1 | scramble.py |
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2 | setup.cfg |
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3 | lib/psyco_full.py |
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4 | lib/bx/__init__.py |
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5 | lib/bx/_seqmapping.c |
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6 | lib/bx/binned_array.py |
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7 | lib/bx/binned_array_tests.py |
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8 | lib/bx/bitset.c |
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9 | lib/bx/bitset_builders.py |
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10 | lib/bx/bitset_tests.py |
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11 | lib/bx/bitset_utils.py |
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12 | lib/bx/filter.py |
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13 | lib/bx/gene_reader.py |
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14 | lib/bx/interval_index_file.py |
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15 | lib/bx/interval_index_file_tests.py |
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16 | lib/bx/seqmapping.py |
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17 | lib/bx/seqmapping_tests.py |
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18 | lib/bx/wiggle.py |
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19 | lib/bx/wiggle_tests.py |
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20 | lib/bx/align/__init__.py |
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21 | lib/bx/align/_core.c |
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22 | lib/bx/align/axt.py |
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23 | lib/bx/align/core.py |
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24 | lib/bx/align/lav.py |
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25 | lib/bx/align/lav_tests.py |
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26 | lib/bx/align/maf.py |
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27 | lib/bx/align/maf_tests.py |
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28 | lib/bx/align/score.py |
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29 | lib/bx/align/score_tests.py |
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30 | lib/bx/align/sitemask/__init__.py |
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31 | lib/bx/align/sitemask/_cpg.c |
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32 | lib/bx/align/sitemask/core.py |
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33 | lib/bx/align/sitemask/cpg.py |
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34 | lib/bx/align/sitemask/find_cpg.c |
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35 | lib/bx/align/sitemask/quality.py |
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36 | lib/bx/align/sitemask/sitemask_tests.py |
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37 | lib/bx/align/tools/__init__.py |
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38 | lib/bx/align/tools/chop.py |
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39 | lib/bx/align/tools/fuse.py |
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40 | lib/bx/align/tools/thread.py |
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41 | lib/bx/align/tools/tile.py |
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42 | lib/bx/arrays/__init__.py |
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43 | lib/bx/arrays/array_tree.c |
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44 | lib/bx/arrays/array_tree_tests.py |
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45 | lib/bx/arrays/bed.c |
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46 | lib/bx/arrays/wiggle.c |
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47 | lib/bx/cookbook/__init__.py |
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48 | lib/bx/cookbook/attribute.py |
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49 | lib/bx/cookbook/doc_optparse.py |
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50 | lib/bx/cookbook/progress_bar.py |
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51 | lib/bx/intervals/__init__.py |
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52 | lib/bx/intervals/cluster.c |
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53 | lib/bx/intervals/cluster_tests.py |
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54 | lib/bx/intervals/intersection.c |
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55 | lib/bx/intervals/intersection_tests.py |
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56 | lib/bx/intervals/io.py |
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57 | lib/bx/intervals/random.py |
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58 | lib/bx/intervals/operations/__init__.py |
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59 | lib/bx/intervals/operations/base_coverage.py |
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60 | lib/bx/intervals/operations/complement.py |
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61 | lib/bx/intervals/operations/concat.py |
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62 | lib/bx/intervals/operations/coverage.py |
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63 | lib/bx/intervals/operations/find_clusters.py |
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64 | lib/bx/intervals/operations/intersect.py |
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65 | lib/bx/intervals/operations/join.py |
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66 | lib/bx/intervals/operations/merge.py |
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67 | lib/bx/intervals/operations/quicksect.py |
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68 | lib/bx/intervals/operations/subtract.py |
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69 | lib/bx/intseq/__init__.py |
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70 | lib/bx/intseq/ngramcount.c |
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71 | lib/bx/misc/__init__.py |
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72 | lib/bx/misc/_seekbzip2.c |
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73 | lib/bx/misc/binary_file.py |
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74 | lib/bx/misc/cdb.py |
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75 | lib/bx/misc/cdb_tests.py |
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76 | lib/bx/misc/filecache.py |
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77 | lib/bx/misc/filecache_tests.py |
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78 | lib/bx/misc/readlengths.py |
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79 | lib/bx/misc/seekbzip2.py |
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80 | lib/bx/misc/seekbzip2_tests.py |
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81 | lib/bx/misc/seeklzop.py |
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82 | lib/bx/misc/seeklzop_tests.py |
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83 | lib/bx/motif/__init__.py |
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84 | lib/bx/motif/_pwm.c |
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85 | lib/bx/motif/pwm.py |
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86 | lib/bx/motif/pwm_tests.py |
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87 | lib/bx/motif/io/__init__.py |
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88 | lib/bx/motif/io/transfac.py |
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89 | lib/bx/motif/io/transfac_tests.py |
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90 | lib/bx/motif/logo/__init__.py |
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91 | lib/bx/phylo/__init__.py |
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92 | lib/bx/phylo/newick.py |
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93 | lib/bx/phylo/newick_tests.py |
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94 | lib/bx/phylo/phast.py |
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95 | lib/bx/phylo/phast_tests.py |
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96 | lib/bx/pwm/__init__.py |
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97 | lib/bx/pwm/_position_weight_matrix.c |
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98 | lib/bx/pwm/bed_score_aligned_pwm.py |
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99 | lib/bx/pwm/bed_score_aligned_string.py |
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100 | lib/bx/pwm/maf_select_motifs.py |
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101 | lib/bx/pwm/position_weight_matrix.py |
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102 | lib/bx/pwm/pwm_score_maf.py |
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103 | lib/bx/pwm/pwm_score_motifs.py |
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104 | lib/bx/pwm/pwm_score_positions.py |
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105 | lib/bx/pwm/pwm_tests.py |
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106 | lib/bx/seq/__init__.py |
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107 | lib/bx/seq/_nib.c |
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108 | lib/bx/seq/_twobit.c |
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109 | lib/bx/seq/core.py |
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110 | lib/bx/seq/fasta.py |
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111 | lib/bx/seq/fasta_tests.py |
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112 | lib/bx/seq/nib.py |
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113 | lib/bx/seq/nib_tests.py |
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114 | lib/bx/seq/qdna.py |
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115 | lib/bx/seq/qdna_tests.py |
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116 | lib/bx/seq/seq.py |
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117 | lib/bx/seq/seq_tests.py |
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118 | lib/bx/seq/twobit.py |
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119 | lib/bx/seq/twobit_tests.py |
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120 | lib/bx/tabular/__init__.py |
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121 | lib/bx/tabular/io.py |
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122 | lib/bx_extras/__init__.py |
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123 | lib/bx_extras/fpconst.py |
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124 | lib/bx_extras/lrucache.py |
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125 | lib/bx_extras/pstat.py |
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126 | lib/bx_extras/pyparsing.py |
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127 | lib/bx_extras/stats.py |
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128 | lib/bx_python.egg-info/PKG-INFO |
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129 | lib/bx_python.egg-info/SOURCES.txt |
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130 | lib/bx_python.egg-info/dependency_links.txt |
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131 | lib/bx_python.egg-info/not-zip-safe |
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132 | lib/bx_python.egg-info/top_level.txt |
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133 | scripts/aggregate_scores_in_intervals.py |
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134 | scripts/align_print_template.py |
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135 | scripts/axt_extract_ranges.py |
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136 | scripts/axt_to_fasta.py |
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137 | scripts/axt_to_lav.py |
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138 | scripts/axt_to_maf.py |
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139 | scripts/bed_build_windows.py |
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140 | scripts/bed_complement.py |
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141 | scripts/bed_count_by_interval.py |
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142 | scripts/bed_count_overlapping.py |
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143 | scripts/bed_coverage.py |
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144 | scripts/bed_coverage_by_interval.py |
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145 | scripts/bed_diff_basewise_summary.py |
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146 | scripts/bed_intersect.py |
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147 | scripts/bed_intersect_basewise.py |
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148 | scripts/bed_merge_overlapping.py |
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149 | scripts/bed_rand_intersect.py |
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150 | scripts/bed_subtract_basewise.py |
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151 | scripts/div_snp_table_chr.py |
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152 | scripts/find_in_sorted_file.py |
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153 | scripts/gene_fourfold_sites.py |
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154 | scripts/get_scores_in_intervals.py |
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155 | scripts/int_seqs_to_char_strings.py |
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156 | scripts/interval_count_intersections.py |
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157 | scripts/interval_join.py |
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158 | scripts/lav_to_axt.py |
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159 | scripts/lav_to_maf.py |
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160 | scripts/line_select.py |
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161 | scripts/lzop_build_offset_table.py |
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162 | scripts/mMK_bitset.py |
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163 | scripts/maf_build_index.py |
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164 | scripts/maf_chop.py |
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165 | scripts/maf_chunk.py |
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166 | scripts/maf_col_counts.py |
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167 | scripts/maf_col_counts_all.py |
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168 | scripts/maf_count.py |
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169 | scripts/maf_covered_regions.py |
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170 | scripts/maf_div_sites.py |
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171 | scripts/maf_drop_overlapping.py |
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172 | scripts/maf_extract_chrom_ranges.py |
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173 | scripts/maf_extract_ranges.py |
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174 | scripts/maf_extract_ranges_indexed.py |
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175 | scripts/maf_filter.py |
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176 | scripts/maf_filter_max_wc.py |
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177 | scripts/maf_gap_frequency.py |
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178 | scripts/maf_gc_content.py |
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179 | scripts/maf_interval_alignibility.py |
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180 | scripts/maf_limit_to_species.py |
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181 | scripts/maf_mapping_word_frequency.py |
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182 | scripts/maf_mask_cpg.py |
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183 | scripts/maf_mean_length_ungapped_piece.py |
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184 | scripts/maf_percent_columns_matching.py |
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185 | scripts/maf_percent_identity.py |
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186 | scripts/maf_print_chroms.py |
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187 | scripts/maf_print_scores.py |
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188 | scripts/maf_randomize.py |
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189 | scripts/maf_region_coverage_by_src.py |
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190 | scripts/maf_select.py |
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191 | scripts/maf_shuffle_columns.py |
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192 | scripts/maf_species_in_all_files.py |
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193 | scripts/maf_split_by_src.py |
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194 | scripts/maf_thread_for_species.py |
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195 | scripts/maf_tile.py |
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196 | scripts/maf_tile_2.py |
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197 | scripts/maf_to_axt.py |
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198 | scripts/maf_to_concat_fasta.py |
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199 | scripts/maf_to_fasta.py |
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200 | scripts/maf_to_int_seqs.py |
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201 | scripts/maf_translate_chars.py |
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202 | scripts/maf_truncate.py |
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203 | scripts/maf_word_frequency.py |
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204 | scripts/mask_quality.py |
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205 | scripts/nib_chrom_intervals_to_fasta.py |
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206 | scripts/nib_intervals_to_fasta.py |
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207 | scripts/nib_length.py |
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208 | scripts/one_field_per_line.py |
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209 | scripts/prefix_lines.py |
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210 | scripts/pretty_table.py |
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211 | scripts/qv_to_bqv.py |
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212 | scripts/random_lines.py |
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213 | scripts/table_add_column.py |
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214 | scripts/table_filter.py |
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215 | scripts/tfloc_summary.py |
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216 | scripts/ucsc_gene_table_to_intervals.py |
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217 | scripts/wiggle_to_array_tree.py |
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218 | scripts/wiggle_to_binned_array.py |
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219 | scripts/wiggle_to_chr_binned_array.py |
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220 | scripts/wiggle_to_simple.py |
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221 | src/binBits.c |
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222 | src/cluster.c |
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223 | src/pwm_utils.c |
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224 | src/bunzip/micro-bunzip.c |
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225 | src/kent/bits.c |
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226 | src/kent/common.c |
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