# HG changeset patch # User artbio # Date 1508761779 14400 # Node ID 1827b74f872bd4015d6c5fba8b4ed48935f862ba # Parent a96e6a7df2b724b2a60be57d5b80386d8e424420 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60 diff -r a96e6a7df2b7 -r 1827b74f872b small_rna_maps.py --- a/small_rna_maps.py Tue Oct 10 18:48:37 2017 -0400 +++ b/small_rna_maps.py Mon Oct 23 08:29:39 2017 -0400 @@ -10,6 +10,10 @@ the_parser = argparse.ArgumentParser() the_parser.add_argument('--inputs', dest='inputs', required=True, nargs='+', help='list of input BAM files') + the_parser.add_argument('--minsize', dest='minsize', type=int, + default=0, help='minimal size of reads') + the_parser.add_argument('--maxsize', dest='maxsize', type=int, + default=10000, help='maximal size of reads') the_parser.add_argument('--sample_names', dest='sample_names', required=True, nargs='+', help='list of sample names') @@ -24,14 +28,17 @@ class Map: - def __init__(self, bam_file, sample): + def __init__(self, bam_file, sample, minsize, maxsize): self.sample_name = sample + self.minsize = minsize + self.maxsize = maxsize self.bam_object = pysam.AlignmentFile(bam_file, 'rb') self.chromosomes = dict(zip(self.bam_object.references, self.bam_object.lengths)) - self.map_dict = self.create_map(self.bam_object) + self.map_dict = self.create_map(self.bam_object, self.minsize, + self.maxsize) - def create_map(self, bam_object): + def create_map(self, bam_object, minsize, maxsize): ''' Returns a map_dictionary {(chromosome,read_position,polarity): [read_length, ...]} @@ -43,13 +50,15 @@ map_dictionary[(chrom, self.chromosomes[chrom], 'F')] = [] for chrom in self.chromosomes: for read in bam_object.fetch(chrom): - positions = read.positions # a list of covered positions - if read.is_reverse: - map_dictionary[(chrom, positions[-1]+1, - 'R')].append(read.query_alignment_length) - else: - map_dictionary[(chrom, positions[0]+1, - 'F')].append(read.query_alignment_length) + if (read.query_alignment_length >= minsize and + read.query_alignment_length <= maxsize): + positions = read.positions # a list of covered positions + if read.is_reverse: + map_dictionary[(chrom, positions[-1]+1, 'R')].append( + read.query_alignment_length) + else: + map_dictionary[(chrom, positions[0]+1, 'F')].append( + read.query_alignment_length) return map_dictionary def compute_readcount(self, map_dictionary, out): @@ -182,7 +191,7 @@ out.write('\t'.join(line) + '\n') -def main(inputs, samples, methods, outputs): +def main(inputs, samples, methods, outputs, minsize, maxsize): for method, output in zip(methods, outputs): F = open(output, 'w') if method == 'Size': @@ -192,7 +201,7 @@ "Polarity", method] F.write('\t'.join(header) + '\n') for input, sample in zip(inputs, samples): - mapobj = Map(input, sample) + mapobj = Map(input, sample, minsize, maxsize) token = {"Counts": mapobj.compute_readcount, "Max": mapobj.compute_max, "Mean": mapobj.compute_mean, @@ -209,4 +218,5 @@ if len(set(args.sample_names)) != len(args.sample_names): args.sample_names = [name + '_' + str(i) for i, name in enumerate(args.sample_names)] - main(args.inputs, args.sample_names, args.plot_methods, args.outputs) + main(args.inputs, args.sample_names, args.plot_methods, args.outputs, + args.minsize, args.maxsize) diff -r a96e6a7df2b7 -r 1827b74f872b small_rna_maps.xml --- a/small_rna_maps.xml Tue Oct 10 18:48:37 2017 -0400 +++ b/small_rna_maps.xml Mon Oct 23 08:29:39 2017 -0400 @@ -1,4 +1,4 @@ - + numpy @@ -25,6 +25,8 @@ #for $sample in $inputs '$sample.name' #end for + --minsize $minsize + --maxsize $maxsize #if str($plots_options.plots_options_selector ) == "two_plot": --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}' --outputs '$output_tab' '$extra_output_tab' && @@ -56,6 +58,10 @@ + + @@ -108,6 +114,8 @@ + + @@ -117,6 +125,8 @@ + + @@ -125,7 +135,20 @@ + + + + + + + + + + + + + @@ -135,7 +158,21 @@ + + + + + + + + + + + + + + @@ -146,6 +183,8 @@ + + @@ -156,6 +195,8 @@ + + @@ -166,6 +207,8 @@ + + @@ -176,6 +219,8 @@ + + @@ -186,6 +231,8 @@ + + @@ -196,6 +243,8 @@ + + @@ -204,6 +253,8 @@ + + @@ -212,6 +263,8 @@ + + @@ -220,6 +273,8 @@ + + diff -r a96e6a7df2b7 -r 1827b74f872b test-data/count-mean-20-30.pdf Binary file test-data/count-mean-20-30.pdf has changed diff -r a96e6a7df2b7 -r 1827b74f872b test-data/count20-30.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count20-30.tab Mon Oct 23 08:29:39 2017 -0400 @@ -0,0 +1,350 @@ +Dataset Chromosome Chrom_length Coordinate Polarity Counts +input2.bam FBtr0070001 72 1 F 0 +input2.bam FBtr0070001 72 13 F 1 +input2.bam FBtr0070001 72 19 F 1 +input2.bam FBtr0070001 72 28 F 1 +input2.bam FBtr0070001 72 32 F 3 +input2.bam FBtr0070001 72 53 F 1 +input2.bam FBtr0070001 72 72 F 0 +input2.bam FBtr0070533 72 1 F 0 +input2.bam FBtr0070533 72 16 F 1 +input2.bam FBtr0070533 72 19 F 1 +input2.bam FBtr0070533 72 20 F 1 +input2.bam FBtr0070533 72 21 F 2 +input2.bam FBtr0070533 72 22 F 10 +input2.bam FBtr0070533 72 72 F 0 +input2.bam FBtr0070603 72 1 F 0 +input2.bam FBtr0070603 72 17 F 4 +input2.bam FBtr0070603 72 19 F 2 +input2.bam FBtr0070603 72 20 F 1 +input2.bam FBtr0070603 72 22 F 9 +input2.bam FBtr0070603 72 27 F 1 +input2.bam FBtr0070603 72 28 F 2 +input2.bam FBtr0070603 72 30 F 1 +input2.bam FBtr0070603 72 31 F 1 +input2.bam FBtr0070603 72 34 F 2 +input2.bam FBtr0070603 72 35 F 1 +input2.bam FBtr0070603 72 37 F 1 +input2.bam FBtr0070603 72 41 F 1 +input2.bam FBtr0070603 72 51 F 2 +input2.bam FBtr0070603 72 72 F 0 +input2.bam FBtr0070604 72 1 F 0 +input2.bam FBtr0070604 72 31 F 1 +input2.bam FBtr0070604 72 32 F 5 +input2.bam FBtr0070604 72 53 F 2 +input2.bam FBtr0070604 72 72 F 0 +input2.bam FBtr0070911 73 1 F 0 +input2.bam FBtr0070911 73 32 F 1 +input2.bam FBtr0070911 73 73 F 0 +input2.bam FBtr0078490 72 1 F 3 +input2.bam FBtr0078490 72 13 F 1 +input2.bam FBtr0078490 72 20 F 1 +input2.bam FBtr0078490 72 30 F 1 +input2.bam FBtr0078490 72 72 F 0 +input2.bam FBtr0078580 72 1 F 3 +input2.bam FBtr0078580 72 11 F 1 +input2.bam FBtr0078580 72 13 F 1 +input2.bam FBtr0078580 72 15 F 2 +input2.bam FBtr0078580 72 16 F 3 +input2.bam FBtr0078580 72 17 F 2 +input2.bam FBtr0078580 72 18 F 9 +input2.bam FBtr0078580 72 19 F 19 +input2.bam FBtr0078580 72 20 F 19 +input2.bam FBtr0078580 72 21 F 39 +input2.bam FBtr0078580 72 25 F 1 +input2.bam FBtr0078580 72 26 F 1 +input2.bam FBtr0078580 72 28 F 2 +input2.bam FBtr0078580 72 29 F 1 +input2.bam FBtr0078580 72 40 F 1 +input2.bam FBtr0078580 72 72 F 0 +input2.bam FBtr0078790 73 1 F 0 +input2.bam FBtr0078790 73 42 F 1 +input2.bam FBtr0078790 73 51 F 1 +input2.bam FBtr0078790 73 52 F 2 +input2.bam FBtr0078790 73 73 F 0 +input2.bam FBtr0079064 72 1 F 0 +input2.bam FBtr0079064 72 72 F 0 +input2.bam FBtr0079090 72 1 F 0 +input2.bam FBtr0079090 72 16 F 1 +input2.bam FBtr0079090 72 72 F 0 +input2.bam FBtr0079338 73 1 F 0 +input2.bam FBtr0079338 73 41 F 2 +input2.bam FBtr0079338 73 42 F 1 +input2.bam FBtr0079338 73 73 F 0 +input2.bam FBtr0079528 71 1 F 0 +input2.bam FBtr0079528 71 3 F 1 +input2.bam FBtr0079528 71 10 F 4 +input2.bam FBtr0079528 71 11 F 3 +input2.bam FBtr0079528 71 13 F 2 +input2.bam FBtr0079528 71 14 F 2 +input2.bam FBtr0079528 71 15 F 1 +input2.bam FBtr0079528 71 18 F 3 +input2.bam FBtr0079528 71 19 F 1 +input2.bam FBtr0079528 71 30 F 1 +input2.bam FBtr0079528 71 31 F 1 +input2.bam FBtr0079528 71 32 F 7 +input2.bam FBtr0079528 71 36 F 2 +input2.bam FBtr0079528 71 37 F 3 +input2.bam FBtr0079528 71 38 F 3 +input2.bam FBtr0079528 71 71 F 0 +input2.bam FBtr0079596 73 1 F 0 +input2.bam FBtr0079596 73 3 F 3 +input2.bam FBtr0079596 73 4 F 3 +input2.bam FBtr0079596 73 5 F 9 +input2.bam FBtr0079596 73 9 F 1 +input2.bam FBtr0079596 73 11 F 18 +input2.bam FBtr0079596 73 12 F 41 +input2.bam FBtr0079596 73 13 F 36 +input2.bam FBtr0079596 73 14 F 4 +input2.bam FBtr0079596 73 22 F 1 +input2.bam FBtr0079596 73 53 F 2 +input2.bam FBtr0079596 73 59 R 1 +input2.bam FBtr0079596 73 73 F 0 +input2.bam FBtr0079677 72 1 F 0 +input2.bam FBtr0079677 72 15 F 1 +input2.bam FBtr0079677 72 72 F 0 +input2.bam FBtr0079690 72 1 F 0 +input2.bam FBtr0079690 72 15 F 1 +input2.bam FBtr0079690 72 17 F 1 +input2.bam FBtr0079690 72 19 F 1 +input2.bam FBtr0079690 72 72 F 0 +input2.bam FBtr0079692 73 1 F 0 +input2.bam FBtr0079692 73 12 F 1 +input2.bam FBtr0079692 73 15 F 1 +input2.bam FBtr0079692 73 73 F 0 +input2.bam FBtr0079693 72 1 F 0 +input2.bam FBtr0079693 72 17 F 1 +input2.bam FBtr0079693 72 52 F 1 +input2.bam FBtr0079693 72 72 F 0 +input2.bam FBtr0079694 72 1 F 0 +input2.bam FBtr0079694 72 72 F 0 +input2.bam FBtr0079702 72 1 F 0 +input2.bam FBtr0079702 72 72 F 0 +input2.bam FBtr0079728 72 1 F 0 +input2.bam FBtr0079728 72 72 F 0 +input2.bam FBtr0079729 72 1 F 0 +input2.bam FBtr0079729 72 72 F 0 +input2.bam FBtr0079752 72 1 F 0 +input2.bam FBtr0079752 72 49 F 1 +input2.bam FBtr0079752 72 72 F 0 +input2.bam FBtr0079820 74 1 F 0 +input2.bam FBtr0079820 74 52 F 1 +input2.bam FBtr0079820 74 53 F 24 +input2.bam FBtr0079820 74 54 F 6 +input2.bam FBtr0079820 74 55 F 1 +input2.bam FBtr0079820 74 74 F 0 +input2.bam FBtr0080609 72 1 F 0 +input2.bam FBtr0080609 72 21 F 1 +input2.bam FBtr0080609 72 22 F 1 +input2.bam FBtr0080609 72 33 F 1 +input2.bam FBtr0080609 72 72 F 0 +input2.bam FBtr0080644 72 1 F 0 +input2.bam FBtr0080644 72 72 F 0 +input2.bam FBtr0080646 72 1 F 0 +input2.bam FBtr0080646 72 51 F 1 +input2.bam FBtr0080646 72 72 F 0 +input2.bam FBtr0080647 72 1 F 0 +input2.bam FBtr0080647 72 72 F 0 +input2.bam FBtr0080660 72 1 F 0 +input2.bam FBtr0080660 72 72 F 0 +input2.bam FBtr0080663 71 1 F 2 +input2.bam FBtr0080663 71 11 F 1 +input2.bam FBtr0080663 71 12 F 4 +input2.bam FBtr0080663 71 13 F 3 +input2.bam FBtr0080663 71 14 F 2 +input2.bam FBtr0080663 71 15 F 1 +input2.bam FBtr0080663 71 16 F 1 +input2.bam FBtr0080663 71 18 F 1 +input2.bam FBtr0080663 71 19 F 1 +input2.bam FBtr0080663 71 21 F 1 +input2.bam FBtr0080663 71 71 F 0 +input2.bam FBtr0080664 71 1 F 1 +input2.bam FBtr0080664 71 3 F 2 +input2.bam FBtr0080664 71 10 F 1 +input2.bam FBtr0080664 71 11 F 2 +input2.bam FBtr0080664 71 12 F 3 +input2.bam FBtr0080664 71 13 F 8 +input2.bam FBtr0080664 71 15 F 2 +input2.bam FBtr0080664 71 16 F 4 +input2.bam FBtr0080664 71 18 F 4 +input2.bam FBtr0080664 71 19 F 3 +input2.bam FBtr0080664 71 30 F 1 +input2.bam FBtr0080664 71 32 F 3 +input2.bam FBtr0080664 71 33 F 1 +input2.bam FBtr0080664 71 36 F 4 +input2.bam FBtr0080664 71 37 F 2 +input2.bam FBtr0080664 71 38 F 2 +input2.bam FBtr0080664 71 42 F 1 +input2.bam FBtr0080664 71 62 R 1 +input2.bam FBtr0080664 71 71 F 0 +input2.bam FBtr0080664 71 71 R 1 +input1.bam FBtr0070001 72 1 F 0 +input1.bam FBtr0070001 72 7 F 5 +input1.bam FBtr0070001 72 8 F 3 +input1.bam FBtr0070001 72 11 F 2 +input1.bam FBtr0070001 72 17 F 1 +input1.bam FBtr0070001 72 27 F 2 +input1.bam FBtr0070001 72 30 F 1 +input1.bam FBtr0070001 72 31 F 11 +input1.bam FBtr0070001 72 32 F 27 +input1.bam FBtr0070001 72 34 F 1 +input1.bam FBtr0070001 72 72 F 0 +input1.bam FBtr0070533 72 1 F 0 +input1.bam FBtr0070533 72 19 F 5 +input1.bam FBtr0070533 72 20 F 1 +input1.bam FBtr0070533 72 22 F 1 +input1.bam FBtr0070533 72 28 F 1 +input1.bam FBtr0070533 72 32 F 3 +input1.bam FBtr0070533 72 72 F 0 +input1.bam FBtr0070603 72 1 F 0 +input1.bam FBtr0070603 72 3 F 1 +input1.bam FBtr0070603 72 4 F 1 +input1.bam FBtr0070603 72 12 F 1 +input1.bam FBtr0070603 72 13 F 1 +input1.bam FBtr0070603 72 15 F 1 +input1.bam FBtr0070603 72 16 F 1 +input1.bam FBtr0070603 72 17 F 3 +input1.bam FBtr0070603 72 19 F 8 +input1.bam FBtr0070603 72 20 F 2 +input1.bam FBtr0070603 72 21 F 1 +input1.bam FBtr0070603 72 22 F 2 +input1.bam FBtr0070603 72 24 F 1 +input1.bam FBtr0070603 72 25 F 1 +input1.bam FBtr0070603 72 26 F 6 +input1.bam FBtr0070603 72 27 F 3 +input1.bam FBtr0070603 72 32 F 1 +input1.bam FBtr0070603 72 34 F 2 +input1.bam FBtr0070603 72 42 F 1 +input1.bam FBtr0070603 72 72 F 0 +input1.bam FBtr0070604 72 1 F 0 +input1.bam FBtr0070604 72 18 F 1 +input1.bam FBtr0070604 72 31 F 9 +input1.bam FBtr0070604 72 32 F 24 +input1.bam FBtr0070604 72 72 F 0 +input1.bam FBtr0070911 73 1 F 0 +input1.bam FBtr0070911 73 15 F 1 +input1.bam FBtr0070911 73 73 F 0 +input1.bam FBtr0078490 72 1 F 0 +input1.bam FBtr0078490 72 28 F 1 +input1.bam FBtr0078490 72 72 F 0 +input1.bam FBtr0078580 72 1 F 417 +input1.bam FBtr0078580 72 3 F 3 +input1.bam FBtr0078580 72 4 F 4 +input1.bam FBtr0078580 72 5 F 4 +input1.bam FBtr0078580 72 6 F 2 +input1.bam FBtr0078580 72 7 F 1 +input1.bam FBtr0078580 72 11 F 1 +input1.bam FBtr0078580 72 12 F 2 +input1.bam FBtr0078580 72 16 F 1 +input1.bam FBtr0078580 72 19 F 1 +input1.bam FBtr0078580 72 20 F 2 +input1.bam FBtr0078580 72 21 F 4 +input1.bam FBtr0078580 72 25 F 2 +input1.bam FBtr0078580 72 72 F 0 +input1.bam FBtr0078790 73 1 F 0 +input1.bam FBtr0078790 73 33 F 1 +input1.bam FBtr0078790 73 42 F 2 +input1.bam FBtr0078790 73 44 F 1 +input1.bam FBtr0078790 73 52 F 1 +input1.bam FBtr0078790 73 73 F 0 +input1.bam FBtr0079064 72 1 F 0 +input1.bam FBtr0079064 72 3 F 1 +input1.bam FBtr0079064 72 72 F 0 +input1.bam FBtr0079090 72 1 F 1 +input1.bam FBtr0079090 72 26 F 1 +input1.bam FBtr0079090 72 56 R 1 +input1.bam FBtr0079090 72 72 F 0 +input1.bam FBtr0079338 73 1 F 0 +input1.bam FBtr0079338 73 42 F 8 +input1.bam FBtr0079338 73 43 F 1 +input1.bam FBtr0079338 73 73 F 0 +input1.bam FBtr0079528 71 1 F 10 +input1.bam FBtr0079528 71 3 F 54 +input1.bam FBtr0079528 71 4 F 2 +input1.bam FBtr0079528 71 8 F 2 +input1.bam FBtr0079528 71 10 F 1 +input1.bam FBtr0079528 71 11 F 1 +input1.bam FBtr0079528 71 18 F 3 +input1.bam FBtr0079528 71 36 F 1 +input1.bam FBtr0079528 71 71 F 0 +input1.bam FBtr0079596 73 1 F 0 +input1.bam FBtr0079596 73 3 F 11 +input1.bam FBtr0079596 73 4 F 30 +input1.bam FBtr0079596 73 13 F 1 +input1.bam FBtr0079596 73 53 F 1 +input1.bam FBtr0079596 73 54 F 1 +input1.bam FBtr0079596 73 73 F 0 +input1.bam FBtr0079677 72 1 F 1 +input1.bam FBtr0079677 72 72 F 0 +input1.bam FBtr0079690 72 1 F 0 +input1.bam FBtr0079690 72 27 F 1 +input1.bam FBtr0079690 72 72 F 0 +input1.bam FBtr0079692 73 1 F 1 +input1.bam FBtr0079692 73 32 F 1 +input1.bam FBtr0079692 73 73 F 0 +input1.bam FBtr0079693 72 1 F 1 +input1.bam FBtr0079693 72 25 F 1 +input1.bam FBtr0079693 72 72 F 0 +input1.bam FBtr0079694 72 1 F 3 +input1.bam FBtr0079694 72 72 F 0 +input1.bam FBtr0079702 72 1 F 0 +input1.bam FBtr0079702 72 72 F 0 +input1.bam FBtr0079728 72 1 F 0 +input1.bam FBtr0079728 72 8 F 1 +input1.bam FBtr0079728 72 19 F 1 +input1.bam FBtr0079728 72 72 F 0 +input1.bam FBtr0079729 72 1 F 0 +input1.bam FBtr0079729 72 13 F 1 +input1.bam FBtr0079729 72 72 F 0 +input1.bam FBtr0079752 72 1 F 1 +input1.bam FBtr0079752 72 7 F 1 +input1.bam FBtr0079752 72 52 F 1 +input1.bam FBtr0079752 72 72 F 0 +input1.bam FBtr0079820 74 1 F 0 +input1.bam FBtr0079820 74 45 F 1 +input1.bam FBtr0079820 74 49 F 1 +input1.bam FBtr0079820 74 51 F 1 +input1.bam FBtr0079820 74 74 F 0 +input1.bam FBtr0080609 72 1 F 3 +input1.bam FBtr0080609 72 3 F 2 +input1.bam FBtr0080609 72 4 F 10 +input1.bam FBtr0080609 72 12 F 1 +input1.bam FBtr0080609 72 16 F 1 +input1.bam FBtr0080609 72 17 F 1 +input1.bam FBtr0080609 72 19 F 1 +input1.bam FBtr0080609 72 20 F 1 +input1.bam FBtr0080609 72 42 F 1 +input1.bam FBtr0080609 72 72 F 0 +input1.bam FBtr0080644 72 1 F 1 +input1.bam FBtr0080644 72 4 F 1 +input1.bam FBtr0080644 72 72 F 0 +input1.bam FBtr0080646 72 1 F 0 +input1.bam FBtr0080646 72 6 F 1 +input1.bam FBtr0080646 72 7 F 1 +input1.bam FBtr0080646 72 72 F 0 +input1.bam FBtr0080647 72 1 F 0 +input1.bam FBtr0080647 72 6 F 1 +input1.bam FBtr0080647 72 8 F 1 +input1.bam FBtr0080647 72 72 F 0 +input1.bam FBtr0080660 72 1 F 0 +input1.bam FBtr0080660 72 4 F 4 +input1.bam FBtr0080660 72 7 F 2 +input1.bam FBtr0080660 72 72 F 0 +input1.bam FBtr0080663 71 1 F 6 +input1.bam FBtr0080663 71 3 F 56 +input1.bam FBtr0080663 71 4 F 4 +input1.bam FBtr0080663 71 8 F 2 +input1.bam FBtr0080663 71 51 F 1 +input1.bam FBtr0080663 71 71 F 0 +input1.bam FBtr0080664 71 1 F 6 +input1.bam FBtr0080664 71 3 F 56 +input1.bam FBtr0080664 71 4 F 4 +input1.bam FBtr0080664 71 6 F 1 +input1.bam FBtr0080664 71 7 F 1 +input1.bam FBtr0080664 71 8 F 3 +input1.bam FBtr0080664 71 9 F 1 +input1.bam FBtr0080664 71 12 F 1 +input1.bam FBtr0080664 71 13 F 2 +input1.bam FBtr0080664 71 33 F 1 +input1.bam FBtr0080664 71 36 F 1 +input1.bam FBtr0080664 71 71 F 0 diff -r a96e6a7df2b7 -r 1827b74f872b test-data/global_merge_20-30.pdf Binary file test-data/global_merge_20-30.pdf has changed diff -r a96e6a7df2b7 -r 1827b74f872b test-data/mean20-30.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mean20-30.tab Mon Oct 23 08:29:39 2017 -0400 @@ -0,0 +1,350 @@ +Dataset Chromosome Chrom_length Coordinate Polarity Mean +input2.bam FBtr0070001 72 1 F 0 +input2.bam FBtr0070001 72 13 F 22.0 +input2.bam FBtr0070001 72 19 F 23.0 +input2.bam FBtr0070001 72 28 F 23.0 +input2.bam FBtr0070001 72 32 F 22.0 +input2.bam FBtr0070001 72 53 F 20.0 +input2.bam FBtr0070001 72 72 F 0 +input2.bam FBtr0070533 72 1 F 0 +input2.bam FBtr0070533 72 16 F 22.0 +input2.bam FBtr0070533 72 19 F 22.0 +input2.bam FBtr0070533 72 20 F 21.0 +input2.bam FBtr0070533 72 21 F 20.0 +input2.bam FBtr0070533 72 22 F 20.0 +input2.bam FBtr0070533 72 72 F 0 +input2.bam FBtr0070603 72 1 F 0 +input2.bam FBtr0070603 72 17 F 21.5 +input2.bam FBtr0070603 72 19 F 23.0 +input2.bam FBtr0070603 72 20 F 21.0 +input2.bam FBtr0070603 72 22 F 20.1 +input2.bam FBtr0070603 72 27 F 23.0 +input2.bam FBtr0070603 72 28 F 24.0 +input2.bam FBtr0070603 72 30 F 20.0 +input2.bam FBtr0070603 72 31 F 20.0 +input2.bam FBtr0070603 72 34 F 21.0 +input2.bam FBtr0070603 72 35 F 21.0 +input2.bam FBtr0070603 72 37 F 20.0 +input2.bam FBtr0070603 72 41 F 22.0 +input2.bam FBtr0070603 72 51 F 20.0 +input2.bam FBtr0070603 72 72 F 0 +input2.bam FBtr0070604 72 1 F 0 +input2.bam FBtr0070604 72 31 F 23.0 +input2.bam FBtr0070604 72 32 F 21.8 +input2.bam FBtr0070604 72 53 F 20.0 +input2.bam FBtr0070604 72 72 F 0 +input2.bam FBtr0070911 73 1 F 0 +input2.bam FBtr0070911 73 32 F 23.0 +input2.bam FBtr0070911 73 73 F 0 +input2.bam FBtr0078490 72 1 F 22.7 +input2.bam FBtr0078490 72 13 F 20.0 +input2.bam FBtr0078490 72 20 F 20.0 +input2.bam FBtr0078490 72 30 F 21.0 +input2.bam FBtr0078490 72 72 F 0 +input2.bam FBtr0078580 72 1 F 24.3 +input2.bam FBtr0078580 72 11 F 23.0 +input2.bam FBtr0078580 72 13 F 23.0 +input2.bam FBtr0078580 72 15 F 22.5 +input2.bam FBtr0078580 72 16 F 23.3 +input2.bam FBtr0078580 72 17 F 23.0 +input2.bam FBtr0078580 72 18 F 22.8 +input2.bam FBtr0078580 72 19 F 21.7 +input2.bam FBtr0078580 72 20 F 21.3 +input2.bam FBtr0078580 72 21 F 20.4 +input2.bam FBtr0078580 72 25 F 26.0 +input2.bam FBtr0078580 72 26 F 25.0 +input2.bam FBtr0078580 72 28 F 21.5 +input2.bam FBtr0078580 72 29 F 23.0 +input2.bam FBtr0078580 72 40 F 20.0 +input2.bam FBtr0078580 72 72 F 0 +input2.bam FBtr0078790 73 1 F 0 +input2.bam FBtr0078790 73 42 F 20.0 +input2.bam FBtr0078790 73 51 F 22.0 +input2.bam FBtr0078790 73 52 F 21.0 +input2.bam FBtr0078790 73 73 F 0 +input2.bam FBtr0079064 72 1 F 0 +input2.bam FBtr0079064 72 72 F 0 +input2.bam FBtr0079090 72 1 F 0 +input2.bam FBtr0079090 72 16 F 21.0 +input2.bam FBtr0079090 72 72 F 0 +input2.bam FBtr0079338 73 1 F 0 +input2.bam FBtr0079338 73 41 F 22.5 +input2.bam FBtr0079338 73 42 F 20.0 +input2.bam FBtr0079338 73 73 F 0 +input2.bam FBtr0079528 71 1 F 0 +input2.bam FBtr0079528 71 3 F 24.0 +input2.bam FBtr0079528 71 10 F 22.5 +input2.bam FBtr0079528 71 11 F 21.0 +input2.bam FBtr0079528 71 13 F 20.0 +input2.bam FBtr0079528 71 14 F 21.5 +input2.bam FBtr0079528 71 15 F 22.0 +input2.bam FBtr0079528 71 18 F 21.3 +input2.bam FBtr0079528 71 19 F 23.0 +input2.bam FBtr0079528 71 30 F 23.0 +input2.bam FBtr0079528 71 31 F 22.0 +input2.bam FBtr0079528 71 32 F 20.6 +input2.bam FBtr0079528 71 36 F 23.0 +input2.bam FBtr0079528 71 37 F 26.0 +input2.bam FBtr0079528 71 38 F 22.3 +input2.bam FBtr0079528 71 71 F 0 +input2.bam FBtr0079596 73 1 F 0 +input2.bam FBtr0079596 73 3 F 22.3 +input2.bam FBtr0079596 73 4 F 20.0 +input2.bam FBtr0079596 73 5 F 20.0 +input2.bam FBtr0079596 73 9 F 24.0 +input2.bam FBtr0079596 73 11 F 22.0 +input2.bam FBtr0079596 73 12 F 21.2 +input2.bam FBtr0079596 73 13 F 20.2 +input2.bam FBtr0079596 73 14 F 20.0 +input2.bam FBtr0079596 73 22 F 20.0 +input2.bam FBtr0079596 73 53 F 20.0 +input2.bam FBtr0079596 73 59 R 21.0 +input2.bam FBtr0079596 73 73 F 0 +input2.bam FBtr0079677 72 1 F 0 +input2.bam FBtr0079677 72 15 F 20.0 +input2.bam FBtr0079677 72 72 F 0 +input2.bam FBtr0079690 72 1 F 0 +input2.bam FBtr0079690 72 15 F 20.0 +input2.bam FBtr0079690 72 17 F 20.0 +input2.bam FBtr0079690 72 19 F 21.0 +input2.bam FBtr0079690 72 72 F 0 +input2.bam FBtr0079692 73 1 F 0 +input2.bam FBtr0079692 73 12 F 22.0 +input2.bam FBtr0079692 73 15 F 21.0 +input2.bam FBtr0079692 73 73 F 0 +input2.bam FBtr0079693 72 1 F 0 +input2.bam FBtr0079693 72 17 F 20.0 +input2.bam FBtr0079693 72 52 F 20.0 +input2.bam FBtr0079693 72 72 F 0 +input2.bam FBtr0079694 72 1 F 0 +input2.bam FBtr0079694 72 72 F 0 +input2.bam FBtr0079702 72 1 F 0 +input2.bam FBtr0079702 72 72 F 0 +input2.bam FBtr0079728 72 1 F 0 +input2.bam FBtr0079728 72 72 F 0 +input2.bam FBtr0079729 72 1 F 0 +input2.bam FBtr0079729 72 72 F 0 +input2.bam FBtr0079752 72 1 F 0 +input2.bam FBtr0079752 72 49 F 24.0 +input2.bam FBtr0079752 72 72 F 0 +input2.bam FBtr0079820 74 1 F 0 +input2.bam FBtr0079820 74 52 F 21.0 +input2.bam FBtr0079820 74 53 F 20.3 +input2.bam FBtr0079820 74 54 F 20.2 +input2.bam FBtr0079820 74 55 F 20.0 +input2.bam FBtr0079820 74 74 F 0 +input2.bam FBtr0080609 72 1 F 0 +input2.bam FBtr0080609 72 21 F 25.0 +input2.bam FBtr0080609 72 22 F 23.0 +input2.bam FBtr0080609 72 33 F 22.0 +input2.bam FBtr0080609 72 72 F 0 +input2.bam FBtr0080644 72 1 F 0 +input2.bam FBtr0080644 72 72 F 0 +input2.bam FBtr0080646 72 1 F 0 +input2.bam FBtr0080646 72 51 F 21.0 +input2.bam FBtr0080646 72 72 F 0 +input2.bam FBtr0080647 72 1 F 0 +input2.bam FBtr0080647 72 72 F 0 +input2.bam FBtr0080660 72 1 F 0 +input2.bam FBtr0080660 72 72 F 0 +input2.bam FBtr0080663 71 1 F 22.0 +input2.bam FBtr0080663 71 11 F 21.0 +input2.bam FBtr0080663 71 12 F 20.5 +input2.bam FBtr0080663 71 13 F 20.0 +input2.bam FBtr0080663 71 14 F 22.0 +input2.bam FBtr0080663 71 15 F 22.0 +input2.bam FBtr0080663 71 16 F 20.0 +input2.bam FBtr0080663 71 18 F 24.0 +input2.bam FBtr0080663 71 19 F 21.0 +input2.bam FBtr0080663 71 21 F 20.0 +input2.bam FBtr0080663 71 71 F 0 +input2.bam FBtr0080664 71 1 F 22.0 +input2.bam FBtr0080664 71 3 F 23.0 +input2.bam FBtr0080664 71 10 F 23.0 +input2.bam FBtr0080664 71 11 F 22.0 +input2.bam FBtr0080664 71 12 F 21.0 +input2.bam FBtr0080664 71 13 F 20.4 +input2.bam FBtr0080664 71 15 F 21.5 +input2.bam FBtr0080664 71 16 F 20.0 +input2.bam FBtr0080664 71 18 F 20.3 +input2.bam FBtr0080664 71 19 F 21.0 +input2.bam FBtr0080664 71 30 F 21.0 +input2.bam FBtr0080664 71 32 F 20.7 +input2.bam FBtr0080664 71 33 F 20.0 +input2.bam FBtr0080664 71 36 F 24.3 +input2.bam FBtr0080664 71 37 F 24.5 +input2.bam FBtr0080664 71 38 F 25.0 +input2.bam FBtr0080664 71 42 F 20.0 +input2.bam FBtr0080664 71 62 R 23.0 +input2.bam FBtr0080664 71 71 F 0 +input2.bam FBtr0080664 71 71 R 22.0 +input1.bam FBtr0070001 72 1 F 0 +input1.bam FBtr0070001 72 7 F 21.2 +input1.bam FBtr0070001 72 8 F 21.3 +input1.bam FBtr0070001 72 11 F 20.5 +input1.bam FBtr0070001 72 17 F 23.0 +input1.bam FBtr0070001 72 27 F 23.5 +input1.bam FBtr0070001 72 30 F 23.0 +input1.bam FBtr0070001 72 31 F 23.0 +input1.bam FBtr0070001 72 32 F 22.0 +input1.bam FBtr0070001 72 34 F 20.0 +input1.bam FBtr0070001 72 72 F 0 +input1.bam FBtr0070533 72 1 F 0 +input1.bam FBtr0070533 72 19 F 21.8 +input1.bam FBtr0070533 72 20 F 23.0 +input1.bam FBtr0070533 72 22 F 20.0 +input1.bam FBtr0070533 72 28 F 25.0 +input1.bam FBtr0070533 72 32 F 21.3 +input1.bam FBtr0070533 72 72 F 0 +input1.bam FBtr0070603 72 1 F 0 +input1.bam FBtr0070603 72 3 F 21.0 +input1.bam FBtr0070603 72 4 F 20.0 +input1.bam FBtr0070603 72 12 F 23.0 +input1.bam FBtr0070603 72 13 F 22.0 +input1.bam FBtr0070603 72 15 F 20.0 +input1.bam FBtr0070603 72 16 F 24.0 +input1.bam FBtr0070603 72 17 F 24.0 +input1.bam FBtr0070603 72 19 F 23.3 +input1.bam FBtr0070603 72 20 F 24.0 +input1.bam FBtr0070603 72 21 F 25.0 +input1.bam FBtr0070603 72 22 F 21.5 +input1.bam FBtr0070603 72 24 F 21.0 +input1.bam FBtr0070603 72 25 F 23.0 +input1.bam FBtr0070603 72 26 F 25.8 +input1.bam FBtr0070603 72 27 F 26.3 +input1.bam FBtr0070603 72 32 F 20.0 +input1.bam FBtr0070603 72 34 F 20.0 +input1.bam FBtr0070603 72 42 F 21.0 +input1.bam FBtr0070603 72 72 F 0 +input1.bam FBtr0070604 72 1 F 0 +input1.bam FBtr0070604 72 18 F 23.0 +input1.bam FBtr0070604 72 31 F 23.0 +input1.bam FBtr0070604 72 32 F 22.0 +input1.bam FBtr0070604 72 72 F 0 +input1.bam FBtr0070911 73 1 F 0 +input1.bam FBtr0070911 73 15 F 21.0 +input1.bam FBtr0070911 73 73 F 0 +input1.bam FBtr0078490 72 1 F 0 +input1.bam FBtr0078490 72 28 F 23.0 +input1.bam FBtr0078490 72 72 F 0 +input1.bam FBtr0078580 72 1 F 24.6 +input1.bam FBtr0078580 72 3 F 22.0 +input1.bam FBtr0078580 72 4 F 25.3 +input1.bam FBtr0078580 72 5 F 21.5 +input1.bam FBtr0078580 72 6 F 21.0 +input1.bam FBtr0078580 72 7 F 22.0 +input1.bam FBtr0078580 72 11 F 23.0 +input1.bam FBtr0078580 72 12 F 22.5 +input1.bam FBtr0078580 72 16 F 23.0 +input1.bam FBtr0078580 72 19 F 24.0 +input1.bam FBtr0078580 72 20 F 21.0 +input1.bam FBtr0078580 72 21 F 20.3 +input1.bam FBtr0078580 72 25 F 27.5 +input1.bam FBtr0078580 72 72 F 0 +input1.bam FBtr0078790 73 1 F 0 +input1.bam FBtr0078790 73 33 F 23.0 +input1.bam FBtr0078790 73 42 F 22.0 +input1.bam FBtr0078790 73 44 F 20.0 +input1.bam FBtr0078790 73 52 F 20.0 +input1.bam FBtr0078790 73 73 F 0 +input1.bam FBtr0079064 72 1 F 0 +input1.bam FBtr0079064 72 3 F 21.0 +input1.bam FBtr0079064 72 72 F 0 +input1.bam FBtr0079090 72 1 F 28.0 +input1.bam FBtr0079090 72 26 F 24.0 +input1.bam FBtr0079090 72 56 R 21.0 +input1.bam FBtr0079090 72 72 F 0 +input1.bam FBtr0079338 73 1 F 0 +input1.bam FBtr0079338 73 42 F 21.8 +input1.bam FBtr0079338 73 43 F 21.0 +input1.bam FBtr0079338 73 73 F 0 +input1.bam FBtr0079528 71 1 F 25.3 +input1.bam FBtr0079528 71 3 F 23.7 +input1.bam FBtr0079528 71 4 F 24.0 +input1.bam FBtr0079528 71 8 F 22.0 +input1.bam FBtr0079528 71 10 F 21.0 +input1.bam FBtr0079528 71 11 F 22.0 +input1.bam FBtr0079528 71 18 F 20.3 +input1.bam FBtr0079528 71 36 F 20.0 +input1.bam FBtr0079528 71 71 F 0 +input1.bam FBtr0079596 73 1 F 0 +input1.bam FBtr0079596 73 3 F 23.1 +input1.bam FBtr0079596 73 4 F 21.6 +input1.bam FBtr0079596 73 13 F 21.0 +input1.bam FBtr0079596 73 53 F 20.0 +input1.bam FBtr0079596 73 54 F 20.0 +input1.bam FBtr0079596 73 73 F 0 +input1.bam FBtr0079677 72 1 F 23.0 +input1.bam FBtr0079677 72 72 F 0 +input1.bam FBtr0079690 72 1 F 0 +input1.bam FBtr0079690 72 27 F 25.0 +input1.bam FBtr0079690 72 72 F 0 +input1.bam FBtr0079692 73 1 F 23.0 +input1.bam FBtr0079692 73 32 F 20.0 +input1.bam FBtr0079692 73 73 F 0 +input1.bam FBtr0079693 72 1 F 24.0 +input1.bam FBtr0079693 72 25 F 23.0 +input1.bam FBtr0079693 72 72 F 0 +input1.bam FBtr0079694 72 1 F 24.0 +input1.bam FBtr0079694 72 72 F 0 +input1.bam FBtr0079702 72 1 F 0 +input1.bam FBtr0079702 72 72 F 0 +input1.bam FBtr0079728 72 1 F 0 +input1.bam FBtr0079728 72 8 F 20.0 +input1.bam FBtr0079728 72 19 F 24.0 +input1.bam FBtr0079728 72 72 F 0 +input1.bam FBtr0079729 72 1 F 0 +input1.bam FBtr0079729 72 13 F 22.0 +input1.bam FBtr0079729 72 72 F 0 +input1.bam FBtr0079752 72 1 F 24.0 +input1.bam FBtr0079752 72 7 F 20.0 +input1.bam FBtr0079752 72 52 F 20.0 +input1.bam FBtr0079752 72 72 F 0 +input1.bam FBtr0079820 74 1 F 0 +input1.bam FBtr0079820 74 45 F 20.0 +input1.bam FBtr0079820 74 49 F 24.0 +input1.bam FBtr0079820 74 51 F 20.0 +input1.bam FBtr0079820 74 74 F 0 +input1.bam FBtr0080609 72 1 F 22.3 +input1.bam FBtr0080609 72 3 F 21.0 +input1.bam FBtr0080609 72 4 F 20.0 +input1.bam FBtr0080609 72 12 F 23.0 +input1.bam FBtr0080609 72 16 F 23.0 +input1.bam FBtr0080609 72 17 F 24.0 +input1.bam FBtr0080609 72 19 F 26.0 +input1.bam FBtr0080609 72 20 F 25.0 +input1.bam FBtr0080609 72 42 F 21.0 +input1.bam FBtr0080609 72 72 F 0 +input1.bam FBtr0080644 72 1 F 27.0 +input1.bam FBtr0080644 72 4 F 24.0 +input1.bam FBtr0080644 72 72 F 0 +input1.bam FBtr0080646 72 1 F 0 +input1.bam FBtr0080646 72 6 F 22.0 +input1.bam FBtr0080646 72 7 F 21.0 +input1.bam FBtr0080646 72 72 F 0 +input1.bam FBtr0080647 72 1 F 0 +input1.bam FBtr0080647 72 6 F 22.0 +input1.bam FBtr0080647 72 8 F 20.0 +input1.bam FBtr0080647 72 72 F 0 +input1.bam FBtr0080660 72 1 F 0 +input1.bam FBtr0080660 72 4 F 24.0 +input1.bam FBtr0080660 72 7 F 21.0 +input1.bam FBtr0080660 72 72 F 0 +input1.bam FBtr0080663 71 1 F 26.0 +input1.bam FBtr0080663 71 3 F 23.7 +input1.bam FBtr0080663 71 4 F 23.3 +input1.bam FBtr0080663 71 8 F 20.0 +input1.bam FBtr0080663 71 51 F 20.0 +input1.bam FBtr0080663 71 71 F 0 +input1.bam FBtr0080664 71 1 F 24.7 +input1.bam FBtr0080664 71 3 F 23.8 +input1.bam FBtr0080664 71 4 F 23.5 +input1.bam FBtr0080664 71 6 F 23.0 +input1.bam FBtr0080664 71 7 F 21.0 +input1.bam FBtr0080664 71 8 F 21.0 +input1.bam FBtr0080664 71 9 F 20.0 +input1.bam FBtr0080664 71 12 F 20.0 +input1.bam FBtr0080664 71 13 F 20.0 +input1.bam FBtr0080664 71 33 F 20.0 +input1.bam FBtr0080664 71 36 F 21.0 +input1.bam FBtr0080664 71 71 F 0 diff -r a96e6a7df2b7 -r 1827b74f872b test-data/size20-30.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/size20-30.tab Mon Oct 23 08:29:39 2017 -0400 @@ -0,0 +1,263 @@ +Dataset Chromosome Polarity Size Counts +input1.bam FBtr0070001 F 20 4 +input1.bam FBtr0070001 F 21 4 +input1.bam FBtr0070001 F 22 29 +input1.bam FBtr0070001 F 23 15 +input1.bam FBtr0070001 F 24 1 +input1.bam FBtr0070001 R 20 0 +input1.bam FBtr0070001 R 21 0 +input1.bam FBtr0070001 R 22 0 +input1.bam FBtr0070001 R 23 0 +input1.bam FBtr0070001 R 24 0 +input1.bam FBtr0070533 F 20 2 +input1.bam FBtr0070533 F 21 2 +input1.bam FBtr0070533 F 22 4 +input1.bam FBtr0070533 F 23 2 +input1.bam FBtr0070533 F 24 0 +input1.bam FBtr0070533 F 25 1 +input1.bam FBtr0070533 R 20 0 +input1.bam FBtr0070533 R 21 0 +input1.bam FBtr0070533 R 22 0 +input1.bam FBtr0070533 R 23 0 +input1.bam FBtr0070533 R 24 0 +input1.bam FBtr0070533 R 25 0 +input1.bam FBtr0070603 F 20 6 +input1.bam FBtr0070603 F 21 3 +input1.bam FBtr0070603 F 22 3 +input1.bam FBtr0070603 F 23 10 +input1.bam FBtr0070603 F 24 2 +input1.bam FBtr0070603 F 25 5 +input1.bam FBtr0070603 F 26 5 +input1.bam FBtr0070603 F 27 3 +input1.bam FBtr0070603 R 20 0 +input1.bam FBtr0070603 R 21 0 +input1.bam FBtr0070603 R 22 0 +input1.bam FBtr0070603 R 23 0 +input1.bam FBtr0070603 R 24 0 +input1.bam FBtr0070603 R 25 0 +input1.bam FBtr0070603 R 26 0 +input1.bam FBtr0070603 R 27 0 +input1.bam FBtr0070604 F 21 1 +input1.bam FBtr0070604 F 22 23 +input1.bam FBtr0070604 F 23 10 +input1.bam FBtr0070604 R 21 0 +input1.bam FBtr0070604 R 22 0 +input1.bam FBtr0070604 R 23 0 +input1.bam FBtr0070911 F 21 1 +input1.bam FBtr0070911 R 21 0 +input1.bam FBtr0078490 F 23 1 +input1.bam FBtr0078490 R 23 0 +input1.bam FBtr0078580 F 20 9 +input1.bam FBtr0078580 F 21 5 +input1.bam FBtr0078580 F 22 13 +input1.bam FBtr0078580 F 23 5 +input1.bam FBtr0078580 F 24 180 +input1.bam FBtr0078580 F 25 212 +input1.bam FBtr0078580 F 26 1 +input1.bam FBtr0078580 F 27 2 +input1.bam FBtr0078580 F 28 17 +input1.bam FBtr0078580 R 20 0 +input1.bam FBtr0078580 R 21 0 +input1.bam FBtr0078580 R 22 0 +input1.bam FBtr0078580 R 23 0 +input1.bam FBtr0078580 R 24 0 +input1.bam FBtr0078580 R 25 0 +input1.bam FBtr0078580 R 26 0 +input1.bam FBtr0078580 R 27 0 +input1.bam FBtr0078580 R 28 0 +input1.bam FBtr0078790 F 20 2 +input1.bam FBtr0078790 F 21 0 +input1.bam FBtr0078790 F 22 2 +input1.bam FBtr0078790 F 23 1 +input1.bam FBtr0078790 R 20 0 +input1.bam FBtr0078790 R 21 0 +input1.bam FBtr0078790 R 22 0 +input1.bam FBtr0078790 R 23 0 +input1.bam FBtr0079064 F 21 1 +input1.bam FBtr0079064 R 21 0 +input1.bam FBtr0079090 F 21 0 +input1.bam FBtr0079090 F 22 0 +input1.bam FBtr0079090 F 23 0 +input1.bam FBtr0079090 F 24 1 +input1.bam FBtr0079090 F 25 0 +input1.bam FBtr0079090 F 26 0 +input1.bam FBtr0079090 F 27 0 +input1.bam FBtr0079090 F 28 1 +input1.bam FBtr0079090 R 21 1 +input1.bam FBtr0079090 R 22 0 +input1.bam FBtr0079090 R 23 0 +input1.bam FBtr0079090 R 24 0 +input1.bam FBtr0079090 R 25 0 +input1.bam FBtr0079090 R 26 0 +input1.bam FBtr0079090 R 27 0 +input1.bam FBtr0079090 R 28 0 +input1.bam FBtr0079338 F 21 3 +input1.bam FBtr0079338 F 22 6 +input1.bam FBtr0079338 R 21 0 +input1.bam FBtr0079338 R 22 0 +input1.bam FBtr0079528 F 20 12 +input1.bam FBtr0079528 F 21 3 +input1.bam FBtr0079528 F 22 2 +input1.bam FBtr0079528 F 23 3 +input1.bam FBtr0079528 F 24 36 +input1.bam FBtr0079528 F 25 8 +input1.bam FBtr0079528 F 26 5 +input1.bam FBtr0079528 F 27 2 +input1.bam FBtr0079528 F 28 2 +input1.bam FBtr0079528 F 29 1 +input1.bam FBtr0079528 R 20 0 +input1.bam FBtr0079528 R 21 0 +input1.bam FBtr0079528 R 22 0 +input1.bam FBtr0079528 R 23 0 +input1.bam FBtr0079528 R 24 0 +input1.bam FBtr0079528 R 25 0 +input1.bam FBtr0079528 R 26 0 +input1.bam FBtr0079528 R 27 0 +input1.bam FBtr0079528 R 28 0 +input1.bam FBtr0079528 R 29 0 +input1.bam FBtr0079596 F 20 13 +input1.bam FBtr0079596 F 21 3 +input1.bam FBtr0079596 F 22 16 +input1.bam FBtr0079596 F 23 8 +input1.bam FBtr0079596 F 24 0 +input1.bam FBtr0079596 F 25 0 +input1.bam FBtr0079596 F 26 3 +input1.bam FBtr0079596 F 27 1 +input1.bam FBtr0079596 R 20 0 +input1.bam FBtr0079596 R 21 0 +input1.bam FBtr0079596 R 22 0 +input1.bam FBtr0079596 R 23 0 +input1.bam FBtr0079596 R 24 0 +input1.bam FBtr0079596 R 25 0 +input1.bam FBtr0079596 R 26 0 +input1.bam FBtr0079596 R 27 0 +input1.bam FBtr0079677 F 23 1 +input1.bam FBtr0079677 R 23 0 +input1.bam FBtr0079690 F 25 1 +input1.bam FBtr0079690 R 25 0 +input1.bam FBtr0079692 F 20 1 +input1.bam FBtr0079692 F 21 0 +input1.bam FBtr0079692 F 22 0 +input1.bam FBtr0079692 F 23 1 +input1.bam FBtr0079692 R 20 0 +input1.bam FBtr0079692 R 21 0 +input1.bam FBtr0079692 R 22 0 +input1.bam FBtr0079692 R 23 0 +input1.bam FBtr0079693 F 23 1 +input1.bam FBtr0079693 F 24 1 +input1.bam FBtr0079693 R 23 0 +input1.bam FBtr0079693 R 24 0 +input1.bam FBtr0079694 F 23 1 +input1.bam FBtr0079694 F 24 1 +input1.bam FBtr0079694 F 25 1 +input1.bam FBtr0079694 R 23 0 +input1.bam FBtr0079694 R 24 0 +input1.bam FBtr0079694 R 25 0 +input1.bam FBtr0079728 F 20 1 +input1.bam FBtr0079728 F 21 0 +input1.bam FBtr0079728 F 22 0 +input1.bam FBtr0079728 F 23 0 +input1.bam FBtr0079728 F 24 1 +input1.bam FBtr0079728 R 20 0 +input1.bam FBtr0079728 R 21 0 +input1.bam FBtr0079728 R 22 0 +input1.bam FBtr0079728 R 23 0 +input1.bam FBtr0079728 R 24 0 +input1.bam FBtr0079729 F 22 1 +input1.bam FBtr0079729 R 22 0 +input1.bam FBtr0079752 F 20 2 +input1.bam FBtr0079752 F 21 0 +input1.bam FBtr0079752 F 22 0 +input1.bam FBtr0079752 F 23 0 +input1.bam FBtr0079752 F 24 1 +input1.bam FBtr0079752 R 20 0 +input1.bam FBtr0079752 R 21 0 +input1.bam FBtr0079752 R 22 0 +input1.bam FBtr0079752 R 23 0 +input1.bam FBtr0079752 R 24 0 +input1.bam FBtr0079820 F 20 2 +input1.bam FBtr0079820 F 21 0 +input1.bam FBtr0079820 F 22 0 +input1.bam FBtr0079820 F 23 0 +input1.bam FBtr0079820 F 24 1 +input1.bam FBtr0079820 R 20 0 +input1.bam FBtr0079820 R 21 0 +input1.bam FBtr0079820 R 22 0 +input1.bam FBtr0079820 R 23 0 +input1.bam FBtr0079820 R 24 0 +input1.bam FBtr0080609 F 20 10 +input1.bam FBtr0080609 F 21 4 +input1.bam FBtr0080609 F 22 0 +input1.bam FBtr0080609 F 23 4 +input1.bam FBtr0080609 F 24 1 +input1.bam FBtr0080609 F 25 1 +input1.bam FBtr0080609 F 26 1 +input1.bam FBtr0080609 R 20 0 +input1.bam FBtr0080609 R 21 0 +input1.bam FBtr0080609 R 22 0 +input1.bam FBtr0080609 R 23 0 +input1.bam FBtr0080609 R 24 0 +input1.bam FBtr0080609 R 25 0 +input1.bam FBtr0080609 R 26 0 +input1.bam FBtr0080644 F 24 1 +input1.bam FBtr0080644 F 25 0 +input1.bam FBtr0080644 F 26 0 +input1.bam FBtr0080644 F 27 1 +input1.bam FBtr0080644 R 24 0 +input1.bam FBtr0080644 R 25 0 +input1.bam FBtr0080644 R 26 0 +input1.bam FBtr0080644 R 27 0 +input1.bam FBtr0080646 F 21 1 +input1.bam FBtr0080646 F 22 1 +input1.bam FBtr0080646 R 21 0 +input1.bam FBtr0080646 R 22 0 +input1.bam FBtr0080647 F 20 1 +input1.bam FBtr0080647 F 21 0 +input1.bam FBtr0080647 F 22 1 +input1.bam FBtr0080647 R 20 0 +input1.bam FBtr0080647 R 21 0 +input1.bam FBtr0080647 R 22 0 +input1.bam FBtr0080660 F 21 2 +input1.bam FBtr0080660 F 22 0 +input1.bam FBtr0080660 F 23 0 +input1.bam FBtr0080660 F 24 4 +input1.bam FBtr0080660 R 21 0 +input1.bam FBtr0080660 R 22 0 +input1.bam FBtr0080660 R 23 0 +input1.bam FBtr0080660 R 24 0 +input1.bam FBtr0080663 F 20 10 +input1.bam FBtr0080663 F 21 0 +input1.bam FBtr0080663 F 22 1 +input1.bam FBtr0080663 F 23 7 +input1.bam FBtr0080663 F 24 33 +input1.bam FBtr0080663 F 25 10 +input1.bam FBtr0080663 F 26 6 +input1.bam FBtr0080663 F 27 0 +input1.bam FBtr0080663 F 28 2 +input1.bam FBtr0080663 R 20 0 +input1.bam FBtr0080663 R 21 0 +input1.bam FBtr0080663 R 22 0 +input1.bam FBtr0080663 R 23 0 +input1.bam FBtr0080663 R 24 0 +input1.bam FBtr0080663 R 25 0 +input1.bam FBtr0080663 R 26 0 +input1.bam FBtr0080663 R 27 0 +input1.bam FBtr0080663 R 28 0 +input1.bam FBtr0080664 F 20 12 +input1.bam FBtr0080664 F 21 5 +input1.bam FBtr0080664 F 22 0 +input1.bam FBtr0080664 F 23 11 +input1.bam FBtr0080664 F 24 33 +input1.bam FBtr0080664 F 25 10 +input1.bam FBtr0080664 F 26 4 +input1.bam FBtr0080664 F 27 0 +input1.bam FBtr0080664 F 28 2 +input1.bam FBtr0080664 R 20 0 +input1.bam FBtr0080664 R 21 0 +input1.bam FBtr0080664 R 22 0 +input1.bam FBtr0080664 R 23 0 +input1.bam FBtr0080664 R 24 0 +input1.bam FBtr0080664 R 25 0 +input1.bam FBtr0080664 R 26 0 +input1.bam FBtr0080664 R 27 0 +input1.bam FBtr0080664 R 28 0