# HG changeset patch
# User iuc
# Date 1450821826 18000
# Node ID 8600bfe7ed5253d72f1fc8cee53d828b5ed3d62b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
diff -r 000000000000 -r 8600bfe7ed52 cwpair2.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cwpair2.py Tue Dec 22 17:03:46 2015 -0500
@@ -0,0 +1,68 @@
+"""
+cwpair2.py
+
+Takes a list of called peaks on both strands and produces a list of matched pairs and a list
+of unmatched orphans using a specified method for finding matched pairs. Methods for finding
+matched pairs are mode, closest, largest or all, where the analysis is run for each method
+
+Input: list of one or more gff format files
+
+Output: files produced for each input/mode combination:
+MP (matched_pair), D (details), O (orphans), P (frequency preview plot), F (frequency final plot),
+C (statistics graph), statistics.tabular
+"""
+
+import argparse
+import csv
+import cwpair2_util
+
+if __name__ == '__main__':
+ parser = argparse.ArgumentParser()
+ parser.add_argument('--input', dest='inputs', action='append', nargs=2, help="Input datasets")
+ parser.add_argument('--method', dest='method', default='mode', help='Method of finding match.')
+ parser.add_argument('--up_distance', dest='up_distance', type=int, default=50, help='Distance upstream from a pair.')
+ parser.add_argument('--down_distance', dest='down_distance', type=int, default=100, help='Distance downstream of a pair.')
+ parser.add_argument('--binsize', dest='binsize', type=int, default=1, help='Width of bins for plots and mode.')
+ parser.add_argument('--threshold_format', dest='threshold_format', help='Percentage to filter the 95th percentile.')
+ parser.add_argument('--relative_threshold', dest='relative_threshold', type=float, default=0.0, help='Percentage to filter the 95th percentile.')
+ parser.add_argument('--absolute_threshold', dest='absolute_threshold', type=float, default=0.0, help='Absolute value to filter.')
+ parser.add_argument('--output_files', dest='output_files', default='matched_pair', help='Restrict output dataset collections.')
+ parser.add_argument('--statistics_output', dest='statistics_output', help='Statistics output file.')
+ args = parser.parse_args()
+
+ cwpair2_util.create_directories()
+
+ statistics = []
+ if args.absolute_threshold > 0:
+ threshold = args.absolute_threshold
+ elif args.relative_threshold > 0:
+ threshold = args.relative_threshold / 100.0
+ else:
+ threshold = 0
+ for (dataset_path, hid) in args.inputs:
+ stats = cwpair2_util.process_file(dataset_path,
+ hid,
+ args.method,
+ threshold,
+ args.up_distance,
+ args.down_distance,
+ args.binsize,
+ args.output_files)
+ statistics.extend(stats)
+ # Accumulate statistics.
+ by_file = {}
+ for stats in statistics:
+ # Skip "None" statistics from failed files
+ if not stats:
+ continue
+ path = stats['stats_path']
+ if path not in by_file:
+ by_file[path] = []
+ 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.writerow(keys)
+ for file_path, statistics in by_file.items():
+ for stats in statistics:
+ statistics_out.writerow([stats[key] for key in keys])
diff -r 000000000000 -r 8600bfe7ed52 cwpair2.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cwpair2.xml Tue Dec 22 17:03:46 2015 -0500
@@ -0,0 +1,185 @@
+
+
+ find matched pairs and unmatched orphans
+
+ cwpair2_macros.xml
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+ output_files == "all"
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+ output_files in ["all", "matched_pair_orphan_detail"]
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+ output_files in ["all", "matched_pair_orphan", "matched_pair_orphan_detail"]
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+**What it does**
+
+CWPair accepts one or more gff files as input and takes the peak location to be the midpoint between the
+exclusion zone start and end coordinate (columns D and E). CWPair starts with the highest peak (primary peak)
+in the dataset, and then looks on the opposite strand for another peak located within the distance defined by
+a combination of the tool's **Distance upstream from a peak to allow a pair** (the distance upstream or 5’ to
+the primary peak) and **Distance downstream from a peak to allow a pair** (the distance downstream or 3’ to the
+primary peak) parameters. So "upstream" value 30 "downstream" value 20 makes the tool look 30 bp upstream and
+20 bp downstream (inclusive). Consequently, the search space would be 51 bp, since it includes the primary peak
+coordinate. The use of a negative number changes the direction of the search limits. So, "upstream" -30 and
+"downstream" 20 produces an 11 bp downstream search window (20-30 bp downstream, inclusive).
+
+.. image:: $PATH_TO_IMAGES/cwpair2.png
+
+When encountering multiple candidate peaks within the search window, CWPair uses the resolution method defined by
+the tool's **Method of finding a match** parameter as follows:
+
+
+ * **mode** - This is an iterative process in which all peak-pair distances within the search window are determined, and the mode calculated. The pair whose distance apart is closest to the mode is then selected.
+ * **closest** - Pairs the peak that has the closest absolute distance from the primary peak.
+ * **largest** - Pairs the peak that has the highest tag count.
+ * **all** - Runs all three methods, producing separate outputs for each.
+
+When considering the candidate peaks for pairing to a primary peak, a tag-count threshold may also be set using
+the tool's **Filter using relative/absolute threshold** parameter. A relative threshold determines the tag counts
+at the 95th percentile of peak occupancy (i.e. top 5% in terms of tag counts), then uses a tag count threshold at
+the specified percentage of this 95th percentile. So if the peak at the 95th percentile has 200 tags, and "relative
+threshold" 50 is used, then it will not consider any peak having less than 100 tags.
+
+-----
+
+**Options**
+
+ * **Method of finding match** - Method of finding matched pair, mode, closest, largest, or all (run with each method).
+ * **Distance upstream from a peak to allow a pair** - The maximum distance (inclusive) upstream on the opposite strand from the primary peak to locate another peak, resulting in a pair.
+ * **Distance downstream from a peak to allow a pair** - The maximum distance (inclusive) downstream on the opposite strand from the primary peak to locate another peak, resulting in a pair.
+ * **Percentage of the 95 percentile value to filter below** - Percentage of the 95 percentile value below which to filter when using a relative threshold.
+ * **Absolute value to filter below** - Absolute value below which to filter when using an absolute threshold.
+ * **Output files** - Restrict output dataset collections to matched pairs only or one of several combinations of collection types.
+
+-----
+
+**Output Data Files**
+
+ * **closest/largest/mode MP** - gff file containing the Matched Pairs and includes the peak-pair midpoint coordinate (column D) and the coordinate +1 (column E). The tag count sum is reported in column F, along with the C-W distance in bp in column I.
+ * **closest/largest/mode O** - tabular file containing the Orphans (all peaks that are not in pairs).
+ * **closest/largest/mode D** - tabular file containing the Details, which lists + and – strand information separately. The start and end represent the lower and higher coordinates of the exclusion zone from GeneTrack, and “Value” is the tag count sum within the exclusion zone. The peak pair midpoint is calculated along with the distance between the two paired peaks (midpoint-to-midpoint or C-W distance).
+
+**Output Statistics Files**
+
+ * **closest/largest/mode C** - pdf file that provides the frequency distribution of peak pair distances.
+ * **closest/largest/mode P** - pdf file that provides the preview plots graph (the initial iteration of the process for finding the mode).
+ * **closest/largest/mode F** - pdf file that provides the final plots graph.
+ * **Statistics Table** - provides the number of peaks in pairs (dividing this by 2 provides the number of peak-pairs).
+
+
+
+
diff -r 000000000000 -r 8600bfe7ed52 cwpair2_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cwpair2_macros.xml Tue Dec 22 17:03:46 2015 -0500
@@ -0,0 +1,29 @@
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+ 1.0
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+ anaconda
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+ @unpublished{None,
+ author = {None},
+ title = {None},
+ year = {None},
+ eprint = {None},
+ url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
+ }
+
+
+
diff -r 000000000000 -r 8600bfe7ed52 cwpair2_util.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cwpair2_util.py Tue Dec 22 17:03:46 2015 -0500
@@ -0,0 +1,393 @@
+import bisect
+import csv
+import os
+import sys
+import traceback
+import matplotlib
+matplotlib.use('Agg')
+from matplotlib import pyplot
+
+# Data outputs
+DETAILS = 'D'
+MATCHED_PAIRS = 'MP'
+ORPHANS = 'O'
+# Data output formats
+GFF_EXT = 'gff'
+TABULAR_EXT = 'tabular'
+# Statistics historgrams output directory.
+HISTOGRAM = 'H'
+# Statistics outputs
+FINAL_PLOTS = 'F'
+PREVIEW_PLOTS = 'P'
+STATS_GRAPH = 'C'
+
+# Graph settings.
+COLORS = 'krg'
+Y_LABEL = 'Peak-pair counts'
+X_LABEL = 'Peak-pair distance (bp)'
+TICK_WIDTH = 3
+ADJUST = [0.140, 0.9, 0.9, 0.1]
+PLOT_FORMAT = 'pdf'
+pyplot.rc('xtick.major', size=10.00)
+pyplot.rc('ytick.major', size=10.00)
+pyplot.rc('lines', linewidth=4.00)
+pyplot.rc('axes', linewidth=3.00)
+pyplot.rc('font', family='Bitstream Vera Sans', size=32.0)
+
+
+class FrequencyDistribution(object):
+
+ def __init__(self, start, end, binsize=10, d=None):
+ self.start = start
+ self.end = end
+ self.dist = d or {}
+ self.binsize = binsize
+
+ def get_bin(self, x):
+ """
+ Returns the bin in which a data point falls
+ """
+ return self.start + (x-self.start) // self.binsize * self.binsize + self.binsize/2.0
+
+ def add(self, x):
+ x = self.get_bin(x)
+ self.dist[x] = self.dist.get(x, 0) + 1
+
+ def graph_series(self):
+ x = []
+ y = []
+ for i in range(self.start, self.end, self.binsize):
+ center = self.get_bin(i)
+ x.append(center)
+ y.append(self.dist.get(center, 0))
+ return x, y
+
+ def mode(self):
+ return max(self.dist.items(), key=lambda data: data[1])[0]
+
+ def size(self):
+ return sum(self.dist.values())
+
+
+def stop_err(msg):
+ sys.stderr.write(msg)
+ sys.exit(1)
+
+
+def distance(peak1, peak2):
+ return (peak2[1]+peak2[2])/2 - (peak1[1]+peak1[2])/2
+
+
+def gff_row(cname, start, end, score, source, type='.', strand='.', phase='.', attrs={}):
+ return (cname, source, type, start, end, score, strand, phase, gff_attrs(attrs))
+
+
+def gff_attrs(d):
+ if not d:
+ return '.'
+ return ';'.join('%s=%s' % item for item in d.items())
+
+
+def parse_chromosomes(reader):
+ # This version of cwpair2 accepts only gff format as input.
+ chromosomes = {}
+ reader.next()
+ for line in reader:
+ cname, junk, junk, start, end, value, strand, junk, junk = line
+ start = int(start)
+ end = int(end)
+ value = float(value)
+ if cname not in chromosomes:
+ chromosomes[cname] = []
+ peaks = chromosomes[cname]
+ peaks.append((strand, start, end, value))
+ return chromosomes
+
+
+def perc95(chromosomes):
+ """
+ Returns the 95th percentile value of the given chromosomes.
+ """
+ values = []
+ for peaks in chromosomes.values():
+ for peak in peaks:
+ values.append(peak[3])
+ values.sort()
+ # Get 95% value
+ return values[int(len(values)*0.95)]
+
+
+def filter(chromosomes, threshold=0.05):
+ """
+ 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.
+ """
+ if threshold < 1:
+ p95 = perc95(chromosomes)
+ threshold = p95 * threshold
+ # Make the threshold a proportion of the
+ for cname, peaks in chromosomes.items():
+ chromosomes[cname] = [peak for peak in peaks if peak[3] > threshold]
+
+
+def split_strands(chromosome):
+ watson = [peak for peak in chromosome if peak[0] == '+']
+ crick = [peak for peak in chromosome if peak[0] == '-']
+ return watson, crick
+
+
+def all_pair_distribution(chromosomes, up_distance, down_distance, binsize):
+ dist = FrequencyDistribution(-up_distance, down_distance, binsize=binsize)
+ for cname, data in chromosomes.items():
+ watson, crick = split_strands(data)
+ crick.sort(key=lambda data: float(data[1]))
+ keys = make_keys(crick)
+ for peak in watson:
+ for cpeak in get_window(crick, peak, up_distance, down_distance, keys):
+ dist.add(distance(peak, cpeak))
+ return dist
+
+
+def make_keys(crick):
+ return [(data[1] + data[2])//2 for data in crick]
+
+
+def get_window(crick, peak, up_distance, down_distance, keys=None):
+ """
+ Returns a window of all crick peaks within a distance of a watson peak.
+ crick strand MUST be sorted by distance
+ """
+ strand, start, end, value = peak
+ midpoint = (start + end) // 2
+ lower = midpoint - up_distance
+ upper = midpoint + down_distance
+ keys = keys or make_keys(crick)
+ start_index = bisect.bisect_left(keys, lower)
+ end_index = bisect.bisect_right(keys, upper)
+ return [cpeak for cpeak in crick[start_index:end_index]]
+
+
+def match_largest(window, peak):
+ if not window:
+ return None
+ return max(window, key=lambda cpeak: cpeak[3])
+
+
+def match_closest(window, peak):
+ if not window:
+ return None
+
+ def key(cpeak):
+ d = distance(peak, cpeak)
+ # Search negative distances last
+ if d < 0:
+ # And then prefer less negative distances
+ d = 10000 - d
+ return d
+ return min(window, key=key)
+
+
+def match_mode(window, peak, mode):
+ if not window:
+ return None
+ return min(window, key=lambda cpeak: abs(distance(peak, cpeak)-mode))
+
+METHODS = {'mode': match_mode, 'closest': match_closest, 'largest': match_largest}
+
+
+def frequency_plot(freqs, fname, labels=[], title=''):
+ pyplot.clf()
+ pyplot.figure(figsize=(10, 10))
+ for i, freq in enumerate(freqs):
+ x, y = freq.graph_series()
+ pyplot.plot(x, y, '%s-' % COLORS[i])
+ if len(freqs) > 1:
+ pyplot.legend(labels)
+ pyplot.xlim(freq.start, freq.end)
+ pyplot.ylim(ymin=0)
+ pyplot.ylabel(Y_LABEL)
+ pyplot.xlabel(X_LABEL)
+ pyplot.subplots_adjust(left=ADJUST[0], right=ADJUST[1], top=ADJUST[2], bottom=ADJUST[3])
+ # Get the current axes
+ ax = pyplot.gca()
+ for l in ax.get_xticklines() + ax.get_yticklines():
+ l.set_markeredgewidth(TICK_WIDTH)
+ pyplot.savefig(fname)
+
+
+def create_directories():
+ # Output histograms in pdf.
+ os.mkdir(HISTOGRAM)
+ os.mkdir('data_%s' % DETAILS)
+ os.mkdir('data_%s' % ORPHANS)
+ os.mkdir('data_%s' % MATCHED_PAIRS)
+
+
+def process_file(dataset_path, galaxy_hid, method, threshold, up_distance,
+ down_distance, binsize, output_files):
+ if method == 'all':
+ match_methods = METHODS.keys()
+ else:
+ match_methods = [method]
+ statistics = []
+ for match_method in match_methods:
+ stats = perform_process(dataset_path,
+ galaxy_hid,
+ match_method,
+ threshold,
+ up_distance,
+ down_distance,
+ binsize,
+ output_files)
+ statistics.append(stats)
+ if output_files == 'all' and method == 'all':
+ frequency_plot([s['dist'] for s in statistics],
+ statistics[0]['graph_path'],
+ labels=METHODS.keys())
+ return statistics
+
+
+def perform_process(dataset_path, galaxy_hid, method, threshold, up_distance,
+ down_distance, binsize, output_files):
+ output_details = output_files in ["all", "matched_pair_orphan_detail"]
+ output_plots = output_files in ["all"]
+ 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
+ if threshold >= 1:
+ filter_string = 'fa%d' % threshold
+ else:
+ filter_string = 'f%d' % (threshold * 100)
+ fname = '%s_%su%dd%d_on_data_%s' % (method, filter_string, up_distance, down_distance, galaxy_hid)
+
+ def make_histogram_path(output_type, fname):
+ return os.path.join(HISTOGRAM, 'histogram_%s_%s.%s' % (output_type, fname, PLOT_FORMAT))
+
+ def make_path(output_type, extension, fname):
+ # Returns the full path for an output.
+ return os.path.join(output_type, '%s_%s.%s' % (output_type, fname, extension))
+
+ 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')
+
+ 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)
+ detailed_output.writerow(('chrom', 'start', 'end', 'value', 'strand') * 2 + ('midpoint', 'c-w reads sum', 'c-w distance (bp)'))
+ if output_plots:
+ # Final Plot
+ final_plot_path = make_histogram_path(FINAL_PLOTS, fname)
+ if output_orphans:
+ # Orphans
+ orphan_output = td_writer('data_%s' % ORPHANS, TABULAR_EXT, fname)
+ orphan_output.writerow(('chrom', 'strand', 'start', 'end', 'value'))
+ if output_plots:
+ # Preview Plot
+ preview_plot_path = make_histogram_path(PREVIEW_PLOTS, fname)
+ # Matched Pairs.
+ matched_pairs_output = td_writer('data_%s' % MATCHED_PAIRS, GFF_EXT, fname)
+ statistics['stats_path'] = 'statistics.%s' % TABULAR_EXT
+ if output_plots:
+ statistics['graph_path'] = make_histogram_path(STATS_GRAPH, fname)
+ statistics['perc95'] = perc95(chromosomes)
+ if threshold > 0:
+ # Apply filter
+ filter(chromosomes, threshold)
+ if method == 'mode':
+ freq = all_pair_distribution(chromosomes, up_distance, down_distance, binsize)
+ mode = freq.mode()
+ statistics['preview_mode'] = mode
+ if output_plots:
+ frequency_plot([freq], preview_plot_path, title='Preview frequency plot')
+ else:
+ statistics['preview_mode'] = 'NA'
+ dist = FrequencyDistribution(-up_distance, down_distance, binsize=binsize)
+ orphans = 0
+ # x will be used to archive the summary dataset
+ x = []
+ for cname, chromosome in chromosomes.items():
+ # Each peak is (strand, start, end, value)
+ watson, crick = split_strands(chromosome)
+ # Sort by value of each peak
+ watson.sort(key=lambda data: -float(data[3]))
+ # Sort by position to facilitate binary search
+ crick.sort(key=lambda data: float(data[1]))
+ keys = make_keys(crick)
+ for peak in watson:
+ window = get_window(crick, peak, up_distance, down_distance, keys)
+ if method == 'mode':
+ match = match_mode(window, peak, mode)
+ else:
+ match = METHODS[method](window, peak)
+ if match:
+ midpoint = (match[1] + match[2] + peak[1] + peak[2]) // 4
+ d = distance(peak, match)
+ dist.add(d)
+ # Simple output in gff format.
+ x.append(gff_row(cname,
+ source='cwpair',
+ start=midpoint,
+ end=midpoint + 1,
+ score=peak[3] + match[3],
+ attrs={'cw_distance': d}))
+ if output_details:
+ detailed_output.writerow((cname,
+ peak[1],
+ peak[2],
+ peak[3],
+ '+',
+ cname,
+ match[1],
+ match[2],
+ match[3], '-',
+ midpoint,
+ peak[3]+match[3],
+ d))
+ i = bisect.bisect_left(keys, (match[1]+match[2])/2)
+ del crick[i]
+ del keys[i]
+ else:
+ if output_orphans:
+ orphan_output.writerow((cname, peak[0], peak[1], peak[2], peak[3]))
+ # Keep track of orphans for statistics.
+ orphans += 1
+ # Remaining crick peaks are orphans
+ if output_orphans:
+ for cpeak in crick:
+ orphan_output.writerow((cname, cpeak[0], cpeak[1], cpeak[2], cpeak[3]))
+ # Keep track of orphans for statistics.
+ orphans += len(crick)
+ # Sort output descending by score.
+ x.sort(key=lambda data: float(data[5]), reverse=True)
+ # Writing a summary to gff format file
+ for row in x:
+ row_tmp = list(row)
+ # Dataset in tuple cannot be modified in Python, so row will
+ # be converted to list format to add 'chr'.
+ if row_tmp[0] == "999":
+ row_tmp[0] = 'chrM'
+ elif row_tmp[0] == "998":
+ row_tmp[0] = 'chrY'
+ elif row_tmp[0] == "997":
+ row_tmp[0] = 'chrX'
+ else:
+ row_tmp[0] = row_tmp[0]
+ # Print row_tmp.
+ matched_pairs_output.writerow(row_tmp)
+ statistics['paired'] = dist.size() * 2
+ statistics['orphans'] = orphans
+ statistics['final_mode'] = dist.mode()
+ if output_plots:
+ frequency_plot([dist], final_plot_path, title='Frequency distribution')
+ statistics['dist'] = dist
+ return statistics
diff -r 000000000000 -r 8600bfe7ed52 static/images/cwpair2.png
Binary file static/images/cwpair2.png has changed
diff -r 000000000000 -r 8600bfe7ed52 test-data/closest_d_output2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closest_d_output2.tabular Tue Dec 22 17:03:46 2015 -0500
@@ -0,0 +1,66 @@
+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
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+chr1 231 251 1146.0 + chr1 279 299 1328.0 - 265 2474.0 48
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+chr1 101411 101431 973.0 + chr1 101367 101387 1388.0 - 101399 2361.0 -44
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+chr1 348 368 699.0 + chr1 373 393 200.0 - 370 899.0 25
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+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
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+chr1 228633 228653 371.0 + chr1 228691 228711 255.0 - 228672 626.0 58
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+chr1 136366 136386 248.0 + chr1 136352 136372 117.0 - 136369 365.0 -14
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+chr1 368 388 192.0 + chr1 388 408 167.0 - 388 359.0 20
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+chr1 55495 55515 125.0 + chr1 55581 55601 831.0 - 55548 956.0 86
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+chr1 39197 39217 101.0 + chr1 39258 39278 261.0 - 39237 362.0 61
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+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
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diff -r 000000000000 -r 8600bfe7ed52 test-data/closest_f_output2.pdf
Binary file test-data/closest_f_output2.pdf has changed
diff -r 000000000000 -r 8600bfe7ed52 test-data/closest_mp_output1.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closest_mp_output1.gff Tue Dec 22 17:03:46 2015 -0500
@@ -0,0 +1,55 @@
+chr1 cwpair . 87162 87163 5531.0 . . cw_distance=11
+chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16
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+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
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+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
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+chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4
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+chr1 cwpair . 173276 173277 546.0 . . cw_distance=8
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+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
diff -r 000000000000 -r 8600bfe7ed52 test-data/closest_mp_output2.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closest_mp_output2.gff Tue Dec 22 17:03:46 2015 -0500
@@ -0,0 +1,65 @@
+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
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+chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44
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+chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12
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+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
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+chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45
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+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
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+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
diff -r 000000000000 -r 8600bfe7ed52 test-data/closest_o_output2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closest_o_output2.tabular Tue Dec 22 17:03:46 2015 -0500
@@ -0,0 +1,100 @@
+chrom strand start end value
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diff -r 000000000000 -r 8600bfe7ed52 test-data/cwpair2_input1.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cwpair2_input1.gff Tue Dec 22 17:03:46 2015 -0500
@@ -0,0 +1,499 @@
+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
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+chr1 genetrack . 438 458 334 + . stddev=0.109271183179
+chr1 genetrack . 467 487 98 + . stddev=0.0
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+chr1 genetrack . 601 621 96 + . stddev=0.0
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+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 000000000000 -r 8600bfe7ed52 test-data/largest_d_output2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/largest_d_output2.tabular Tue Dec 22 17:03:46 2015 -0500
@@ -0,0 +1,64 @@
+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
diff -r 000000000000 -r 8600bfe7ed52 test-data/largest_f_output2.pdf
Binary file test-data/largest_f_output2.pdf has changed
diff -r 000000000000 -r 8600bfe7ed52 test-data/largest_mp_output1.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/largest_mp_output1.gff Tue Dec 22 17:03:46 2015 -0500
@@ -0,0 +1,54 @@
+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
diff -r 000000000000 -r 8600bfe7ed52 test-data/largest_mp_output2.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/largest_mp_output2.gff Tue Dec 22 17:03:46 2015 -0500
@@ -0,0 +1,63 @@
+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
diff -r 000000000000 -r 8600bfe7ed52 test-data/largest_o_output2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/largest_o_output2.tabular Tue Dec 22 17:03:46 2015 -0500
@@ -0,0 +1,100 @@
+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 1109.0
+chr1 + 92775 92795 1105.0
+chr1 + 4748 4768 1077.0
+chr1 + 126733 126753 952.0
+chr1 + 71041 71061 881.0
+chr1 + 35773 35793 866.0
+chr1 + 53097 53117 835.0
+chr1 + 71556 71576 835.0
+chr1 + 30964 30984 829.0
+chr1 + 31019 31039 810.0
+chr1 + 55349 55369 794.0
+chr1 + 203193 203213 789.0
+chr1 + 39794 39814 780.0
+chr1 + 153928 153948 768.0
+chr1 + 179472 179492 696.0
+chr1 + 178117 178137 686.0
+chr1 + 1298 1318 684.0
+chr1 + 87085 87105 676.0
+chr1 + 192754 192774 668.0
+chr1 + 89611 89631 640.0
+chr1 + 20205 20225 634.0
+chr1 + 118428 118448 633.0
+chr1 + 110736 110756 621.0
+chr1 + 48642 48662 610.0
+chr1 + 159372 159392 605.0
+chr1 + 6453 6473 601.0
+chr1 + 112137 112157 601.0
+chr1 + 142905 142925 599.0
+chr1 + 167443 167463 597.0
+chr1 + 126073 126093 590.0
+chr1 + 6233 6253 589.0
+chr1 + 43657 43677 586.0
+chr1 + 134021 134041 572.0
+chr1 + 29864 29884 570.0
+chr1 + 70953 70973 555.0
+chr1 + 87002 87022 550.0
+chr1 + 129555 129575 536.0
+chr1 + 119754 119774 515.0
+chr1 + 43523 43543 505.0
+chr1 + 97898 97918 501.0
+chr1 + 40830 40850 491.0
+chr1 + 153095 153115 490.0
+chr1 + 7303 7323 484.0
+chr1 + 115866 115886 480.0
+chr1 + 129680 129700 464.0
+chr1 + 187155 187175 455.0
+chr1 + 192271 192291 453.0
+chr1 + 160 180 451.0
+chr1 + 150449 150469 436.0
+chr1 + 9367 9387 425.0
+chr1 + 93793 93813 415.0
+chr1 + 87572 87592 407.0
+chr1 + 124845 124865 383.0
+chr1 + 4053 4073 381.0
+chr1 + 136072 136092 380.0
+chr1 + 39942 39962 375.0
+chr1 + 61977 61997 368.0
+chr1 + 2976 2996 356.0
+chr1 + 27978 27998 354.0
+chr1 + 195756 195776 348.0
+chr1 + 172223 172243 338.0
+chr1 + 143657 143677 328.0
+chr1 + 45409 45429 307.0
+chr1 + 45248 45268 305.0
+chr1 + 72671 72691 304.0
+chr1 + 68564 68584 303.0
+chr1 + 119953 119973 295.0
+chr1 + 48319 48339 290.0
+chr1 + 48772 48792 284.0
+chr1 + 126369 126389 284.0
+chr1 + 116432 116452 267.0
+chr1 + 199649 199669 264.0
+chr1 + 204126 204146 261.0
+chr1 + 130514 130534 243.0
+chr1 + 55692 55712 228.0
+chr1 + 117198 117218 228.0
+chr1 + 42843 42863 218.0
+chr1 + 59583 59603 204.0
+chr1 + 124669 124689 203.0
+chr1 + 2613 2633 202.0
+chr1 + 40264 40284 199.0
+chr1 + 21406 21426 177.0
+chr1 + 20391 20411 173.0
+chr1 + 20626 20646 171.0
diff -r 000000000000 -r 8600bfe7ed52 test-data/mode_c_output2.pdf
Binary file test-data/mode_c_output2.pdf has changed
diff -r 000000000000 -r 8600bfe7ed52 test-data/mode_d_output2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mode_d_output2.tabular Tue Dec 22 17:03:46 2015 -0500
@@ -0,0 +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 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 323 343 486.0 - 299 3296.0 68
+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 87234 87254 637.0 - 87212 2073.0 63
+chr1 201 221 1411.0 + chr1 261 281 1278.0 - 241 2689.0 60
+chr1 229741 229761 1380.0 + chr1 229784 229804 615.0 - 229772 1995.0 43
+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 87158 87178 2039.0 - 87138 3164.0 60
+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 87101 87121 1134.0 - 87070 1903.0 82
+chr1 124318 124338 749.0 + chr1 124275 124295 12.0 - 124306 761.0 -43
+chr1 348 368 699.0 + chr1 410 430 8.0 - 389 707.0 62
+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 87085 87105 676.0 + chr1 87049 87069 422.0 - 87077 1098.0 -36
+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 160 180 451.0 + chr1 215 235 2611.0 - 197 3062.0 55
+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 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 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 229757 229777 3151.0 - 229749 3235.0 36
+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 230132 230152 2.0 - 230148 10.0 -13
+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
diff -r 000000000000 -r 8600bfe7ed52 test-data/mode_f_output2.pdf
Binary file test-data/mode_f_output2.pdf has changed
diff -r 000000000000 -r 8600bfe7ed52 test-data/mode_mp_output1.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mode_mp_output1.gff Tue Dec 22 17:03:46 2015 -0500
@@ -0,0 +1,56 @@
+chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51
+chr1 cwpair . 123 124 4204.0 . . cw_distance=52
+chr1 cwpair . 299 300 3296.0 . . cw_distance=68
+chr1 cwpair . 229749 229750 3235.0 . . cw_distance=36
+chr1 cwpair . 87138 87139 3164.0 . . cw_distance=60
+chr1 cwpair . 197 198 3062.0 . . cw_distance=55
+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 . 265 266 2474.0 . . cw_distance=48
+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 . 87212 87213 2073.0 . . cw_distance=63
+chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37
+chr1 cwpair . 229772 229773 1995.0 . . cw_distance=43
+chr1 cwpair . 87070 87071 1903.0 . . cw_distance=82
+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 . 87035 87036 972.0 . . cw_distance=47
+chr1 cwpair . 55548 55549 956.0 . . cw_distance=86
+chr1 cwpair . 350 351 885.0 . . cw_distance=66
+chr1 cwpair . 72805 72806 869.0 . . cw_distance=29
+chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2
+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 . 72731 72732 710.0 . . cw_distance=100
+chr1 cwpair . 389 390 707.0 . . cw_distance=62
+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 . 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 . 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 . 230148 230149 10.0 . . cw_distance=-13
diff -r 000000000000 -r 8600bfe7ed52 test-data/mode_mp_output2.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mode_mp_output2.gff Tue Dec 22 17:03:46 2015 -0500
@@ -0,0 +1,66 @@
+chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51
+chr1 cwpair . 123 124 4204.0 . . cw_distance=52
+chr1 cwpair . 299 300 3296.0 . . cw_distance=68
+chr1 cwpair . 229749 229750 3235.0 . . cw_distance=36
+chr1 cwpair . 87138 87139 3164.0 . . cw_distance=60
+chr1 cwpair . 197 198 3062.0 . . cw_distance=55
+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 . 265 266 2474.0 . . cw_distance=48
+chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44
+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 . 87212 87213 2073.0 . . cw_distance=63
+chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37
+chr1 cwpair . 229772 229773 1995.0 . . cw_distance=43
+chr1 cwpair . 87070 87071 1903.0 . . cw_distance=82
+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 . 25305 25306 1183.0 . . cw_distance=99
+chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15
+chr1 cwpair . 87077 87078 1098.0 . . cw_distance=-36
+chr1 cwpair . 55548 55549 956.0 . . cw_distance=86
+chr1 cwpair . 350 351 885.0 . . cw_distance=66
+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 . 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 . 72731 72732 710.0 . . cw_distance=100
+chr1 cwpair . 389 390 707.0 . . cw_distance=62
+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 . 230148 230149 10.0 . . cw_distance=-13
diff -r 000000000000 -r 8600bfe7ed52 test-data/mode_o_output2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mode_o_output2.tabular Tue Dec 22 17:03:46 2015 -0500
@@ -0,0 +1,100 @@
+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 1109.0
+chr1 + 92775 92795 1105.0
+chr1 + 4748 4768 1077.0
+chr1 + 126733 126753 952.0
+chr1 + 71041 71061 881.0
+chr1 + 35773 35793 866.0
+chr1 + 53097 53117 835.0
+chr1 + 71556 71576 835.0
+chr1 + 30964 30984 829.0
+chr1 + 31019 31039 810.0
+chr1 + 55349 55369 794.0
+chr1 + 203193 203213 789.0
+chr1 + 39794 39814 780.0
+chr1 + 153928 153948 768.0
+chr1 + 179472 179492 696.0
+chr1 + 178117 178137 686.0
+chr1 + 1298 1318 684.0
+chr1 + 192754 192774 668.0
+chr1 + 89611 89631 640.0
+chr1 + 20205 20225 634.0
+chr1 + 118428 118448 633.0
+chr1 + 110736 110756 621.0
+chr1 + 48642 48662 610.0
+chr1 + 159372 159392 605.0
+chr1 + 6453 6473 601.0
+chr1 + 112137 112157 601.0
+chr1 + 142905 142925 599.0
+chr1 + 167443 167463 597.0
+chr1 + 126073 126093 590.0
+chr1 + 6233 6253 589.0
+chr1 + 43657 43677 586.0
+chr1 + 134021 134041 572.0
+chr1 + 29864 29884 570.0
+chr1 + 70953 70973 555.0
+chr1 + 87002 87022 550.0
+chr1 + 129555 129575 536.0
+chr1 + 119754 119774 515.0
+chr1 + 43523 43543 505.0
+chr1 + 97898 97918 501.0
+chr1 + 40830 40850 491.0
+chr1 + 153095 153115 490.0
+chr1 + 7303 7323 484.0
+chr1 + 115866 115886 480.0
+chr1 + 129680 129700 464.0
+chr1 + 187155 187175 455.0
+chr1 + 192271 192291 453.0
+chr1 + 150449 150469 436.0
+chr1 + 9367 9387 425.0
+chr1 + 93793 93813 415.0
+chr1 + 87572 87592 407.0
+chr1 + 124845 124865 383.0
+chr1 + 4053 4073 381.0
+chr1 + 136072 136092 380.0
+chr1 + 39942 39962 375.0
+chr1 + 61977 61997 368.0
+chr1 + 2976 2996 356.0
+chr1 + 27978 27998 354.0
+chr1 + 195756 195776 348.0
+chr1 + 172223 172243 338.0
+chr1 + 143657 143677 328.0
+chr1 + 45409 45429 307.0
+chr1 + 45248 45268 305.0
+chr1 + 68564 68584 303.0
+chr1 + 119953 119973 295.0
+chr1 + 48319 48339 290.0
+chr1 + 48772 48792 284.0
+chr1 + 126369 126389 284.0
+chr1 + 116432 116452 267.0
+chr1 + 199649 199669 264.0
+chr1 + 204126 204146 261.0
+chr1 + 130514 130534 243.0
+chr1 + 55692 55712 228.0
+chr1 + 117198 117218 228.0
+chr1 + 42843 42863 218.0
+chr1 + 59583 59603 204.0
+chr1 + 124669 124689 203.0
+chr1 + 2613 2633 202.0
+chr1 + 40264 40284 199.0
+chr1 + 21406 21426 177.0
+chr1 + 20391 20411 173.0
+chr1 + 20626 20646 171.0
+chr1 + 198594 198614 170.0
+chr1 + 149343 149363 159.0
+chr1 + 121016 121036 155.0
diff -r 000000000000 -r 8600bfe7ed52 test-data/mode_p_output2.pdf
Binary file test-data/mode_p_output2.pdf has changed
diff -r 000000000000 -r 8600bfe7ed52 test-data/statistics1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/statistics1.tabular Tue Dec 22 17:03:46 2015 -0500
@@ -0,0 +1,4 @@
+fname final_mode preview_mode perc95 paired orphans
+mode: data 1 63.5 63.5 1437.0 114 384
+closest: data 1 10.5 NA 1437.0 112 386
+largest: data 1 -3.5 NA 1437.0 110 388
diff -r 000000000000 -r 8600bfe7ed52 test-data/statistics2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/statistics2.tabular Tue Dec 22 17:03:46 2015 -0500
@@ -0,0 +1,4 @@
+fname final_mode preview_mode perc95 paired orphans
+mode: data 1 63.5 63.5 1437.0 134 364
+closest: data 1 8.5 NA 1437.0 132 366
+largest: data 1 -24.5 NA 1437.0 128 370
diff -r 000000000000 -r 8600bfe7ed52 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Dec 22 17:03:46 2015 -0500
@@ -0,0 +1,6 @@
+
+
+
+
+
+