 - . stddev=0.0 -chr1 genetrack . 102903 102923 846 - . stddev=0.0 -chr1 genetrack . 104110 104130 117 - . stddev=0.0 -chr1 genetrack . 105663 105683 417 - . stddev=0.0 -chr1 genetrack . 105814 105834 529 - . stddev=0.0 -chr1 genetrack . 105846 105866 177 - . stddev=0.0 -chr1 genetrack . 105889 105909 84 - . stddev=0.0 -chr1 genetrack . 106041 106061 14 - . stddev=0.0 -chr1 genetrack . 106340 106360 421 - . stddev=0.0 -chr1 genetrack . 108072 108092 72 - . stddev=0.0 -chr1 genetrack . 108263 108283 145 - . stddev=0.0 -chr1 genetrack . 108579 108599 367 - . stddev=0.0 -chr1 genetrack . 111947 111967 585 - . stddev=1.43661357803 -chr1 genetrack . 113762 113782 296 - . stddev=0.0 -chr1 genetrack . 114306 114326 2 - . stddev=0.0 -chr1 genetrack . 116148 116168 248 - . stddev=0.0 -chr1 genetrack . 116619 116639 699 - . stddev=0.0 -chr1 genetrack . 117522 117542 1573 - . stddev=0.0 -chr1 genetrack . 117845 117865 16 - . stddev=0.0 -chr1 genetrack . 118841 118861 7 - . stddev=0.0 -chr1 genetrack . 119430 119450 1093 - . stddev=0.0 -chr1 genetrack . 119596 119616 842 - . stddev=0.0 -chr1 genetrack . 119657 119677 499 - . stddev=0.0 -chr1 genetrack . 119669 119689 665 - . stddev=0.0 -chr1 genetrack . 119866 119886 846 - . stddev=0.0 -chr1 genetrack . 119880 119900 1136 - . stddev=0.0 -chr1 genetrack . 120788 120808 105 - . stddev=0.0 -chr1 genetrack . 122624 122644 201 - . stddev=0.0 -chr1 genetrack . 122777 122797 20 - . stddev=0.0 -chr1 genetrack . 123718 123738 751 - . stddev=0.0 -chr1 genetrack . 124275 124295 12 - . stddev=0.0 -chr1 genetrack . 125840 125860 273 - . stddev=0.0 -chr1 genetrack . 127027 127047 590 - . stddev=0.0 -chr1 genetrack . 130869 130889 718 - . stddev=0.0 -chr1 genetrack . 133644 133664 122 - . stddev=0.0 -chr1 genetrack . 134270 134290 508 - . stddev=0.0 -chr1 genetrack . 135051 135071 63 - . stddev=0.0 -chr1 genetrack . 136352 136372 117 - . stddev=0.0 -chr1 genetrack . 137428 137448 1200 - . stddev=0.028855482822 -chr1 genetrack . 137816 137836 695 - . stddev=0.0 -chr1 genetrack . 138864 138884 13 - . stddev=0.0 -chr1 genetrack . 139228 139248 214 - . stddev=0.0 -chr1 genetrack . 139627 139647 531 - . stddev=0.0 -chr1 genetrack . 140133 140153 441 - . stddev=0.0 -chr1 genetrack . 140770 140790 556 - . stddev=0.0 -chr1 genetrack . 141182 141202 14 - . stddev=0.0 -chr1 genetrack . 143551 143571 3 - . stddev=0.0 -chr1 genetrack . 144669 144689 1192 - . stddev=0.0959718343646 -chr1 genetrack . 145383 145403 326 - . stddev=0.0 -chr1 genetrack . 147573 147593 255 - . stddev=0.0 -chr1 genetrack . 148690 148710 2 - . stddev=0.0 -chr1 genetrack . 149704 149724 74 - . stddev=0.0 -chr1 genetrack . 150358 150378 153 - . stddev=0.0 -chr1 genetrack . 151341 151361 593 - . stddev=0.0 -chr1 genetrack . 152984 153004 106 - . stddev=0.0 -chr1 genetrack . 153812 153832 168 - . stddev=0.0 -chr1 genetrack . 154862 154882 14 - . stddev=0.0 -chr1 genetrack . 155111 155131 1051 - . stddev=0.0 -chr1 genetrack . 155456 155476 23 - . stddev=0.0 -chr1 genetrack . 155897 155917 10 - . stddev=0.0 -chr1 genetrack . 157559 157579 337 - . stddev=0.0 -chr1 genetrack . 166467 166487 582 - . stddev=0.0 -chr1 genetrack . 166631 166651 173 - . stddev=0.0 -chr1 genetrack . 169064 169084 76 - . stddev=0.0 -chr1 genetrack . 169500 169520 814 - . stddev=0.0 -chr1 genetrack . 170129 170149 373 - . stddev=0.0 -chr1 genetrack . 170282 170302 63 - . stddev=0.0 -chr1 genetrack . 171063 171083 212 - . stddev=0.0 -chr1 genetrack . 173270 173290 535 - . stddev=0.0863866916508 -chr1 genetrack . 175188 175208 117 - . stddev=0.0 -chr1 genetrack . 175474 175494 1119 - . stddev=0.0 -chr1 genetrack . 176004 176024 1473 - . stddev=0.0 -chr1 genetrack . 177140 177160 93 - . stddev=0.0 -chr1 genetrack . 177386 177406 289 - . stddev=0.0 -chr1 genetrack . 178846 178866 601 - . stddev=0.0 -chr1 genetrack . 178971 178991 723 - . stddev=0.0 -chr1 genetrack . 179116 179136 71 - . stddev=0.0 -chr1 genetrack . 180272 180292 25 - . stddev=0.0 -chr1 genetrack . 180362 180382 59 - . stddev=0.0 -chr1 genetrack . 180995 181015 299 - . stddev=0.0 -chr1 genetrack . 182588 182608 465 - . stddev=0.0 -chr1 genetrack . 182790 182810 355 - . stddev=0.0 -chr1 genetrack . 185122 185142 62 - . stddev=0.0 -chr1 genetrack . 185673 185693 190 - . stddev=0.0 -chr1 genetrack . 187422 187442 20 - . stddev=0.0 -chr1 genetrack . 187976 187996 728 - . stddev=0.0 -chr1 genetrack . 196499 196519 224 - . stddev=0.0 -chr1 genetrack . 197060 197080 224 - . stddev=0.0 -chr1 genetrack . 197151 197171 1464 - . stddev=0.0 -chr1 genetrack . 197342 197362 204 - . stddev=0.0 -chr1 genetrack . 197562 197582 2 - . stddev=0.0 -chr1 genetrack . 198423 198443 598 - . stddev=0.0 -chr1 genetrack . 198953 198973 3 - . stddev=0.0 -chr1 genetrack . 199388 199408 805 - . stddev=0.0 -chr1 genetrack . 199935 199955 31 - . stddev=0.0 -chr1 genetrack . 201308 201328 1287 - . stddev=0.0 -chr1 genetrack . 201651 201671 892 - . stddev=0.0 -chr1 genetrack . 202977 202997 163 - . stddev=0.0 -chr1 genetrack . 203452 203472 76 - . stddev=0.0 -chr1 genetrack . 203835 203855 242 - . stddev=0.0 -chr1 genetrack . 206245 206265 22 - . stddev=0.0 -chr1 genetrack . 207675 207695 313 - . stddev=0.0 -chr1 genetrack . 208559 208579 121 - . stddev=0.89393833276 -chr1 genetrack . 209205 209225 176 - . stddev=0.0 -chr1 genetrack . 220863 220883 2 - . stddev=0.0 -chr1 genetrack . 223035 223055 62 - . stddev=0.0 -chr1 genetrack . 225156 225176 2 - . stddev=0.0 -chr1 genetrack . 226777 226797 444 - . stddev=0.0 -chr1 genetrack . 227608 227628 1311 - . stddev=0.0 -chr1 genetrack . 228405 228425 1447 - . stddev=2.78971080368 -chr1 genetrack . 228691 228711 255 - . stddev=0.0 -chr1 genetrack . 229031 229051 6 - . stddev=0.0 -chr1 genetrack . 229583 229603 62 - . stddev=0.0 -chr1 genetrack . 229665 229685 131 - . stddev=0.0 -chr1 genetrack . 229757 229777 3151 - . stddev=2.79078905805 -chr1 genetrack . 229784 229804 615 - . stddev=0.0 -chr1 genetrack . 229965 229985 13 - . stddev=0.0 -chr1 genetrack . 230120 230140 2 - . stddev=0.0 -chr1 genetrack . 230132 230152 2 - . stddev=0.0 -chr1 genetrack . 230150 230170 7 - . stddev=0.699854212224 -chr1 genetrack . 230173 230193 33 - . stddev=0.477212598425 +##gff-version 3.2.1 +chr1 genetrack . 11 31 414 + . stddev=2.26073020752 +chr1 genetrack . 30 50 2140 + . stddev=4.43077587195 +chr1 genetrack . 48 68 2842 + . stddev=4.88263527016 +chr1 genetrack . 87 107 3211 + . stddev=5.51553909779 +chr1 genetrack . 117 137 2163 + . stddev=4.21572697137 +chr1 genetrack . 160 180 451 + . stddev=0.724882503432 +chr1 genetrack . 201 221 1411 + . stddev=5.79752503059 +chr1 genetrack . 231 251 1146 + . stddev=1.48216146131 +chr1 genetrack . 255 275 2810 + . stddev=1.35163759113 +chr1 genetrack . 307 327 685 + . stddev=0.0 +chr1 genetrack . 348 368 699 + . stddev=2.60206286017 +chr1 genetrack . 368 388 192 + . stddev=0.0 +chr1 genetrack . 438 458 334 + . stddev=0.109271183179 +chr1 genetrack . 467 487 98 + . stddev=0.0 +chr1 genetrack . 512 532 101 + . stddev=0.792079207921 +chr1 genetrack . 601 621 96 + . stddev=0.0 +chr1 genetrack . 682 702 168 + . stddev=0.0 +chr1 genetrack . 1298 1318 684 + . stddev=0.0 +chr1 genetrack . 2293 2313 12 + . stddev=0.0 +chr1 genetrack . 2613 2633 202 + . stddev=0.0 +chr1 genetrack . 2976 2996 356 + . stddev=0.0 +chr1 genetrack . 4053 4073 381 + . stddev=0.0 +chr1 genetrack . 4445 4465 94 + . stddev=0.0 +chr1 genetrack . 4748 4768 1077 + . stddev=0.0 +chr1 genetrack . 5379 5399 1572 + . stddev=0.0 +chr1 genetrack . 5750 5770 25 + . stddev=0.0 +chr1 genetrack . 5794 5814 148 + . stddev=0.0 +chr1 genetrack . 6163 6183 1049 + . stddev=0.645595472695 +chr1 genetrack . 6233 6253 589 + . stddev=2.54134583729 +chr1 genetrack . 6255 6275 26 + . stddev=0.0 +chr1 genetrack . 6413 6433 682 + . stddev=0.0 +chr1 genetrack . 6453 6473 601 + . stddev=0.0 +chr1 genetrack . 6706 6726 431 + . stddev=0.0 +chr1 genetrack . 7303 7323 484 + . stddev=0.0 +chr1 genetrack . 7753 7773 14 + . stddev=0.0 +chr1 genetrack . 9367 9387 425 + . stddev=0.0 +chr1 genetrack . 10641 10661 1359 + . stddev=0.0 +chr1 genetrack . 12305 12325 13 + . stddev=0.0 +chr1 genetrack . 16173 16193 12 + . stddev=0.0 +chr1 genetrack . 16501 16521 15 + . stddev=0.0 +chr1 genetrack . 19216 19236 42 + . stddev=0.0 +chr1 genetrack . 20117 20137 8 + . stddev=0.0 +chr1 genetrack . 20205 20225 634 + . stddev=0.0 +chr1 genetrack . 20391 20411 173 + . stddev=0.0 +chr1 genetrack . 20626 20646 171 + . stddev=0.0 +chr1 genetrack . 21406 21426 177 + . stddev=0.0 +chr1 genetrack . 22268 22288 15 + . stddev=0.0 +chr1 genetrack . 22571 22591 609 + . stddev=0.0 +chr1 genetrack . 24765 24785 4 + . stddev=0.0 +chr1 genetrack . 25246 25266 995 + . stddev=0.0 +chr1 genetrack . 27978 27998 354 + . stddev=0.0 +chr1 genetrack . 29570 29590 1130 + . stddev=0.0 +chr1 genetrack . 29864 29884 570 + . stddev=0.0 +chr1 genetrack . 30964 30984 829 + . stddev=0.0 +chr1 genetrack . 31019 31039 810 + . stddev=0.0 +chr1 genetrack . 31096 31116 1481 + . stddev=0.0 +chr1 genetrack . 31627 31647 40 + . stddev=0.0 +chr1 genetrack . 32145 32165 66 + . stddev=0.0 +chr1 genetrack . 32449 32469 476 + . stddev=0.0 +chr1 genetrack . 33426 33446 2 + . stddev=0.0 +chr1 genetrack . 33829 33849 48 + . stddev=0.0 +chr1 genetrack . 35773 35793 866 + . stddev=0.0 +chr1 genetrack . 39081 39101 1268 + . stddev=0.0 +chr1 genetrack . 39197 39217 101 + . stddev=0.0 +chr1 genetrack . 39591 39611 10 + . stddev=0.0 +chr1 genetrack . 39794 39814 780 + . stddev=0.0 +chr1 genetrack . 39942 39962 375 + . stddev=0.0 +chr1 genetrack . 40264 40284 199 + . stddev=0.0 +chr1 genetrack . 40830 40850 491 + . stddev=0.0 +chr1 genetrack . 41008 41028 132 + . stddev=0.0 +chr1 genetrack . 42843 42863 218 + . stddev=0.0 +chr1 genetrack . 42925 42945 77 + . stddev=0.0 +chr1 genetrack . 43147 43167 9 + . stddev=0.0 +chr1 genetrack . 43523 43543 505 + . stddev=0.0 +chr1 genetrack . 43657 43677 586 + . stddev=0.0 +chr1 genetrack . 43835 43855 1173 + . stddev=0.0 +chr1 genetrack . 44687 44707 100 + . stddev=0.0 +chr1 genetrack . 45248 45268 305 + . stddev=0.139642881568 +chr1 genetrack . 45409 45429 307 + . stddev=0.0 +chr1 genetrack . 45678 45698 198 + . stddev=0.0 +chr1 genetrack . 47015 47035 133 + . stddev=0.0 +chr1 genetrack . 48319 48339 290 + . stddev=0.0 +chr1 genetrack . 48431 48451 57 + . stddev=0.0 +chr1 genetrack . 48642 48662 610 + . stddev=0.0 +chr1 genetrack . 48772 48792 284 + . stddev=0.0 +chr1 genetrack . 49283 49303 2 + . stddev=0.0 +chr1 genetrack . 52440 52460 1562 + . stddev=0.0 +chr1 genetrack . 53097 53117 835 + . stddev=0.0 +chr1 genetrack . 55349 55369 794 + . stddev=0.0 +chr1 genetrack . 55495 55515 125 + . stddev=0.0 +chr1 genetrack . 55692 55712 228 + . stddev=0.0 +chr1 genetrack . 59190 59210 168 + . stddev=0.0 +chr1 genetrack . 59248 59268 80 + . stddev=0.0 +chr1 genetrack . 59583 59603 204 + . stddev=0.0 +chr1 genetrack . 61977 61997 368 + . stddev=0.0 +chr1 genetrack . 64772 64792 1292 + . stddev=0.0 +chr1 genetrack . 65152 65172 575 + . stddev=0.0 +chr1 genetrack . 68018 68038 62 + . stddev=0.0 +chr1 genetrack . 68564 68584 303 + . stddev=0.0 +chr1 genetrack . 70776 70796 1148 + . stddev=0.0 +chr1 genetrack . 70953 70973 555 + . stddev=0.0 +chr1 genetrack . 71041 71061 881 + . stddev=0.0 +chr1 genetrack . 71556 71576 835 + . stddev=0.0345856983909 +chr1 genetrack . 72671 72691 304 + . stddev=0.0572595236366 +chr1 genetrack . 72781 72801 657 + . stddev=0.0 +chr1 genetrack . 73234 73254 1492 + . stddev=0.0 +chr1 genetrack . 76365 76385 47 + . stddev=0.0 +chr1 genetrack . 76501 76521 33 + . stddev=0.0 +chr1 genetrack . 77731 77751 113 + . stddev=0.0 +chr1 genetrack . 81481 81501 5 + . stddev=0.0 +chr1 genetrack . 83774 83794 1125 + . stddev=0.0 +chr1 genetrack . 86865 86885 81 + . stddev=0.0 +chr1 genetrack . 86886 86906 1253 + . stddev=0.0 +chr1 genetrack . 86954 86974 1948 + . stddev=5.39208071191 +chr1 genetrack . 87002 87022 550 + . stddev=0.0 +chr1 genetrack . 87019 87039 769 + . stddev=0.0 +chr1 genetrack . 87085 87105 676 + . stddev=0.0 +chr1 genetrack . 87098 87118 1125 + . stddev=1.98839815175 +chr1 genetrack . 87147 87167 3492 + . stddev=2.59487167975 +chr1 genetrack . 87171 87191 1436 + . stddev=1.75985539692 +chr1 genetrack . 87572 87592 407 + . stddev=0.0 +chr1 genetrack . 89611 89631 640 + . stddev=0.0 +chr1 genetrack . 89663 89683 2 + . stddev=0.0 +chr1 genetrack . 90040 90060 82 + . stddev=0.0 +chr1 genetrack . 90412 90432 86 + . stddev=0.0 +chr1 genetrack . 91215 91235 11 + . stddev=0.0 +chr1 genetrack . 91379 91399 120 + . stddev=0.0 +chr1 genetrack . 92411 92431 1252 + . stddev=0.169502292497 +chr1 genetrack . 92543 92563 699 + . stddev=0.0 +chr1 genetrack . 92631 92651 260 + . stddev=0.0 +chr1 genetrack . 92775 92795 1105 + . stddev=0.923076923077 +chr1 genetrack . 92982 93002 44 + . stddev=0.0 +chr1 genetrack . 93793 93813 415 + . stddev=0.0 +chr1 genetrack . 95920 95940 5 + . stddev=0.0 +chr1 genetrack . 96908 96928 2 + . stddev=0.0 +chr1 genetrack . 97898 97918 501 + . stddev=0.0 +chr1 genetrack . 97967 97987 50 + . stddev=0.0 +chr1 genetrack . 98528 98548 34 + . stddev=0.0 +chr1 genetrack . 100364 100384 2695 + . stddev=4.98845945981 +chr1 genetrack . 101411 101431 973 + . stddev=0.0 +chr1 genetrack . 102337 102357 36 + . stddev=0.0 +chr1 genetrack . 103108 103128 90 + . stddev=0.0 +chr1 genetrack . 103207 103227 1229 + . stddev=0.0 +chr1 genetrack . 105499 105519 46 + . stddev=0.145830520272 +chr1 genetrack . 105942 105962 25 + . stddev=0.0 +chr1 genetrack . 106034 106054 558 + . stddev=0.0 +chr1 genetrack . 108624 108644 206 + . stddev=0.0 +chr1 genetrack . 110130 110150 42 + . stddev=0.0 +chr1 genetrack . 110540 110560 91 + . stddev=0.0 +chr1 genetrack . 110602 110622 8 + . stddev=0.0 +chr1 genetrack . 110736 110756 621 + . stddev=0.0400962950016 +chr1 genetrack . 111317 111337 17 + . stddev=0.0 +chr1 genetrack . 112137 112157 601 + . stddev=0.0 +chr1 genetrack . 112900 112920 125 + . stddev=0.0 +chr1 genetrack . 113226 113246 28 + . stddev=0.0 +chr1 genetrack . 113782 113802 420 + . stddev=0.0 +chr1 genetrack . 115866 115886 480 + . stddev=0.0 +chr1 genetrack . 116432 116452 267 + . stddev=0.0 +chr1 genetrack . 116660 116680 74 + . stddev=0.0 +chr1 genetrack . 117198 117218 228 + . stddev=0.0 +chr1 genetrack . 118428 118448 633 + . stddev=0.039715023981 +chr1 genetrack . 119155 119175 9 + . stddev=0.0 +chr1 genetrack . 119736 119756 135 + . stddev=0.0 +chr1 genetrack . 119754 119774 515 + . stddev=0.0 +chr1 genetrack . 119953 119973 295 + . stddev=0.0 +chr1 genetrack . 121016 121036 155 + . stddev=0.0 +chr1 genetrack . 121289 121309 89 + . stddev=0.0 +chr1 genetrack . 124318 124338 749 + . stddev=0.0 +chr1 genetrack . 124669 124689 203 + . stddev=0.0 +chr1 genetrack . 124845 124865 383 + . stddev=0.0 +chr1 genetrack . 125727 125747 3 + . stddev=0.0 +chr1 genetrack . 126073 126093 590 + . stddev=0.329075555241 +chr1 genetrack . 126369 126389 284 + . stddev=0.0592345205678 +chr1 genetrack . 126733 126753 952 + . stddev=0.484392920736 +chr1 genetrack . 129555 129575 536 + . stddev=0.0431531100978 +chr1 genetrack . 129680 129700 464 + . stddev=0.0 +chr1 genetrack . 130514 130534 243 + . stddev=0.0 +chr1 genetrack . 133139 133159 84 + . stddev=0.0 +chr1 genetrack . 134021 134041 572 + . stddev=0.0 +chr1 genetrack . 134170 134190 151 + . stddev=0.0 +chr1 genetrack . 134559 134579 87 + . stddev=0.0 +chr1 genetrack . 134868 134888 36 + . stddev=0.0 +chr1 genetrack . 136072 136092 380 + . stddev=0.0 +chr1 genetrack . 136366 136386 248 + . stddev=0.0 +chr1 genetrack . 138030 138050 2 + . stddev=0.0 +chr1 genetrack . 138051 138071 5 + . stddev=0.0 +chr1 genetrack . 138868 138888 698 + . stddev=0.0 +chr1 genetrack . 139213 139233 965 + . stddev=0.0 +chr1 genetrack . 140857 140877 23 + . stddev=0.0 +chr1 genetrack . 142139 142159 43 + . stddev=0.0 +chr1 genetrack . 142905 142925 599 + . stddev=0.0 +chr1 genetrack . 142950 142970 12 + . stddev=0.0 +chr1 genetrack . 143657 143677 328 + . stddev=0.0 +chr1 genetrack . 145253 145273 1394 + . stddev=0.0 +chr1 genetrack . 146517 146537 69 + . stddev=0.0 +chr1 genetrack . 147211 147231 130 + . stddev=0.0 +chr1 genetrack . 147227 147247 101 + . stddev=0.0 +chr1 genetrack . 147322 147342 15 + . stddev=0.0 +chr1 genetrack . 149343 149363 159 + . stddev=0.0 +chr1 genetrack . 150449 150469 436 + . stddev=0.0 +chr1 genetrack . 151369 151389 2 + . stddev=0.0 +chr1 genetrack . 151431 151451 38 + . stddev=0.0 +chr1 genetrack . 152678 152698 135 + . stddev=0.0 +chr1 genetrack . 153095 153115 490 + . stddev=0.0 +chr1 genetrack . 153928 153948 768 + . stddev=0.0 +chr1 genetrack . 155028 155048 522 + . stddev=0.0 +chr1 genetrack . 156097 156117 2 + . stddev=0.0 +chr1 genetrack . 156252 156272 133 + . stddev=0.0 +chr1 genetrack . 158038 158058 2 + . stddev=0.0 +chr1 genetrack . 159372 159392 605 + . stddev=0.0 +chr1 genetrack . 165827 165847 1109 + . stddev=0.0 +chr1 genetrack . 166238 166258 21 + . stddev=0.0 +chr1 genetrack . 167443 167463 597 + . stddev=0.0 +chr1 genetrack . 167652 167672 5 + . stddev=0.0 +chr1 genetrack . 169107 169127 1811 + . stddev=0.0 +chr1 genetrack . 169159 169179 91 + . stddev=0.0 +chr1 genetrack . 169338 169358 2 + . stddev=0.0 +chr1 genetrack . 170119 170139 284 + . stddev=0.0 +chr1 genetrack . 172223 172243 338 + . stddev=0.0 +chr1 genetrack . 173262 173282 11 + . stddev=0.0 +chr1 genetrack . 175899 175919 2 + . stddev=0.0 +chr1 genetrack . 176858 176878 46 + . stddev=0.0 +chr1 genetrack . 177627 177647 51 + . stddev=0.0 +chr1 genetrack . 178117 178137 686 + . stddev=0.0 +chr1 genetrack . 179472 179492 696 + . stddev=0.0 +chr1 genetrack . 179554 179574 31 + . stddev=0.176684695969 +chr1 genetrack . 180280 180300 38 + . stddev=0.0 +chr1 genetrack . 180652 180672 154 + . stddev=0.0 +chr1 genetrack . 183610 183630 4 + . stddev=0.433012701892 +chr1 genetrack . 185076 185096 1309 + . stddev=0.0 +chr1 genetrack . 187009 187029 139 + . stddev=0.0 +chr1 genetrack . 187155 187175 455 + . stddev=0.0 +chr1 genetrack . 188920 188940 7 + . stddev=1.97948663722 +chr1 genetrack . 189494 189514 70 + . stddev=0.0 +chr1 genetrack . 191408 191428 50 + . stddev=0.0 +chr1 genetrack . 192271 192291 453 + . stddev=0.0 +chr1 genetrack . 192754 192774 668 + . stddev=0.0 +chr1 genetrack . 195756 195776 348 + . stddev=0.0 +chr1 genetrack . 197489 197509 3 + . stddev=0.0 +chr1 genetrack . 198594 198614 170 + . stddev=0.0 +chr1 genetrack . 199141 199161 2 + . stddev=0.0 +chr1 genetrack . 199418 199438 5 + . stddev=0.0 +chr1 genetrack . 199649 199669 264 + . stddev=0.0 +chr1 genetrack . 200580 200600 1298 + . stddev=0.0 +chr1 genetrack . 201841 201861 15 + . stddev=0.0 +chr1 genetrack . 203193 203213 789 + . stddev=0.0 +chr1 genetrack . 203872 203892 1234 + . stddev=0.0 +chr1 genetrack . 204126 204146 261 + . stddev=0.0 +chr1 genetrack . 204214 204234 36 + . stddev=0.0 +chr1 genetrack . 206684 206704 8 + . stddev=0.0 +chr1 genetrack . 210175 210195 62 + . stddev=0.0 +chr1 genetrack . 219301 219321 37 + . stddev=0.0 +chr1 genetrack . 227346 227366 114 + . stddev=0.0 +chr1 genetrack . 228150 228170 5 + . stddev=0.0 +chr1 genetrack . 228633 228653 371 + . stddev=0.0 +chr1 genetrack . 229721 229741 84 + . stddev=0.0 +chr1 genetrack . 229741 229761 1380 + . stddev=0.0 +chr1 genetrack . 229862 229882 110 + . stddev=0.0 +chr1 genetrack . 230110 230130 42 + . stddev=3.55113280767 +chr1 genetrack . 230145 230165 8 + . stddev=3.08220700148 +chr1 genetrack . 230163 230183 23 + . stddev=1.62796915016 +chr1 genetrack . 50 70 39 - . stddev=1.95948442816 +chr1 genetrack . 139 159 993 - . stddev=4.91699987402 +chr1 genetrack . 176 196 14 - . stddev=0.0 +chr1 genetrack . 215 235 2611 - . stddev=5.10619852562 +chr1 genetrack . 261 281 1278 - . stddev=3.36870454509 +chr1 genetrack . 279 299 1328 - . stddev=2.15740829792 +chr1 genetrack . 323 343 486 - . stddev=0.0453142295176 +chr1 genetrack . 373 393 200 - . stddev=0.551339278485 +chr1 genetrack . 388 408 167 - . stddev=0.0 +chr1 genetrack . 410 430 8 - . stddev=0.0 +chr1 genetrack . 446 466 170 - . stddev=0.748724405435 +chr1 genetrack . 468 488 468 - . stddev=0.0 +chr1 genetrack . 634 654 151 - . stddev=0.0 +chr1 genetrack . 1457 1477 111 - . stddev=0.0 +chr1 genetrack . 1970 1990 629 - . stddev=0.0 +chr1 genetrack . 3148 3168 1420 - . stddev=0.0265278988758 +chr1 genetrack . 4892 4912 272 - . stddev=0.0 +chr1 genetrack . 5546 5566 27 - . stddev=0.0 +chr1 genetrack . 6254 6274 1076 - . stddev=1.26363262979 +chr1 genetrack . 6476 6496 567 - . stddev=0.0 +chr1 genetrack . 6702 6722 2 - . stddev=0.0 +chr1 genetrack . 7659 7679 243 - . stddev=0.0 +chr1 genetrack . 8596 8616 114 - . stddev=0.0 +chr1 genetrack . 8904 8924 80 - . stddev=0.0 +chr1 genetrack . 9119 9139 22 - . stddev=0.0 +chr1 genetrack . 10107 10127 1622 - . stddev=0.0 +chr1 genetrack . 12157 12177 40 - . stddev=0.0 +chr1 genetrack . 13415 13435 634 - . stddev=0.0 +chr1 genetrack . 16739 16759 3 - . stddev=0.0 +chr1 genetrack . 19145 19165 618 - . stddev=0.0 +chr1 genetrack . 19191 19211 736 - . stddev=0.0 +chr1 genetrack . 20550 20570 865 - . stddev=0.0 +chr1 genetrack . 22383 22403 141 - . stddev=0.0 +chr1 genetrack . 22569 22589 254 - . stddev=0.0 +chr1 genetrack . 23046 23066 213 - . stddev=0.0 +chr1 genetrack . 25345 25365 188 - . stddev=0.0 +chr1 genetrack . 27517 27537 1459 - . stddev=0.0 +chr1 genetrack . 29325 29345 1074 - . stddev=0.0 +chr1 genetrack . 30046 30066 17 - . stddev=0.0 +chr1 genetrack . 31693 31713 450 - . stddev=0.0 +chr1 genetrack . 31876 31896 1344 - . stddev=0.0 +chr1 genetrack . 32497 32517 2 - . stddev=0.0 +chr1 genetrack . 37166 37186 1000 - . stddev=0.0 +chr1 genetrack . 38768 38788 1064 - . stddev=0.0 +chr1 genetrack . 38799 38819 9 - . stddev=0.0 +chr1 genetrack . 39000 39020 3 - . stddev=0.0 +chr1 genetrack . 39052 39072 82 - . stddev=0.0 +chr1 genetrack . 39258 39278 261 - . stddev=0.0 +chr1 genetrack . 39293 39313 2 - . stddev=0.0 +chr1 genetrack . 41867 41887 7 - . stddev=0.0 +chr1 genetrack . 45565 45585 246 - . stddev=1.46097357384 +chr1 genetrack . 45579 45599 78 - . stddev=0.0 +chr1 genetrack . 45643 45663 295 - . stddev=1.27157056343 +chr1 genetrack . 46616 46636 741 - . stddev=0.0 +chr1 genetrack . 49660 49680 6 - . stddev=0.0 +chr1 genetrack . 50091 50111 156 - . stddev=0.0 +chr1 genetrack . 51978 51998 633 - . stddev=0.0 +chr1 genetrack . 52308 52328 549 - . stddev=0.0 +chr1 genetrack . 53045 53065 31 - . stddev=0.0 +chr1 genetrack . 55581 55601 831 - . stddev=0.124372757427 +chr1 genetrack . 55616 55636 984 - . stddev=0.0 +chr1 genetrack . 56542 56562 606 - . stddev=0.0 +chr1 genetrack . 56664 56684 67 - . stddev=0.0 +chr1 genetrack . 56995 57015 1393 - . stddev=0.0 +chr1 genetrack . 57121 57141 4 - . stddev=0.0 +chr1 genetrack . 57212 57232 667 - . stddev=0.0 +chr1 genetrack . 57543 57563 2 - . stddev=0.0 +chr1 genetrack . 59157 59177 168 - . stddev=0.0 +chr1 genetrack . 59246 59266 397 - . stddev=0.0 +chr1 genetrack . 61877 61897 607 - . stddev=0.0 +chr1 genetrack . 65148 65168 43 - . stddev=0.0 +chr1 genetrack . 65687 65707 596 - . stddev=0.0 +chr1 genetrack . 66306 66326 2 - . stddev=0.0 +chr1 genetrack . 68423 68443 139 - . stddev=0.0 +chr1 genetrack . 70336 70356 652 - . stddev=0.0 +chr1 genetrack . 70788 70808 998 - . stddev=0.0 +chr1 genetrack . 72771 72791 406 - . stddev=0.0 +chr1 genetrack . 72810 72830 212 - . stddev=0.0 +chr1 genetrack . 74763 74783 430 - . stddev=0.0 +chr1 genetrack . 75897 75917 10 - . stddev=0.0 +chr1 genetrack . 77515 77535 797 - . stddev=0.0 +chr1 genetrack . 77530 77550 513 - . stddev=0.0 +chr1 genetrack . 78813 78833 113 - . stddev=0.0 +chr1 genetrack . 80958 80978 137 - . stddev=0.0 +chr1 genetrack . 81037 81057 4 - . stddev=0.0 +chr1 genetrack . 81972 81992 49 - . stddev=0.0 +chr1 genetrack . 85759 85779 77 - . stddev=0.0 +chr1 genetrack . 86166 86186 969 - . stddev=0.0 +chr1 genetrack . 86280 86300 14 - . stddev=0.0 +chr1 genetrack . 86991 87011 65 - . stddev=0.0 +chr1 genetrack . 87049 87069 422 - . stddev=2.00428551887 +chr1 genetrack . 87101 87121 1134 - . stddev=0.0296825973187 +chr1 genetrack . 87158 87178 2039 - . stddev=2.64919364477 +chr1 genetrack . 87198 87218 2207 - . stddev=4.88766842837 +chr1 genetrack . 87234 87254 637 - . stddev=0.0 +chr1 genetrack . 87262 87282 505 - . stddev=0.0 +chr1 genetrack . 87289 87309 1270 - . stddev=0.0 +chr1 genetrack . 87327 87347 729 - . stddev=0.517094014402 +chr1 genetrack . 87468 87488 304 - . stddev=0.0 +chr1 genetrack . 88213 88233 301 - . stddev=0.0 +chr1 genetrack . 88376 88396 56 - . stddev=0.0 +chr1 genetrack . 89175 89195 23 - . stddev=0.0 +chr1 genetrack . 91926 91946 10 - . stddev=0.0 +chr1 genetrack . 92411 92431 136 - . stddev=0.0 +chr1 genetrack . 92541 92561 602 - . stddev=0.0 +chr1 genetrack . 92571 92591 90 - . stddev=0.0 +chr1 genetrack . 92639 92659 2137 - . stddev=3.28540359906 +chr1 genetrack . 92664 92684 187 - . stddev=0.390044546071 +chr1 genetrack . 94913 94933 1437 - . stddev=0.0 +chr1 genetrack . 95971 95991 684 - . stddev=0.0 +chr1 genetrack . 96278 96298 166 - . stddev=0.0 +chr1 genetrack . 96315 96335 2 - . stddev=0.0 +chr1 genetrack . 96566 96586 6 - . stddev=0.0 +chr1 genetrack . 96911 96931 10 - . stddev=0.0 +chr1 genetrack . 98555 98575 88 - . stddev=0.0 +chr1 genetrack . 101301 101321 48 - . stddev=0.0 +chr1 genetrack . 101367 101387 1388 - . stddev=0.0268317355181 +chr1 genetrack . 102072 102092 14 - . stddev=0.0 +chr1 genetrack . 102903 102923 846 - . stddev=0.0 +chr1 genetrack . 104110 104130 117 - . stddev=0.0 +chr1 genetrack . 105663 105683 417 - . stddev=0.0 +chr1 genetrack . 105814 105834 529 - . stddev=0.0 +chr1 genetrack . 105846 105866 177 - . stddev=0.0 +chr1 genetrack . 105889 105909 84 - . stddev=0.0 +chr1 genetrack . 106041 106061 14 - . stddev=0.0 +chr1 genetrack . 106340 106360 421 - . stddev=0.0 +chr1 genetrack . 108072 108092 72 - . stddev=0.0 +chr1 genetrack . 108263 108283 145 - . stddev=0.0 +chr1 genetrack . 108579 108599 367 - . stddev=0.0 +chr1 genetrack . 111947 111967 585 - . stddev=1.43661357803 +chr1 genetrack . 113762 113782 296 - . stddev=0.0 +chr1 genetrack . 114306 114326 2 - . stddev=0.0 +chr1 genetrack . 116148 116168 248 - . stddev=0.0 +chr1 genetrack . 116619 116639 699 - . stddev=0.0 +chr1 genetrack . 117522 117542 1573 - . stddev=0.0 +chr1 genetrack . 117845 117865 16 - . stddev=0.0 +chr1 genetrack . 118841 118861 7 - . stddev=0.0 +chr1 genetrack . 119430 119450 1093 - . stddev=0.0 +chr1 genetrack . 119596 119616 842 - . stddev=0.0 +chr1 genetrack . 119657 119677 499 - . stddev=0.0 +chr1 genetrack . 119669 119689 665 - . stddev=0.0 +chr1 genetrack . 119866 119886 846 - . stddev=0.0 +chr1 genetrack . 119880 119900 1136 - . stddev=0.0 +chr1 genetrack . 120788 120808 105 - . stddev=0.0 +chr1 genetrack . 122624 122644 201 - . stddev=0.0 +chr1 genetrack . 122777 122797 20 - . stddev=0.0 +chr1 genetrack . 123718 123738 751 - . stddev=0.0 +chr1 genetrack . 124275 124295 12 - . stddev=0.0 +chr1 genetrack . 125840 125860 273 - . stddev=0.0 +chr1 genetrack . 127027 127047 590 - . stddev=0.0 +chr1 genetrack . 130869 130889 718 - . stddev=0.0 +chr1 genetrack . 133644 133664 122 - . stddev=0.0 +chr1 genetrack . 134270 134290 508 - . stddev=0.0 +chr1 genetrack . 135051 135071 63 - . stddev=0.0 +chr1 genetrack . 136352 136372 117 - . stddev=0.0 +chr1 genetrack . 137428 137448 1200 - . stddev=0.028855482822 +chr1 genetrack . 137816 137836 695 - . stddev=0.0 +chr1 genetrack . 138864 138884 13 - . stddev=0.0 +chr1 genetrack . 139228 139248 214 - . stddev=0.0 +chr1 genetrack . 139627 139647 531 - . stddev=0.0 +chr1 genetrack . 140133 140153 441 - . stddev=0.0 +chr1 genetrack . 140770 140790 556 - . stddev=0.0 +chr1 genetrack . 141182 141202 14 - . stddev=0.0 +chr1 genetrack . 143551 143571 3 - . stddev=0.0 +chr1 genetrack . 144669 144689 1192 - . stddev=0.0959718343646 +chr1 genetrack . 145383 145403 326 - . stddev=0.0 +chr1 genetrack . 147573 147593 255 - . stddev=0.0 +chr1 genetrack . 148690 148710 2 - . stddev=0.0 +chr1 genetrack . 149704 149724 74 - . stddev=0.0 +chr1 genetrack . 150358 150378 153 - . stddev=0.0 +chr1 genetrack . 151341 151361 593 - . stddev=0.0 +chr1 genetrack . 152984 153004 106 - . stddev=0.0 +chr1 genetrack . 153812 153832 168 - . stddev=0.0 +chr1 genetrack . 154862 154882 14 - . stddev=0.0 +chr1 genetrack . 155111 155131 1051 - . stddev=0.0 +chr1 genetrack . 155456 155476 23 - . stddev=0.0 +chr1 genetrack . 155897 155917 10 - . stddev=0.0 +chr1 genetrack . 157559 157579 337 - . stddev=0.0 +chr1 genetrack . 166467 166487 582 - . stddev=0.0 +chr1 genetrack . 166631 166651 173 - . stddev=0.0 +chr1 genetrack . 169064 169084 76 - . stddev=0.0 +chr1 genetrack . 169500 169520 814 - . stddev=0.0 +chr1 genetrack . 170129 170149 373 - . stddev=0.0 +chr1 genetrack . 170282 170302 63 - . stddev=0.0 +chr1 genetrack . 171063 171083 212 - . stddev=0.0 +chr1 genetrack . 173270 173290 535 - . stddev=0.0863866916508 +chr1 genetrack . 175188 175208 117 - . stddev=0.0 +chr1 genetrack . 175474 175494 1119 - . stddev=0.0 +chr1 genetrack . 176004 176024 1473 - . stddev=0.0 +chr1 genetrack . 177140 177160 93 - . stddev=0.0 +chr1 genetrack . 177386 177406 289 - . stddev=0.0 +chr1 genetrack . 178846 178866 601 - . stddev=0.0 +chr1 genetrack . 178971 178991 723 - . stddev=0.0 +chr1 genetrack . 179116 179136 71 - . stddev=0.0 +chr1 genetrack . 180272 180292 25 - . stddev=0.0 +chr1 genetrack . 180362 180382 59 - . stddev=0.0 +chr1 genetrack . 180995 181015 299 - . stddev=0.0 +chr1 genetrack . 182588 182608 465 - . stddev=0.0 +chr1 genetrack . 182790 182810 355 - . stddev=0.0 +chr1 genetrack . 185122 185142 62 - . stddev=0.0 +chr1 genetrack . 185673 185693 190 - . stddev=0.0 +chr1 genetrack . 187422 187442 20 - . stddev=0.0 +chr1 genetrack . 187976 187996 728 - . stddev=0.0 +chr1 genetrack . 196499 196519 224 - . stddev=0.0 +chr1 genetrack . 197060 197080 224 - . stddev=0.0 +chr1 genetrack . 197151 197171 1464 - . stddev=0.0 +chr1 genetrack . 197342 197362 204 - . stddev=0.0 +chr1 genetrack . 197562 197582 2 - . stddev=0.0 +chr1 genetrack . 198423 198443 598 - . stddev=0.0 +chr1 genetrack . 198953 198973 3 - . stddev=0.0 +chr1 genetrack . 199388 199408 805 - . stddev=0.0 +chr1 genetrack . 199935 199955 31 - . stddev=0.0 +chr1 genetrack . 201308 201328 1287 - . stddev=0.0 +chr1 genetrack . 201651 201671 892 - . stddev=0.0 +chr1 genetrack . 202977 202997 163 - . stddev=0.0 +chr1 genetrack . 203452 203472 76 - . stddev=0.0 +chr1 genetrack . 203835 203855 242 - . stddev=0.0 +chr1 genetrack . 206245 206265 22 - . stddev=0.0 +chr1 genetrack . 207675 207695 313 - . stddev=0.0 +chr1 genetrack . 208559 208579 121 - . stddev=0.89393833276 +chr1 genetrack . 209205 209225 176 - . stddev=0.0 +chr1 genetrack . 220863 220883 2 - . stddev=0.0 +chr1 genetrack . 223035 223055 62 - . stddev=0.0 +chr1 genetrack . 225156 225176 2 - . stddev=0.0 +chr1 genetrack . 226777 226797 444 - . stddev=0.0 +chr1 genetrack . 227608 227628 1311 - . stddev=0.0 +chr1 genetrack . 228405 228425 1447 - . stddev=2.78971080368 +chr1 genetrack . 228691 228711 255 - . stddev=0.0 +chr1 genetrack . 229031 229051 6 - . stddev=0.0 +chr1 genetrack . 229583 229603 62 - . stddev=0.0 +chr1 genetrack . 229665 229685 131 - . stddev=0.0 +chr1 genetrack . 229757 229777 3151 - . stddev=2.79078905805 +chr1 genetrack . 229784 229804 615 - . stddev=0.0 +chr1 genetrack . 229965 229985 13 - . stddev=0.0 +chr1 genetrack . 230120 230140 2 - . stddev=0.0 +chr1 genetrack . 230132 230152 2 - . stddev=0.0 +chr1 genetrack . 230150 230170 7 - . stddev=0.699854212224 +chr1 genetrack . 230173 230193 33 - . stddev=0.477212598425 diff -r 71188f3f4b76 -r c4b926c9831c test-data/largest_d_output2.tabular --- a/test-data/largest_d_output2.tabular Mon Nov 06 23:19:50 2017 -0500 +++ b/test-data/largest_d_output2.tabular Thu May 02 08:30:22 2019 -0400 @@ -1,64 +1,65 @@ -chrom start end value strand chrom start end value strand midpoint c-w reads sum c-w distance (bp) -chr1 87147 87167 3492.0 + chr1 87198 87218 2207.0 - 87182 5699.0 51 -chr1 87 107 3211.0 + chr1 139 159 993.0 - 123 4204.0 52 -chr1 48 68 2842.0 + chr1 50 70 39.0 - 59 2881.0 2 -chr1 255 275 2810.0 + chr1 215 235 2611.0 - 245 5421.0 -40 -chr1 117 137 2163.0 + chr1 176 196 14.0 - 156 2177.0 59 -chr1 86954 86974 1948.0 + chr1 87049 87069 422.0 - 87011 2370.0 95 -chr1 169107 169127 1811.0 + chr1 169064 169084 76.0 - 169095 1887.0 -43 -chr1 87171 87191 1436.0 + chr1 87158 87178 2039.0 - 87174 3475.0 -13 -chr1 201 221 1411.0 + chr1 279 299 1328.0 - 250 2739.0 78 -chr1 229741 229761 1380.0 + chr1 229757 229777 3151.0 - 229759 4531.0 16 -chr1 185076 185096 1309.0 + chr1 185122 185142 62.0 - 185109 1371.0 46 -chr1 39081 39101 1268.0 + chr1 39052 39072 82.0 - 39076 1350.0 -29 -chr1 92411 92431 1252.0 + chr1 92411 92431 136.0 - 92421 1388.0 0 -chr1 203872 203892 1234.0 + chr1 203835 203855 242.0 - 203863 1476.0 -37 -chr1 70776 70796 1148.0 + chr1 70788 70808 998.0 - 70792 2146.0 12 -chr1 231 251 1146.0 + chr1 261 281 1278.0 - 256 2424.0 30 -chr1 87098 87118 1125.0 + chr1 87101 87121 1134.0 - 87109 2259.0 3 -chr1 6163 6183 1049.0 + chr1 6254 6274 1076.0 - 6218 2125.0 91 -chr1 25246 25266 995.0 + chr1 25345 25365 188.0 - 25305 1183.0 99 -chr1 101411 101431 973.0 + chr1 101367 101387 1388.0 - 101399 2361.0 -44 -chr1 139213 139233 965.0 + chr1 139228 139248 214.0 - 139230 1179.0 15 -chr1 87019 87039 769.0 + chr1 86991 87011 65.0 - 87015 834.0 -28 -chr1 124318 124338 749.0 + chr1 124275 124295 12.0 - 124306 761.0 -43 -chr1 348 368 699.0 + chr1 323 343 486.0 - 345 1185.0 -25 -chr1 92543 92563 699.0 + chr1 92639 92659 2137.0 - 92601 2836.0 96 -chr1 138868 138888 698.0 + chr1 138864 138884 13.0 - 138876 711.0 -4 -chr1 307 327 685.0 + chr1 373 393 200.0 - 350 885.0 66 -chr1 6413 6433 682.0 + chr1 6476 6496 567.0 - 6454 1249.0 63 -chr1 72781 72801 657.0 + chr1 72771 72791 406.0 - 72786 1063.0 -10 -chr1 22571 22591 609.0 + chr1 22569 22589 254.0 - 22580 863.0 -2 -chr1 65152 65172 575.0 + chr1 65148 65168 43.0 - 65160 618.0 -4 -chr1 106034 106054 558.0 + chr1 106041 106061 14.0 - 106047 572.0 7 -chr1 155028 155048 522.0 + chr1 155111 155131 1051.0 - 155079 1573.0 83 -chr1 32449 32469 476.0 + chr1 32497 32517 2.0 - 32483 478.0 48 -chr1 6706 6726 431.0 + chr1 6702 6722 2.0 - 6714 433.0 -4 -chr1 113782 113802 420.0 + chr1 113762 113782 296.0 - 113782 716.0 -20 -chr1 228633 228653 371.0 + chr1 228691 228711 255.0 - 228672 626.0 58 -chr1 438 458 334.0 + chr1 468 488 468.0 - 463 802.0 30 -chr1 170119 170139 284.0 + chr1 170129 170149 373.0 - 170134 657.0 10 -chr1 92631 92651 260.0 + chr1 92664 92684 187.0 - 92657 447.0 33 -chr1 136366 136386 248.0 + chr1 136352 136372 117.0 - 136369 365.0 -14 -chr1 108624 108644 206.0 + chr1 108579 108599 367.0 - 108611 573.0 -45 -chr1 45678 45698 198.0 + chr1 45643 45663 295.0 - 45670 493.0 -35 -chr1 368 388 192.0 + chr1 446 466 170.0 - 417 362.0 78 -chr1 682 702 168.0 + chr1 634 654 151.0 - 668 319.0 -48 -chr1 59190 59210 168.0 + chr1 59246 59266 397.0 - 59228 565.0 56 -chr1 134170 134190 151.0 + chr1 134270 134290 508.0 - 134230 659.0 100 -chr1 55495 55515 125.0 + chr1 55581 55601 831.0 - 55548 956.0 86 -chr1 39197 39217 101.0 + chr1 39258 39278 261.0 - 39237 362.0 61 -chr1 229721 229741 84.0 + chr1 229784 229804 615.0 - 229762 699.0 63 -chr1 116660 116680 74.0 + chr1 116619 116639 699.0 - 116649 773.0 -41 -chr1 19216 19236 42.0 + chr1 19191 19211 736.0 - 19213 778.0 -25 -chr1 230110 230130 42.0 + chr1 230173 230193 33.0 - 230151 75.0 63 -chr1 31627 31647 40.0 + chr1 31693 31713 450.0 - 31670 490.0 66 -chr1 180280 180300 38.0 + chr1 180362 180382 59.0 - 180331 97.0 82 -chr1 98528 98548 34.0 + chr1 98555 98575 88.0 - 98551 122.0 27 -chr1 230163 230183 23.0 + chr1 230150 230170 7.0 - 230166 30.0 -13 -chr1 173262 173282 11.0 + chr1 173270 173290 535.0 - 173276 546.0 8 -chr1 230145 230165 8.0 + chr1 230120 230140 2.0 - 230142 10.0 -25 -chr1 95920 95940 5.0 + chr1 95971 95991 684.0 - 95955 689.0 51 -chr1 199418 199438 5.0 + chr1 199388 199408 805.0 - 199413 810.0 -30 -chr1 197489 197509 3.0 + chr1 197562 197582 2.0 - 197535 5.0 73 -chr1 96908 96928 2.0 + chr1 96911 96931 10.0 - 96919 12.0 3 +chrom start end value strand chrom start end value strand midpoint c-w reads sum c-w distance (bp) +chr1 87147 87167 3492.0 + chr1 87198 87218 2207.0 - 87182 5699.0 51.0 +chr1 87 107 3211.0 + chr1 139 159 993.0 - 123 4204.0 52.0 +chr1 48 68 2842.0 + chr1 50 70 39.0 - 59 2881.0 2.0 +chr1 255 275 2810.0 + chr1 215 235 2611.0 - 245 5421.0 -40.0 +chr1 117 137 2163.0 + chr1 176 196 14.0 - 156 2177.0 59.0 +chr1 86954 86974 1948.0 + chr1 87049 87069 422.0 - 87011 2370.0 95.0 +chr1 169107 169127 1811.0 + chr1 169064 169084 76.0 - 169095 1887.0 -43.0 +chr1 87171 87191 1436.0 + chr1 87158 87178 2039.0 - 87174 3475.0 -13.0 +chr1 201 221 1411.0 + chr1 279 299 1328.0 - 250 2739.0 78.0 +chr1 229741 229761 1380.0 + chr1 229757 229777 3151.0 - 229759 4531.0 16.0 +chr1 185076 185096 1309.0 + chr1 185122 185142 62.0 - 185109 1371.0 46.0 +chr1 39081 39101 1268.0 + chr1 39052 39072 82.0 - 39076 1350.0 -29.0 +chr1 92411 92431 1252.0 + chr1 92411 92431 136.0 - 92421 1388.0 0.0 +chr1 203872 203892 1234.0 + chr1 203835 203855 242.0 - 203863 1476.0 -37.0 +chr1 70776 70796 1148.0 + chr1 70788 70808 998.0 - 70792 2146.0 12.0 +chr1 231 251 1146.0 + chr1 261 281 1278.0 - 256 2424.0 30.0 +chr1 87098 87118 1125.0 + chr1 87101 87121 1134.0 - 87109 2259.0 3.0 +chr1 6163 6183 1049.0 + chr1 6254 6274 1076.0 - 6218 2125.0 91.0 +chr1 25246 25266 995.0 + chr1 25345 25365 188.0 - 25305 1183.0 99.0 +chr1 101411 101431 973.0 + chr1 101367 101387 1388.0 - 101399 2361.0 -44.0 +chr1 139213 139233 965.0 + chr1 139228 139248 214.0 - 139230 1179.0 15.0 +chr1 87019 87039 769.0 + chr1 86991 87011 65.0 - 87015 834.0 -28.0 +chr1 124318 124338 749.0 + chr1 124275 124295 12.0 - 124306 761.0 -43.0 +chr1 348 368 699.0 + chr1 323 343 486.0 - 345 1185.0 -25.0 +chr1 92543 92563 699.0 + chr1 92639 92659 2137.0 - 92601 2836.0 96.0 +chr1 138868 138888 698.0 + chr1 138864 138884 13.0 - 138876 711.0 -4.0 +chr1 307 327 685.0 + chr1 373 393 200.0 - 350 885.0 66.0 +chr1 6413 6433 682.0 + chr1 6476 6496 567.0 - 6454 1249.0 63.0 +chr1 72781 72801 657.0 + chr1 72771 72791 406.0 - 72786 1063.0 -10.0 +chr1 22571 22591 609.0 + chr1 22569 22589 254.0 - 22580 863.0 -2.0 +chr1 65152 65172 575.0 + chr1 65148 65168 43.0 - 65160 618.0 -4.0 +chr1 106034 106054 558.0 + chr1 106041 106061 14.0 - 106047 572.0 7.0 +chr1 155028 155048 522.0 + chr1 155111 155131 1051.0 - 155079 1573.0 83.0 +chr1 32449 32469 476.0 + chr1 32497 32517 2.0 - 32483 478.0 48.0 +chr1 6706 6726 431.0 + chr1 6702 6722 2.0 - 6714 433.0 -4.0 +chr1 113782 113802 420.0 + chr1 113762 113782 296.0 - 113782 716.0 -20.0 +chr1 228633 228653 371.0 + chr1 228691 228711 255.0 - 228672 626.0 58.0 +chr1 438 458 334.0 + chr1 468 488 468.0 - 463 802.0 30.0 +chr1 170119 170139 284.0 + chr1 170129 170149 373.0 - 170134 657.0 10.0 +chr1 92631 92651 260.0 + chr1 92664 92684 187.0 - 92657 447.0 33.0 +chr1 136366 136386 248.0 + chr1 136352 136372 117.0 - 136369 365.0 -14.0 +chr1 108624 108644 206.0 + chr1 108579 108599 367.0 - 108611 573.0 -45.0 +chr1 45678 45698 198.0 + chr1 45643 45663 295.0 - 45670 493.0 -35.0 +chr1 368 388 192.0 + chr1 446 466 170.0 - 417 362.0 78.0 +chr1 682 702 168.0 + chr1 634 654 151.0 - 668 319.0 -48.0 +chr1 59190 59210 168.0 + chr1 59246 59266 397.0 - 59228 565.0 56.0 +chr1 134170 134190 151.0 + chr1 134270 134290 508.0 - 134230 659.0 100.0 +chr1 55495 55515 125.0 + chr1 55581 55601 831.0 - 55548 956.0 86.0 +chr1 39197 39217 101.0 + chr1 39258 39278 261.0 - 39237 362.0 61.0 +chr1 229721 229741 84.0 + chr1 229784 229804 615.0 - 229762 699.0 63.0 +chr1 116660 116680 74.0 + chr1 116619 116639 699.0 - 116649 773.0 -41.0 +chr1 19216 19236 42.0 + chr1 19191 19211 736.0 - 19213 778.0 -25.0 +chr1 230110 230130 42.0 + chr1 230173 230193 33.0 - 230151 75.0 63.0 +chr1 31627 31647 40.0 + chr1 31693 31713 450.0 - 31670 490.0 66.0 +chr1 180280 180300 38.0 + chr1 180362 180382 59.0 - 180331 97.0 82.0 +chr1 98528 98548 34.0 + chr1 98555 98575 88.0 - 98551 122.0 27.0 +chr1 230163 230183 23.0 + chr1 230150 230170 7.0 - 230166 30.0 -13.0 +chr1 173262 173282 11.0 + chr1 173270 173290 535.0 - 173276 546.0 8.0 +chr1 230145 230165 8.0 + chr1 230120 230140 2.0 - 230142 10.0 -25.0 +chr1 95920 95940 5.0 + chr1 95971 95991 684.0 - 95955 689.0 51.0 +chr1 199418 199438 5.0 + chr1 199388 199408 805.0 - 199413 810.0 -30.0 +chr1 197489 197509 3.0 + chr1 197562 197582 2.0 - 197535 5.0 73.0 +chr1 96908 96928 2.0 + chr1 96911 96931 10.0 - 96919 12.0 3.0 +chr1 151369 151389 2.0 + chr1 151341 151361 593.0 - 151365 595.0 -28.0 diff -r 71188f3f4b76 -r c4b926c9831c test-data/largest_mp_output1.gff --- a/test-data/largest_mp_output1.gff Mon Nov 06 23:19:50 2017 -0500 +++ b/test-data/largest_mp_output1.gff Thu May 02 08:30:22 2019 -0400 @@ -1,54 +1,55 @@ -chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51 -chr1 cwpair . 176 177 4774.0 . . cw_distance=98 -chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16 -chr1 cwpair . 123 124 4204.0 . . cw_distance=52 -chr1 cwpair . 277 278 4138.0 . . cw_distance=24 -chr1 cwpair . 87174 87175 3475.0 . . cw_distance=-13 -chr1 cwpair . 59 60 2881.0 . . cw_distance=2 -chr1 cwpair . 92601 92602 2836.0 . . cw_distance=96 -chr1 cwpair . 241 242 2689.0 . . cw_distance=60 -chr1 cwpair . 87011 87012 2370.0 . . cw_distance=95 -chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3 -chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 -chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 -chr1 cwpair . 287 288 1632.0 . . cw_distance=92 -chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 -chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 -chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 -chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 -chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 -chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 -chr1 cwpair . 72786 72787 1063.0 . . cw_distance=-10 -chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 -chr1 cwpair . 370 371 899.0 . . cw_distance=25 -chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 -chr1 cwpair . 357 358 852.0 . . cw_distance=81 -chr1 cwpair . 463 464 802.0 . . cw_distance=30 -chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 -chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 -chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 -chr1 cwpair . 229762 229763 699.0 . . cw_distance=63 -chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 -chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 -chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 -chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 -chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 -chr1 cwpair . 87006 87007 615.0 . . cw_distance=-11 -chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 -chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 -chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 -chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 -chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 -chr1 cwpair . 178 179 465.0 . . cw_distance=16 -chr1 cwpair . 92657 92658 447.0 . . cw_distance=33 -chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 -chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 -chr1 cwpair . 417 418 362.0 . . cw_distance=78 -chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 -chr1 cwpair . 627 628 247.0 . . cw_distance=33 -chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 -chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 -chr1 cwpair . 230151 230152 75.0 . . cw_distance=63 -chr1 cwpair . 230166 230167 30.0 . . cw_distance=-13 -chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 -chr1 cwpair . 230142 230143 10.0 . . cw_distance=-25 +chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51.0 +chr1 cwpair . 176 177 4774.0 . . cw_distance=98.0 +chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16.0 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52.0 +chr1 cwpair . 277 278 4138.0 . . cw_distance=24.0 +chr1 cwpair . 87174 87175 3475.0 . . cw_distance=-13.0 +chr1 cwpair . 59 60 2881.0 . . cw_distance=2.0 +chr1 cwpair . 92601 92602 2836.0 . . cw_distance=96.0 +chr1 cwpair . 241 242 2689.0 . . cw_distance=60.0 +chr1 cwpair . 87011 87012 2370.0 . . cw_distance=95.0 +chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3.0 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12.0 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91.0 +chr1 cwpair . 287 288 1632.0 . . cw_distance=92.0 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83.0 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0.0 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46.0 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63.0 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99.0 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15.0 +chr1 cwpair . 72786 72787 1063.0 . . cw_distance=-10.0 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86.0 +chr1 cwpair . 370 371 899.0 . . cw_distance=25.0 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2.0 +chr1 cwpair . 357 358 852.0 . . cw_distance=81.0 +chr1 cwpair . 463 464 802.0 . . cw_distance=30.0 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25.0 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20.0 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4.0 +chr1 cwpair . 229762 229763 699.0 . . cw_distance=63.0 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51.0 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100.0 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10.0 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58.0 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4.0 +chr1 cwpair . 87006 87007 615.0 . . cw_distance=-11.0 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7.0 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56.0 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8.0 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66.0 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48.0 +chr1 cwpair . 178 179 465.0 . . cw_distance=16.0 +chr1 cwpair . 92657 92658 447.0 . . cw_distance=33.0 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4.0 +chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14.0 +chr1 cwpair . 417 418 362.0 . . cw_distance=78.0 +chr1 cwpair . 39237 39238 362.0 . . cw_distance=61.0 +chr1 cwpair . 627 628 247.0 . . cw_distance=33.0 +chr1 cwpair . 98551 98552 122.0 . . cw_distance=27.0 +chr1 cwpair . 180331 180332 97.0 . . cw_distance=82.0 +chr1 cwpair . 230151 230152 75.0 . . cw_distance=63.0 +chr1 cwpair . 230166 230167 30.0 . . cw_distance=-13.0 +chr1 cwpair . 96919 96920 12.0 . . cw_distance=3.0 +chr1 cwpair . 230142 230143 10.0 . . cw_distance=-25.0 +chr1 cwpair . 197535 197536 5.0 . . cw_distance=73.0 diff -r 71188f3f4b76 -r c4b926c9831c test-data/largest_mp_output2.gff --- a/test-data/largest_mp_output2.gff Mon Nov 06 23:19:50 2017 -0500 +++ b/test-data/largest_mp_output2.gff Thu May 02 08:30:22 2019 -0400 @@ -1,63 +1,64 @@ -chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51 -chr1 cwpair . 245 246 5421.0 . . cw_distance=-40 -chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16 -chr1 cwpair . 123 124 4204.0 . . cw_distance=52 -chr1 cwpair . 87174 87175 3475.0 . . cw_distance=-13 -chr1 cwpair . 59 60 2881.0 . . cw_distance=2 -chr1 cwpair . 92601 92602 2836.0 . . cw_distance=96 -chr1 cwpair . 250 251 2739.0 . . cw_distance=78 -chr1 cwpair . 256 257 2424.0 . . cw_distance=30 -chr1 cwpair . 87011 87012 2370.0 . . cw_distance=95 -chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44 -chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3 -chr1 cwpair . 156 157 2177.0 . . cw_distance=59 -chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 -chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 -chr1 cwpair . 169095 169096 1887.0 . . cw_distance=-43 -chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 -chr1 cwpair . 203863 203864 1476.0 . . cw_distance=-37 -chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 -chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 -chr1 cwpair . 39076 39077 1350.0 . . cw_distance=-29 -chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 -chr1 cwpair . 345 346 1185.0 . . cw_distance=-25 -chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 -chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 -chr1 cwpair . 72786 72787 1063.0 . . cw_distance=-10 -chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 -chr1 cwpair . 350 351 885.0 . . cw_distance=66 -chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 -chr1 cwpair . 87015 87016 834.0 . . cw_distance=-28 -chr1 cwpair . 199413 199414 810.0 . . cw_distance=-30 -chr1 cwpair . 463 464 802.0 . . cw_distance=30 -chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 -chr1 cwpair . 116649 116650 773.0 . . cw_distance=-41 -chr1 cwpair . 124306 124307 761.0 . . cw_distance=-43 -chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 -chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 -chr1 cwpair . 229762 229763 699.0 . . cw_distance=63 -chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 -chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 -chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 -chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 -chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 -chr1 cwpair . 151365 151366 595.0 . . cw_distance=-28 -chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45 -chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 -chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 -chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 -chr1 cwpair . 45670 45671 493.0 . . cw_distance=-35 -chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 -chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 -chr1 cwpair . 92657 92658 447.0 . . cw_distance=33 -chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 -chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 -chr1 cwpair . 417 418 362.0 . . cw_distance=78 -chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 -chr1 cwpair . 668 669 319.0 . . cw_distance=-48 -chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 -chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 -chr1 cwpair . 230151 230152 75.0 . . cw_distance=63 -chr1 cwpair . 230166 230167 30.0 . . cw_distance=-13 -chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 -chr1 cwpair . 230142 230143 10.0 . . cw_distance=-25 +chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51.0 +chr1 cwpair . 245 246 5421.0 . . cw_distance=-40.0 +chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16.0 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52.0 +chr1 cwpair . 87174 87175 3475.0 . . cw_distance=-13.0 +chr1 cwpair . 59 60 2881.0 . . cw_distance=2.0 +chr1 cwpair . 92601 92602 2836.0 . . cw_distance=96.0 +chr1 cwpair . 250 251 2739.0 . . cw_distance=78.0 +chr1 cwpair . 256 257 2424.0 . . cw_distance=30.0 +chr1 cwpair . 87011 87012 2370.0 . . cw_distance=95.0 +chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44.0 +chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3.0 +chr1 cwpair . 156 157 2177.0 . . cw_distance=59.0 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12.0 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91.0 +chr1 cwpair . 169095 169096 1887.0 . . cw_distance=-43.0 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83.0 +chr1 cwpair . 203863 203864 1476.0 . . cw_distance=-37.0 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0.0 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46.0 +chr1 cwpair . 39076 39077 1350.0 . . cw_distance=-29.0 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63.0 +chr1 cwpair . 345 346 1185.0 . . cw_distance=-25.0 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99.0 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15.0 +chr1 cwpair . 72786 72787 1063.0 . . cw_distance=-10.0 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86.0 +chr1 cwpair . 350 351 885.0 . . cw_distance=66.0 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2.0 +chr1 cwpair . 87015 87016 834.0 . . cw_distance=-28.0 +chr1 cwpair . 199413 199414 810.0 . . cw_distance=-30.0 +chr1 cwpair . 463 464 802.0 . . cw_distance=30.0 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25.0 +chr1 cwpair . 116649 116650 773.0 . . cw_distance=-41.0 +chr1 cwpair . 124306 124307 761.0 . . cw_distance=-43.0 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20.0 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4.0 +chr1 cwpair . 229762 229763 699.0 . . cw_distance=63.0 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51.0 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100.0 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10.0 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58.0 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4.0 +chr1 cwpair . 151365 151366 595.0 . . cw_distance=-28.0 +chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45.0 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7.0 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56.0 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8.0 +chr1 cwpair . 45670 45671 493.0 . . cw_distance=-35.0 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66.0 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48.0 +chr1 cwpair . 92657 92658 447.0 . . cw_distance=33.0 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4.0 +chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14.0 +chr1 cwpair . 417 418 362.0 . . cw_distance=78.0 +chr1 cwpair . 39237 39238 362.0 . . cw_distance=61.0 +chr1 cwpair . 668 669 319.0 . . cw_distance=-48.0 +chr1 cwpair . 98551 98552 122.0 . . cw_distance=27.0 +chr1 cwpair . 180331 180332 97.0 . . cw_distance=82.0 +chr1 cwpair . 230151 230152 75.0 . . cw_distance=63.0 +chr1 cwpair . 230166 230167 30.0 . . cw_distance=-13.0 +chr1 cwpair . 96919 96920 12.0 . . cw_distance=3.0 +chr1 cwpair . 230142 230143 10.0 . . cw_distance=-25.0 +chr1 cwpair . 197535 197536 5.0 . . cw_distance=73.0 diff -r 71188f3f4b76 -r c4b926c9831c test-data/largest_o_output2.tabular --- a/test-data/largest_o_output2.tabular Mon Nov 06 23:19:50 2017 -0500 +++ b/test-data/largest_o_output2.tabular Thu May 02 08:30:22 2019 -0400 @@ -1,100 +1,372 @@ -chrom strand start end value -chr1 + 100364 100384 2695.0 -chr1 + 30 50 2140.0 -chr1 + 5379 5399 1572.0 -chr1 + 52440 52460 1562.0 -chr1 + 73234 73254 1492.0 -chr1 + 31096 31116 1481.0 -chr1 + 145253 145273 1394.0 -chr1 + 10641 10661 1359.0 -chr1 + 200580 200600 1298.0 -chr1 + 64772 64792 1292.0 -chr1 + 86886 86906 1253.0 -chr1 + 103207 103227 1229.0 -chr1 + 43835 43855 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699.0 63.0 -chr1 116660 116680 74.0 + chr1 116619 116639 699.0 - 116649 773.0 -41.0 -chr1 19216 19236 42.0 + chr1 19191 19211 736.0 - 19213 778.0 -25.0 -chr1 230110 230130 42.0 + chr1 230132 230152 2.0 - 230131 44.0 22.0 -chr1 31627 31647 40.0 + chr1 31693 31713 450.0 - 31670 490.0 66.0 -chr1 180280 180300 38.0 + chr1 180272 180292 25.0 - 180286 63.0 -8.0 -chr1 98528 98548 34.0 + chr1 98555 98575 88.0 - 98551 122.0 27.0 -chr1 230163 230183 23.0 + chr1 230173 230193 33.0 - 230178 56.0 10.0 -chr1 173262 173282 11.0 + chr1 173270 173290 535.0 - 173276 546.0 8.0 -chr1 230145 230165 8.0 + chr1 230150 230170 7.0 - 230157 15.0 5.0 -chr1 95920 95940 5.0 + chr1 95971 95991 684.0 - 95955 689.0 51.0 -chr1 199418 199438 5.0 + chr1 199388 199408 805.0 - 199413 810.0 -30.0 -chr1 197489 197509 3.0 + chr1 197562 197582 2.0 - 197535 5.0 73.0 -chr1 96908 96928 2.0 + chr1 96911 96931 10.0 - 96919 12.0 3.0 -chr1 151369 151389 2.0 + chr1 151341 151361 593.0 - 151365 595.0 -28.0 +chrom start end value strand chrom start end value strand midpoint c-w reads sum c-w distance (bp) +chr1 87147 87167 3492.0 + chr1 87158 87178 2039.0 - 87162 5531.0 11.0 +chr1 87 107 3211.0 + chr1 139 159 993.0 - 123 4204.0 52.0 +chr1 48 68 2842.0 + chr1 50 70 39.0 - 59 2881.0 2.0 +chr1 255 275 2810.0 + chr1 279 299 1328.0 - 277 4138.0 24.0 +chr1 117 137 2163.0 + chr1 176 196 14.0 - 156 2177.0 59.0 +chr1 86954 86974 1948.0 + chr1 86991 87011 65.0 - 86982 2013.0 37.0 +chr1 169107 169127 1811.0 + chr1 169064 169084 76.0 - 169095 1887.0 -43.0 +chr1 87171 87191 1436.0 + chr1 87198 87218 2207.0 - 87194 3643.0 27.0 +chr1 201 221 1411.0 + chr1 215 235 2611.0 - 218 4022.0 14.0 +chr1 229741 229761 1380.0 + chr1 229757 229777 3151.0 - 229759 4531.0 16.0 +chr1 185076 185096 1309.0 + chr1 185122 185142 62.0 - 185109 1371.0 46.0 +chr1 39081 39101 1268.0 + chr1 39052 39072 82.0 - 39076 1350.0 -29.0 +chr1 92411 92431 1252.0 + chr1 92411 92431 136.0 - 92421 1388.0 0.0 +chr1 203872 203892 1234.0 + chr1 203835 203855 242.0 - 203863 1476.0 -37.0 +chr1 70776 70796 1148.0 + chr1 70788 70808 998.0 - 70792 2146.0 12.0 +chr1 231 251 1146.0 + chr1 261 281 1278.0 - 256 2424.0 30.0 +chr1 87098 87118 1125.0 + chr1 87101 87121 1134.0 - 87109 2259.0 3.0 +chr1 6163 6183 1049.0 + chr1 6254 6274 1076.0 - 6218 2125.0 91.0 +chr1 25246 25266 995.0 + chr1 25345 25365 188.0 - 25305 1183.0 99.0 +chr1 101411 101431 973.0 + chr1 101367 101387 1388.0 - 101399 2361.0 -44.0 +chr1 139213 139233 965.0 + chr1 139228 139248 214.0 - 139230 1179.0 15.0 +chr1 87019 87039 769.0 + chr1 87049 87069 422.0 - 87044 1191.0 30.0 +chr1 124318 124338 749.0 + chr1 124275 124295 12.0 - 124306 761.0 -43.0 +chr1 348 368 699.0 + chr1 373 393 200.0 - 370 899.0 25.0 +chr1 92543 92563 699.0 + chr1 92571 92591 90.0 - 92567 789.0 28.0 +chr1 138868 138888 698.0 + chr1 138864 138884 13.0 - 138876 711.0 -4.0 +chr1 307 327 685.0 + chr1 323 343 486.0 - 325 1171.0 16.0 +chr1 6413 6433 682.0 + chr1 6476 6496 567.0 - 6454 1249.0 63.0 +chr1 72781 72801 657.0 + chr1 72810 72830 212.0 - 72805 869.0 29.0 +chr1 22571 22591 609.0 + chr1 22569 22589 254.0 - 22580 863.0 -2.0 +chr1 65152 65172 575.0 + chr1 65148 65168 43.0 - 65160 618.0 -4.0 +chr1 106034 106054 558.0 + chr1 106041 106061 14.0 - 106047 572.0 7.0 +chr1 155028 155048 522.0 + chr1 155111 155131 1051.0 - 155079 1573.0 83.0 +chr1 32449 32469 476.0 + chr1 32497 32517 2.0 - 32483 478.0 48.0 +chr1 6706 6726 431.0 + chr1 6702 6722 2.0 - 6714 433.0 -4.0 +chr1 113782 113802 420.0 + chr1 113762 113782 296.0 - 113782 716.0 -20.0 +chr1 228633 228653 371.0 + chr1 228691 228711 255.0 - 228672 626.0 58.0 +chr1 438 458 334.0 + chr1 446 466 170.0 - 452 504.0 8.0 +chr1 72671 72691 304.0 + chr1 72771 72791 406.0 - 72731 710.0 100.0 +chr1 170119 170139 284.0 + chr1 170129 170149 373.0 - 170134 657.0 10.0 +chr1 92631 92651 260.0 + chr1 92639 92659 2137.0 - 92645 2397.0 8.0 +chr1 136366 136386 248.0 + chr1 136352 136372 117.0 - 136369 365.0 -14.0 +chr1 108624 108644 206.0 + chr1 108579 108599 367.0 - 108611 573.0 -45.0 +chr1 45678 45698 198.0 + chr1 45643 45663 295.0 - 45670 493.0 -35.0 +chr1 368 388 192.0 + chr1 388 408 167.0 - 388 359.0 20.0 +chr1 682 702 168.0 + chr1 634 654 151.0 - 668 319.0 -48.0 +chr1 59190 59210 168.0 + chr1 59246 59266 397.0 - 59228 565.0 56.0 +chr1 134170 134190 151.0 + chr1 134270 134290 508.0 - 134230 659.0 100.0 +chr1 55495 55515 125.0 + chr1 55581 55601 831.0 - 55548 956.0 86.0 +chr1 512 532 101.0 + chr1 468 488 468.0 - 500 569.0 -44.0 +chr1 39197 39217 101.0 + chr1 39258 39278 261.0 - 39237 362.0 61.0 +chr1 229721 229741 84.0 + chr1 229784 229804 615.0 - 229762 699.0 63.0 +chr1 116660 116680 74.0 + chr1 116619 116639 699.0 - 116649 773.0 -41.0 +chr1 19216 19236 42.0 + chr1 19191 19211 736.0 - 19213 778.0 -25.0 +chr1 230110 230130 42.0 + chr1 230132 230152 2.0 - 230131 44.0 22.0 +chr1 31627 31647 40.0 + chr1 31693 31713 450.0 - 31670 490.0 66.0 +chr1 180280 180300 38.0 + chr1 180272 180292 25.0 - 180286 63.0 -8.0 +chr1 98528 98548 34.0 + chr1 98555 98575 88.0 - 98551 122.0 27.0 +chr1 230163 230183 23.0 + chr1 230173 230193 33.0 - 230178 56.0 10.0 +chr1 173262 173282 11.0 + chr1 173270 173290 535.0 - 173276 546.0 8.0 +chr1 230145 230165 8.0 + chr1 230150 230170 7.0 - 230157 15.0 5.0 +chr1 95920 95940 5.0 + chr1 95971 95991 684.0 - 95955 689.0 51.0 +chr1 199418 199438 5.0 + chr1 199388 199408 805.0 - 199413 810.0 -30.0 +chr1 197489 197509 3.0 + chr1 197562 197582 2.0 - 197535 5.0 73.0 +chr1 96908 96928 2.0 + chr1 96911 96931 10.0 - 96919 12.0 3.0 +chr1 151369 151389 2.0 + chr1 151341 151361 593.0 - 151365 595.0 -28.0 diff -r 71188f3f4b76 -r c4b926c9831c test-data/mode_mp_output1.gff --- a/test-data/mode_mp_output1.gff Mon Nov 06 23:19:50 2017 -0500 +++ b/test-data/mode_mp_output1.gff Thu May 02 08:30:22 2019 -0400 @@ -1,56 +1,57 @@ -chr1 cwpair . 87162 87163 5531.0 . . cw_distance=11.0 -chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16.0 -chr1 cwpair . 123 124 4204.0 . . cw_distance=52.0 -chr1 cwpair . 277 278 4138.0 . . cw_distance=24.0 -chr1 cwpair . 218 219 4022.0 . . cw_distance=14.0 -chr1 cwpair . 87194 87195 3643.0 . . cw_distance=27.0 -chr1 cwpair . 59 60 2881.0 . . cw_distance=2.0 -chr1 cwpair . 256 257 2424.0 . . cw_distance=30.0 -chr1 cwpair . 92645 92646 2397.0 . . cw_distance=8.0 -chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3.0 -chr1 cwpair . 156 157 2177.0 . . cw_distance=59.0 -chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12.0 -chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91.0 -chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37.0 -chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83.0 -chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0.0 -chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46.0 -chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63.0 -chr1 cwpair . 87044 87045 1191.0 . . cw_distance=30.0 -chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99.0 -chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15.0 -chr1 cwpair . 325 326 1171.0 . . cw_distance=16.0 -chr1 cwpair . 55548 55549 956.0 . . cw_distance=86.0 -chr1 cwpair . 370 371 899.0 . . cw_distance=25.0 -chr1 cwpair . 72805 72806 869.0 . . cw_distance=29.0 -chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2.0 -chr1 cwpair . 92567 92568 789.0 . . cw_distance=28.0 -chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25.0 -chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20.0 -chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4.0 -chr1 cwpair . 72731 72732 710.0 . . cw_distance=100.0 -chr1 cwpair . 229762 229763 699.0 . . cw_distance=63.0 -chr1 cwpair . 95955 95956 689.0 . . cw_distance=51.0 -chr1 cwpair . 134230 134231 659.0 . . cw_distance=100.0 -chr1 cwpair . 170134 170135 657.0 . . cw_distance=10.0 -chr1 cwpair . 228672 228673 626.0 . . cw_distance=58.0 -chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4.0 -chr1 cwpair . 106047 106048 572.0 . . cw_distance=7.0 -chr1 cwpair . 477 478 566.0 . . cw_distance=1.0 -chr1 cwpair . 59228 59229 565.0 . . cw_distance=56.0 -chr1 cwpair . 173276 173277 546.0 . . cw_distance=8.0 -chr1 cwpair . 452 453 504.0 . . cw_distance=8.0 -chr1 cwpair . 31670 31671 490.0 . . cw_distance=66.0 -chr1 cwpair . 32483 32484 478.0 . . cw_distance=48.0 -chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4.0 -chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14.0 -chr1 cwpair . 39237 39238 362.0 . . cw_distance=61.0 -chr1 cwpair . 388 389 359.0 . . cw_distance=20.0 -chr1 cwpair . 627 628 247.0 . . cw_distance=33.0 -chr1 cwpair . 98551 98552 122.0 . . cw_distance=27.0 -chr1 cwpair . 180286 180287 63.0 . . cw_distance=-8.0 -chr1 cwpair . 230178 230179 56.0 . . cw_distance=10.0 -chr1 cwpair . 230131 230132 44.0 . . cw_distance=22.0 -chr1 cwpair . 230157 230158 15.0 . . cw_distance=5.0 -chr1 cwpair . 96919 96920 12.0 . . cw_distance=3.0 -chr1 cwpair . 197535 197536 5.0 . . cw_distance=73.0 +chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51.0 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52.0 +chr1 cwpair . 299 300 3296.0 . . cw_distance=68.0 +chr1 cwpair . 229749 229750 3235.0 . . cw_distance=36.0 +chr1 cwpair . 87138 87139 3164.0 . . cw_distance=60.0 +chr1 cwpair . 197 198 3062.0 . . cw_distance=55.0 +chr1 cwpair . 59 60 2881.0 . . cw_distance=2.0 +chr1 cwpair . 92601 92602 2836.0 . . cw_distance=96.0 +chr1 cwpair . 241 242 2689.0 . . cw_distance=60.0 +chr1 cwpair . 265 266 2474.0 . . cw_distance=48.0 +chr1 cwpair . 156 157 2177.0 . . cw_distance=59.0 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12.0 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91.0 +chr1 cwpair . 87212 87213 2073.0 . . cw_distance=63.0 +chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37.0 +chr1 cwpair . 229772 229773 1995.0 . . cw_distance=43.0 +chr1 cwpair . 87070 87071 1903.0 . . cw_distance=82.0 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83.0 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0.0 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46.0 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63.0 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99.0 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15.0 +chr1 cwpair . 87035 87036 972.0 . . cw_distance=47.0 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86.0 +chr1 cwpair . 350 351 885.0 . . cw_distance=66.0 +chr1 cwpair . 72805 72806 869.0 . . cw_distance=29.0 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2.0 +chr1 cwpair . 463 464 802.0 . . cw_distance=30.0 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25.0 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20.0 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4.0 +chr1 cwpair . 72731 72732 710.0 . . cw_distance=100.0 +chr1 cwpair . 389 390 707.0 . . cw_distance=62.0 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51.0 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100.0 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10.0 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58.0 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4.0 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7.0 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56.0 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8.0 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66.0 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48.0 +chr1 cwpair . 92657 92658 447.0 . . cw_distance=33.0 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4.0 +chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14.0 +chr1 cwpair . 417 418 362.0 . . cw_distance=78.0 +chr1 cwpair . 39237 39238 362.0 . . cw_distance=61.0 +chr1 cwpair . 627 628 247.0 . . cw_distance=33.0 +chr1 cwpair . 98551 98552 122.0 . . cw_distance=27.0 +chr1 cwpair . 180331 180332 97.0 . . cw_distance=82.0 +chr1 cwpair . 230151 230152 75.0 . . cw_distance=63.0 +chr1 cwpair . 230166 230167 30.0 . . cw_distance=-13.0 +chr1 cwpair . 96919 96920 12.0 . . cw_distance=3.0 +chr1 cwpair . 230148 230149 10.0 . . cw_distance=-13.0 +chr1 cwpair . 197535 197536 5.0 . . cw_distance=73.0 diff -r 71188f3f4b76 -r c4b926c9831c test-data/mode_mp_output2.gff --- a/test-data/mode_mp_output2.gff Mon Nov 06 23:19:50 2017 -0500 +++ b/test-data/mode_mp_output2.gff Thu May 02 08:30:22 2019 -0400 @@ -1,66 +1,66 @@ -chr1 cwpair . 87162 87163 5531.0 . . cw_distance=11.0 -chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16.0 -chr1 cwpair . 123 124 4204.0 . . cw_distance=52.0 -chr1 cwpair . 277 278 4138.0 . . cw_distance=24.0 -chr1 cwpair . 218 219 4022.0 . . cw_distance=14.0 -chr1 cwpair . 87194 87195 3643.0 . . cw_distance=27.0 -chr1 cwpair . 59 60 2881.0 . . cw_distance=2.0 -chr1 cwpair . 256 257 2424.0 . . cw_distance=30.0 -chr1 cwpair . 92645 92646 2397.0 . . cw_distance=8.0 -chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44.0 -chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3.0 -chr1 cwpair . 156 157 2177.0 . . cw_distance=59.0 -chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12.0 -chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91.0 -chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37.0 -chr1 cwpair . 169095 169096 1887.0 . . cw_distance=-43.0 -chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83.0 -chr1 cwpair . 203863 203864 1476.0 . . cw_distance=-37.0 -chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0.0 -chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46.0 -chr1 cwpair . 39076 39077 1350.0 . . cw_distance=-29.0 -chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63.0 -chr1 cwpair . 87044 87045 1191.0 . . cw_distance=30.0 -chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99.0 -chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15.0 -chr1 cwpair . 325 326 1171.0 . . cw_distance=16.0 -chr1 cwpair . 55548 55549 956.0 . . cw_distance=86.0 -chr1 cwpair . 370 371 899.0 . . cw_distance=25.0 -chr1 cwpair . 72805 72806 869.0 . . cw_distance=29.0 -chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2.0 -chr1 cwpair . 199413 199414 810.0 . . cw_distance=-30.0 -chr1 cwpair . 92567 92568 789.0 . . cw_distance=28.0 -chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25.0 -chr1 cwpair . 116649 116650 773.0 . . cw_distance=-41.0 -chr1 cwpair . 124306 124307 761.0 . . cw_distance=-43.0 -chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20.0 -chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4.0 -chr1 cwpair . 72731 72732 710.0 . . cw_distance=100.0 -chr1 cwpair . 229762 229763 699.0 . . cw_distance=63.0 -chr1 cwpair . 95955 95956 689.0 . . cw_distance=51.0 -chr1 cwpair . 134230 134231 659.0 . . cw_distance=100.0 -chr1 cwpair . 170134 170135 657.0 . . cw_distance=10.0 -chr1 cwpair . 228672 228673 626.0 . . cw_distance=58.0 -chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4.0 -chr1 cwpair . 151365 151366 595.0 . . cw_distance=-28.0 -chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45.0 -chr1 cwpair . 106047 106048 572.0 . . cw_distance=7.0 -chr1 cwpair . 500 501 569.0 . . cw_distance=-44.0 -chr1 cwpair . 59228 59229 565.0 . . cw_distance=56.0 -chr1 cwpair . 173276 173277 546.0 . . cw_distance=8.0 -chr1 cwpair . 452 453 504.0 . . cw_distance=8.0 -chr1 cwpair . 45670 45671 493.0 . . cw_distance=-35.0 -chr1 cwpair . 31670 31671 490.0 . . cw_distance=66.0 -chr1 cwpair . 32483 32484 478.0 . . cw_distance=48.0 -chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4.0 -chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14.0 -chr1 cwpair . 39237 39238 362.0 . . cw_distance=61.0 -chr1 cwpair . 388 389 359.0 . . cw_distance=20.0 -chr1 cwpair . 668 669 319.0 . . cw_distance=-48.0 -chr1 cwpair . 98551 98552 122.0 . . cw_distance=27.0 -chr1 cwpair . 180286 180287 63.0 . . cw_distance=-8.0 -chr1 cwpair . 230178 230179 56.0 . . cw_distance=10.0 -chr1 cwpair . 230131 230132 44.0 . . cw_distance=22.0 -chr1 cwpair . 230157 230158 15.0 . . cw_distance=5.0 -chr1 cwpair . 96919 96920 12.0 . . cw_distance=3.0 -chr1 cwpair . 197535 197536 5.0 . . cw_distance=73.0 +chr1 cwpair . 87162 87163 5531.0 . . cw_distance=11.0 +chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16.0 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52.0 +chr1 cwpair . 277 278 4138.0 . . cw_distance=24.0 +chr1 cwpair . 218 219 4022.0 . . cw_distance=14.0 +chr1 cwpair . 87194 87195 3643.0 . . cw_distance=27.0 +chr1 cwpair . 59 60 2881.0 . . cw_distance=2.0 +chr1 cwpair . 256 257 2424.0 . . cw_distance=30.0 +chr1 cwpair . 92645 92646 2397.0 . . cw_distance=8.0 +chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44.0 +chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3.0 +chr1 cwpair . 156 157 2177.0 . . cw_distance=59.0 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12.0 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91.0 +chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37.0 +chr1 cwpair . 169095 169096 1887.0 . . cw_distance=-43.0 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83.0 +chr1 cwpair . 203863 203864 1476.0 . . cw_distance=-37.0 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0.0 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46.0 +chr1 cwpair . 39076 39077 1350.0 . . cw_distance=-29.0 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63.0 +chr1 cwpair . 87044 87045 1191.0 . . cw_distance=30.0 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99.0 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15.0 +chr1 cwpair . 325 326 1171.0 . . cw_distance=16.0 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86.0 +chr1 cwpair . 370 371 899.0 . . cw_distance=25.0 +chr1 cwpair . 72805 72806 869.0 . . cw_distance=29.0 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2.0 +chr1 cwpair . 199413 199414 810.0 . . cw_distance=-30.0 +chr1 cwpair . 92567 92568 789.0 . . cw_distance=28.0 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25.0 +chr1 cwpair . 116649 116650 773.0 . . cw_distance=-41.0 +chr1 cwpair . 124306 124307 761.0 . . cw_distance=-43.0 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20.0 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4.0 +chr1 cwpair . 72731 72732 710.0 . . cw_distance=100.0 +chr1 cwpair . 229762 229763 699.0 . . cw_distance=63.0 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51.0 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100.0 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10.0 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58.0 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4.0 +chr1 cwpair . 151365 151366 595.0 . . cw_distance=-28.0 +chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45.0 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7.0 +chr1 cwpair . 500 501 569.0 . . cw_distance=-44.0 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56.0 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8.0 +chr1 cwpair . 452 453 504.0 . . cw_distance=8.0 +chr1 cwpair . 45670 45671 493.0 . . cw_distance=-35.0 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66.0 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48.0 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4.0 +chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14.0 +chr1 cwpair . 39237 39238 362.0 . . cw_distance=61.0 +chr1 cwpair . 388 389 359.0 . . cw_distance=20.0 +chr1 cwpair . 668 669 319.0 . . cw_distance=-48.0 +chr1 cwpair . 98551 98552 122.0 . . cw_distance=27.0 +chr1 cwpair . 180286 180287 63.0 . . cw_distance=-8.0 +chr1 cwpair . 230178 230179 56.0 . . cw_distance=10.0 +chr1 cwpair . 230131 230132 44.0 . . cw_distance=22.0 +chr1 cwpair . 230157 230158 15.0 . . cw_distance=5.0 +chr1 cwpair . 96919 96920 12.0 . . cw_distance=3.0 +chr1 cwpair . 197535 197536 5.0 . . cw_distance=73.0 diff -r 71188f3f4b76 -r c4b926c9831c test-data/mode_o_output2.tabular --- a/test-data/mode_o_output2.tabular Mon Nov 06 23:19:50 2017 -0500 +++ b/test-data/mode_o_output2.tabular Thu May 02 08:30:22 2019 -0400 @@ -1,100 +1,368 @@ -chrom strand start end value -chr1 + 100364 100384 2695.0 -chr1 + 30 50 2140.0 -chr1 + 5379 5399 1572.0 -chr1 + 52440 52460 1562.0 -chr1 + 73234 73254 1492.0 -chr1 + 31096 31116 1481.0 -chr1 + 145253 145273 1394.0 -chr1 + 10641 10661 1359.0 -chr1 + 200580 200600 1298.0 -chr1 + 64772 64792 1292.0 -chr1 + 86886 86906 1253.0 -chr1 + 103207 103227 1229.0 -chr1 + 43835 43855 1173.0 -chr1 + 29570 29590 1130.0 -chr1 + 83774 83794 1125.0 -chr1 + 165827 165847 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-r c4b926c9831c test-data/statistics1.tabular --- a/test-data/statistics1.tabular Mon Nov 06 23:19:50 2017 -0500 +++ b/test-data/statistics1.tabular Thu May 02 08:30:22 2019 -0400 @@ -1,4 +1,4 @@ -fname final_mode preview_mode perc95 paired orphans -mode: data 1 -3.5 16.5 1437.0 112 386 -closest: data 1 -3.5 NA 1437.0 112 386 -largest: data 1 -3.5 NA 1437.0 110 388 +fname final_mode preview_mode perc95 paired orphans +mode: data 1 63.5 63.5 1437.0 114 385 +closest: data 1 8.5 NA 1437.0 112 387 +largest: data 1 63.5 NA 1437.0 110 389 diff -r 71188f3f4b76 -r c4b926c9831c test-data/statistics2.tabular --- a/test-data/statistics2.tabular Mon Nov 06 23:19:50 2017 -0500 +++ b/test-data/statistics2.tabular Thu May 02 08:30:22 2019 -0400 @@ -1,4 +1,4 @@ -fname final_mode preview_mode perc95 paired orphans -mode: data 1 -3.5 16.5 1437.0 132 366 -closest: data 1 -3.5 NA 1437.0 132 366 -largest: data 1 -24.5 NA 1437.0 128 370 +fname final_mode preview_mode perc95 paired orphans +mode: data 1 8.5 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