SYMBOL INDEX (420 symbols across 53 files)

FILE: deeptools/SES_scaleFactor.py
  function estimateScaleFactor (line 15) | def estimateScaleFactor(bamFilesList, binLength, numberOfSamples,
  class Tester (line 187) | class Tester(object):
    method __init__ (line 189) | def __init__(self):

FILE: deeptools/alignmentSieve.py
  function parseArguments (line 14) | def parseArguments():
  function shiftRead (line 155) | def shiftRead(b, chromDict, args):
  function filterWorker (line 210) | def filterWorker(arglist):
  function convertBED (line 348) | def convertBED(oname, tmpFiles, chromDict):
  function main (line 377) | def main(args=None):

FILE: deeptools/bamCompare.py
  function parseArguments (line 20) | def parseArguments():
  function getRequiredArgs (line 55) | def getRequiredArgs():
  function getOptionalArgs (line 76) | def getOptionalArgs():
  function process_args (line 157) | def process_args(args=None):
  function get_scale_factors (line 182) | def get_scale_factors(args, statsList, mappedList):
  function main (line 234) | def main(args=None):

FILE: deeptools/bamCoverage.py
  function parseArguments (line 16) | def parseArguments():
  function get_required_args (line 46) | def get_required_args():
  function get_optional_args (line 60) | def get_optional_args():
  function scaleFactor (line 117) | def scaleFactor(string):
  function process_args (line 129) | def process_args(args=None):
  function main (line 143) | def main(args=None):
  class OffsetFragment (line 261) | class OffsetFragment(writeBedGraph.WriteBedGraph):
    method filterStrand (line 265) | def filterStrand(self, read, rv):
    method get_fragment_from_read_list (line 293) | def get_fragment_from_read_list(self, read, offset):
    method get_fragment_from_read (line 363) | def get_fragment_from_read(self, read):
  class CenterFragment (line 389) | class CenterFragment(writeBedGraph.WriteBedGraph):
    method get_fragment_from_read (line 396) | def get_fragment_from_read(self, read):

FILE: deeptools/bamHandler.py
  function countReadsInInterval (line 6) | def countReadsInInterval(args):
  function getMappingStats (line 25) | def getMappingStats(bam, nThreads):
  function openBam (line 47) | def openBam(bamFile, returnStats=False, nThreads=1, minimalDecoding=True):

FILE: deeptools/bamPEFragmentSize.py
  function parse_arguments (line 24) | def parse_arguments():
  function getDensity (line 120) | def getDensity(lengths, minVal, maxVal):
  function getFragSize (line 130) | def getFragSize(bam, args, idx, outRawFrags):
  function printTable (line 230) | def printTable(args, fragDict, readDict):
  function main (line 293) | def main(args=None):

FILE: deeptools/bigwigAverage.py
  function parse_arguments (line 12) | def parse_arguments(args=None):
  function getType (line 56) | def getType(fname):
  function average (line 68) | def average(tileCoverage, args):
  function main (line 92) | def main(args=None):

FILE: deeptools/bigwigCompare.py
  function parse_arguments (line 11) | def parse_arguments(args=None):
  function getType (line 100) | def getType(fname):
  function main (line 112) | def main(args=None):

FILE: deeptools/computeGCBias.py
  function parse_arguments (line 23) | def parse_arguments(args=None):
  function getRequiredArgs (line 42) | def getRequiredArgs():
  function getPositionsToSample (line 139) | def getPositionsToSample(chrom, start, end, stepSize):
  function countReadsPerGC_wrapper (line 194) | def countReadsPerGC_wrapper(args):
  function countReadsPerGC_worker (line 198) | def countReadsPerGC_worker(chromNameBam,
  function tabulateGCcontent_wrapper (line 234) | def tabulateGCcontent_wrapper(args):
  function tabulateGCcontent_worker (line 238) | def tabulateGCcontent_worker(chromNameBam, start, end, stepSize,
  function tabulateGCcontent (line 397) | def tabulateGCcontent(fragmentLength, chrNameBitToBam, stepSize,
  function countReadsPerGC (line 456) | def countReadsPerGC(regionSize, chrNameBitToBam, stepSize,
  function smooth (line 494) | def smooth(x, window_len=3):
  function bin_by (line 515) | def bin_by(x, y, nbins=10):
  function plotlyGCbias (line 536) | def plotlyGCbias(file_name, frequencies, reads_per_gc, region_size):
  function plotGCbias (line 580) | def plotGCbias(file_name, frequencies, reads_per_gc, region_size, image_...
  function main (line 640) | def main(args=None):
  class Tester (line 730) | class Tester():
    method __init__ (line 731) | def __init__(self):
    method testTabulateGCcontentWorker (line 757) | def testTabulateGCcontentWorker(self):
    method set_filter_out_file (line 766) | def set_filter_out_file(self):
    method unset_filter_out_file (line 770) | def unset_filter_out_file(self):
    method set_extra_sampling_file (line 774) | def set_extra_sampling_file(self):
    method testTabulateGCcontent (line 778) | def testTabulateGCcontent(self):
    method testCountReadsPerGC (line 788) | def testCountReadsPerGC(self):

FILE: deeptools/computeMatrix.py
  function parse_arguments (line 13) | def parse_arguments(args=None):
  function computeMatrixRequiredArgs (line 77) | def computeMatrixRequiredArgs(args=None):
  function computeMatrixOutputArgs (line 101) | def computeMatrixOutputArgs(args=None):
  function computeMatrixOptArgs (line 130) | def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]):
  function process_args (line 348) | def process_args(args=None):
  function main (line 379) | def main(args=None):

FILE: deeptools/computeMatrixOperations.py
  function parse_arguments (line 12) | def parse_arguments():
  function bindArgs (line 146) | def bindArgs():
  function infoArgs (line 162) | def infoArgs():
  function relabelArgs (line 173) | def relabelArgs():
  function subsetArgs (line 194) | def subsetArgs():
  function filterStrandArgs (line 215) | def filterStrandArgs():
  function filterValuesArgs (line 231) | def filterValuesArgs():
  function sortArgs (line 253) | def sortArgs():
  function printInfo (line 300) | def printInfo(matrix):
  function printDataRange (line 314) | def printDataRange(matrix):
  function relabelMatrix (line 330) | def relabelMatrix(matrix, args):
  function getGroupBounds (line 344) | def getGroupBounds(args, matrix):
  function getSampleBounds (line 363) | def getSampleBounds(args, matrix):
  function subsetRegions (line 380) | def subsetRegions(hm, bounds):
  function filterHeatmap (line 398) | def filterHeatmap(hm, args):
  function filterHeatmapValues (line 422) | def filterHeatmapValues(hm, minVal, maxVal):
  function insertMatrix (line 452) | def insertMatrix(hm, hm2, groupName):
  function appendMatrix (line 480) | def appendMatrix(hm, hm2, groupName):
  function rbindMatrices (line 498) | def rbindMatrices(hm, args):
  function cbindMatrices (line 520) | def cbindMatrices(hm, args):
  function loadBED (line 571) | def loadBED(line, fp, fname, labelColumn, labels, regions, defaultGroup):
  function loadGTFtranscript (line 639) | def loadGTFtranscript(cols, label, defaultGroup, transcript_id_designator):
  function loadGTF (line 654) | def loadGTF(line, fp, fname, labels, regions, transcriptID, transcript_i...
  function sortMatrix (line 691) | def sortMatrix(hm, regionsFileName, transcriptID, transcript_id_designat...
  function main (line 788) | def main(args=None):

FILE: deeptools/correctGCBias.py
  function parse_arguments (line 26) | def parse_arguments(args=None):
  function process_args (line 50) | def process_args(args=None):
  function getRequiredArgs (line 56) | def getRequiredArgs():
  function getReadGCcontent (line 116) | def getReadGCcontent(tbit, read, fragmentLength, chrNameBit):
  function writeCorrected_wrapper (line 163) | def writeCorrected_wrapper(args):
  function writeCorrected_worker (line 167) | def writeCorrected_worker(chrNameBam, chrNameBit, start, end, step):
  function numCopiesOfRead (line 267) | def numCopiesOfRead(value):
  function writeCorrectedSam_wrapper (line 287) | def writeCorrectedSam_wrapper(args):
  function writeCorrectedSam_worker (line 291) | def writeCorrectedSam_worker(chrNameBam, chrNameBit, start, end,
  function getFragmentFromRead (line 464) | def getFragmentFromRead(read, defaultFragmentLength, extendPairedEnds=Tr...
  function run_shell_command (line 536) | def run_shell_command(command):
  function main (line 552) | def main(args=None):
  class Tester (line 681) | class Tester():
    method __init__ (line 682) | def __init__(self):
    method testWriteCorrectedChunk (line 705) | def testWriteCorrectedChunk(self):
    method testWriteCorrectedSam (line 719) | def testWriteCorrectedSam(self):
    method testWriteCorrectedSam_paired (line 732) | def testWriteCorrectedSam_paired(self):

FILE: deeptools/correlation.py
  class Correlation (line 28) | class Correlation:
    method __init__ (line 36) | def __init__(self, matrix_file,
    method load_matrix (line 77) | def load_matrix(self, matrix_file):
    method get_outlier_indices (line 102) | def get_outlier_indices(data, max_deviation=200):
    method remove_outliers (line 131) | def remove_outliers(self, verbose=True):
    method remove_rows_of_zeros (line 163) | def remove_rows_of_zeros(self):
    method save_corr_matrix (line 170) | def save_corr_matrix(self, file_handle):
    method compute_correlation (line 187) | def compute_correlation(self):
    method plotly_correlation (line 239) | def plotly_correlation(self, corr_matrix, plot_filename, labels, plot_...
    method plot_correlation (line 262) | def plot_correlation(self, plot_filename, plot_title='', vmax=None,
    method plotly_scatter (line 375) | def plotly_scatter(self, plot_filename, corr_matrix, plot_title='', mi...
    method plot_scatter (line 430) | def plot_scatter(self, plot_filename, plot_title='', image_format=None...
    method plotly_pca (line 540) | def plotly_pca(self, plotFile, Wt, pvar, PCs, eigenvalues, cols, plotT...
    method plot_pca (line 598) | def plot_pca(self, plot_filename=None, PCs=[1, 2], plot_title='', imag...

FILE: deeptools/correlation_heatmap.py
  function plot_correlation (line 16) | def plot_correlation(corr_matrix, labels, plotFileName, vmax=None,

FILE: deeptools/countReadsPerBin.py
  function countReadsInRegions_wrapper (line 19) | def countReadsInRegions_wrapper(args):
  class CountReadsPerBin (line 31) | class CountReadsPerBin(object):
    method __init__ (line 163) | def __init__(self, bamFilesList, binLength=50, numberOfSamples=None, n...
    method get_chunk_length (line 270) | def get_chunk_length(self, bamFilesHandles, genomeSize, chromSizes, ch...
    method run (line 311) | def run(self, allArgs=None):
    method count_reads_in_region (line 400) | def count_reads_in_region(self, chrom, start, end, bed_regions_list=No...
    method get_coverage_of_region (line 539) | def get_coverage_of_region(self, bamHandle, chrom, regions,
    method getReadLength (line 723) | def getReadLength(self, read):
    method is_proper_pair (line 727) | def is_proper_pair(read, maxPairedFragmentLength):
    method get_fragment_from_read (line 788) | def get_fragment_from_read(self, read):
    method getSmoothRange (line 906) | def getSmoothRange(self, tileIndex, tileSize, smoothRange, maxPosition):
  function remove_row_of_zeros (line 964) | def remove_row_of_zeros(matrix):
  function estimateSizeFactors (line 971) | def estimateSizeFactors(m):
  class Tester (line 994) | class Tester(object):
    method __init__ (line 996) | def __init__(self):
    method getRead (line 1021) | def getRead(self, readType):

FILE: deeptools/deeptools_list_tools.py
  function parse_arguments (line 9) | def parse_arguments(args=None):
  function process_args (line 69) | def process_args(args=None):
  function main (line 75) | def main(args=None):

FILE: deeptools/estimateReadFiltering.py
  function parseArguments (line 11) | def parseArguments():
  function getFiltered_worker (line 151) | def getFiltered_worker(arglist):
  function main (line 258) | def main(args=None):

FILE: deeptools/estimateScaleFactor.py
  function parseArguments (line 13) | def parseArguments(args=None):
  function main (line 94) | def main(args=None):

FILE: deeptools/getFragmentAndReadSize.py
  function getFragmentLength_wrapper (line 10) | def getFragmentLength_wrapper(args):
  function getFragmentLength_worker (line 14) | def getFragmentLength_worker(chrom, start, end, bamFile, distanceBetween...
  function get_read_and_fragment_length (line 59) | def get_read_and_fragment_length(bamFile, return_lengths=False, blackLis...

FILE: deeptools/getRatio.py
  function compute_ratio (line 6) | def compute_ratio(value1, value2, args):
  function getRatio (line 22) | def getRatio(tileCoverage, args):

FILE: deeptools/getScaleFactor.py
  function getFractionKept_wrapper (line 13) | def getFractionKept_wrapper(args):
  function getFractionKept_worker (line 17) | def getFractionKept_worker(chrom, start, end, bamFile, args, offset):
  function fraction_kept (line 104) | def fraction_kept(args, stats):
  function get_num_kept_reads (line 183) | def get_num_kept_reads(args, stats):
  function get_scale_factor (line 213) | def get_scale_factor(args, stats):

FILE: deeptools/getScorePerBigWigBin.py
  function countReadsInRegions_wrapper (line 16) | def countReadsInRegions_wrapper(args):
  function countFragmentsInRegions_worker (line 21) | def countFragmentsInRegions_worker(chrom, start, end,
  function getChromSizes (line 139) | def getChromSizes(bigwigFilesList):
  function getScorePerBin (line 197) | def getScorePerBin(bigWigFiles, binLength,
  class Tester (line 292) | class Tester(object):
    method __init__ (line 294) | def __init__(self):

FILE: deeptools/heatmapper.py
  function chopRegions (line 17) | def chopRegions(exonsInput, left=0, right=0):
  function chopRegionsFromMiddle (line 68) | def chopRegionsFromMiddle(exonsInput, left=0, right=0):
  function trimZones (line 143) | def trimZones(zones, maxLength, binSize, padRight):
  function compute_sub_matrix_wrapper (line 173) | def compute_sub_matrix_wrapper(args):
  class heatmapper (line 177) | class heatmapper(object):
    method __init__ (line 183) | def __init__(self):
    method getTicks (line 193) | def getTicks(self, idx):
    method computeMatrix (line 200) | def computeMatrix(self, score_file_list, regions_file, parameters, bla...
    method compute_sub_matrix_worker (line 354) | def compute_sub_matrix_worker(self, chrom, start, end, score_file_list...
    method coverage_from_array (line 597) | def coverage_from_array(valuesArray, zones, binSize, avgType):
    method change_chrom_names (line 636) | def change_chrom_names(chrom):
    method coverage_from_big_wig (line 655) | def coverage_from_big_wig(bigwig, chrom, zones, binSize, avgType, nans...
    method my_average (line 733) | def my_average(valuesArray, avgType='mean'):
    method matrix_from_dict (line 745) | def matrix_from_dict(self, matrixDict, regionsDict, parameters):
    method read_matrix_file (line 752) | def read_matrix_file(self, matrix_file):
    method save_matrix (line 814) | def save_matrix(self, file_name):
    method save_tabulated_values (line 874) | def save_tabulated_values(self, file_handle, reference_point_label='TS...
    method save_matrix_values (line 963) | def save_matrix_values(self, file_name):
    method save_BED (line 991) | def save_BED(self, file_handle):
    method matrix_avg (line 1030) | def matrix_avg(matrix, avgType='mean'):
    method get_individual_matrices (line 1034) | def get_individual_matrices(self, matrix):
    method get_num_individual_matrix_cols (line 1048) | def get_num_individual_matrix_cols(self):
  function computeSilhouetteScore (line 1062) | def computeSilhouetteScore(d, idx, labels):
  class _matrix (line 1079) | class _matrix(object):
    method __init__ (line 1093) | def __init__(self, regions, matrix, group_boundaries, sample_boundaries,
    method get_matrix (line 1126) | def get_matrix(self, group, sample):
    method get_num_samples (line 1147) | def get_num_samples(self):
    method get_num_groups (line 1150) | def get_num_groups(self):
    method set_group_labels (line 1153) | def set_group_labels(self, new_labels):
    method set_sample_labels (line 1160) | def set_sample_labels(self, new_labels):
    method set_sorting_method (line 1167) | def set_sorting_method(self, sort_method, sort_using):
    method get_regions (line 1171) | def get_regions(self):
    method sort_groups (line 1193) | def sort_groups(self, sort_using='mean', sort_method='no', sample_list...
    method hmcluster (line 1252) | def hmcluster(self, k, evaluate_silhouette=True, method='kmeans', clus...
    method computeSilhouette (line 1325) | def computeSilhouette(self, k):
    method removeempty (line 1341) | def removeempty(self):
    method flatten (line 1358) | def flatten(self):

FILE: deeptools/heatmapper_utilities.py
  function plot_single (line 13) | def plot_single(ax, ma, average_type, color, label, plot_type='lines'):
  function plotly_single (line 94) | def plotly_single(ma, average_type, color, label, plot_type='line'):
  function getProfileTicks (line 124) | def getProfileTicks(hm, referencePointLabel, startLabel, endLabel, idx):

FILE: deeptools/mapReduce.py
  function mapReduce (line 8) | def mapReduce(staticArgs, func, chromSize,
  function getUserRegion (line 156) | def getUserRegion(chrom_sizes, region_string, max_chunk_size=1e6):
  function blSubtract (line 239) | def blSubtract(t, chrom, chunk):

FILE: deeptools/multiBamSummary.py
  function parse_arguments (line 16) | def parse_arguments(args=None):
  function bamcorrelate_args (line 94) | def bamcorrelate_args(case='bins'):
  function process_args (line 193) | def process_args(args=None):
  function main (line 212) | def main(args=None):

FILE: deeptools/multiBigwigSummary.py
  function parse_arguments (line 16) | def parse_arguments(args=None):
  function process_args (line 94) | def process_args(args=None):
  function multiBigwigSummaryArgs (line 117) | def multiBigwigSummaryArgs(case='bins'):
  function main (line 207) | def main(args=None):

FILE: deeptools/parserCommon.py
  function check_float_0_1 (line 7) | def check_float_0_1(value):
  function check_list_of_comma_values (line 14) | def check_list_of_comma_values(value):
  function output (line 25) | def output(args=None):
  function read_options (line 42) | def read_options():
  function gtf_options (line 141) | def gtf_options(suppress=False):
  function normalization_options (line 203) | def normalization_options():
  function getParentArgParse (line 292) | def getParentArgParse(args=None, binSize=True, blackList=True):
  function numberOfProcessors (line 344) | def numberOfProcessors(string):
  function genomicRegion (line 377) | def genomicRegion(string):
  function writableFile (line 395) | def writableFile(string):
  function heatmapperMatrixArgs (line 413) | def heatmapperMatrixArgs(args=None):
  function heatmapperOutputArgs (line 431) | def heatmapperOutputArgs(args=None,
  function heatmapperOptionalArgs (line 482) | def heatmapperOptionalArgs(mode=['heatmap', 'profile'][0]):
  function requiredLength (line 870) | def requiredLength(minL, maxL):

FILE: deeptools/plotCorrelation.py
  function parse_arguments (line 20) | def parse_arguments(args=None):
  function plot_correlation_args (line 50) | def plot_correlation_args():
  function scatterplot_options (line 133) | def scatterplot_options():
  function heatmap_options (line 159) | def heatmap_options():
  function main (line 204) | def main(args=None):

FILE: deeptools/plotCoverage.py
  function parse_arguments (line 25) | def parse_arguments(args=None):
  function process_args (line 58) | def process_args(args=None):
  function required_args (line 72) | def required_args():
  function main (line 173) | def main(args=None):

FILE: deeptools/plotEnrichment.py
  function parse_arguments (line 30) | def parse_arguments(args=None):
  function plot_enrichment_args (line 61) | def plot_enrichment_args():
  function getBAMBlocks (line 203) | def getBAMBlocks(read, defaultFragmentLength, centerRead, offset=None):
  function getEnrichment_worker (line 288) | def getEnrichment_worker(arglist):
  function plotEnrichment (line 359) | def plotEnrichment(args, featureCounts, totalCounts, features):
  function getChunkLength (line 455) | def getChunkLength(args, chromSize):
  function main (line 492) | def main(args=None):

FILE: deeptools/plotFingerprint.py
  function parse_arguments (line 28) | def parse_arguments(args=None):
  function process_args (line 53) | def process_args(args=None):
  function get_required_args (line 74) | def get_required_args():
  function get_optional_args (line 87) | def get_optional_args():
  function get_output_args (line 164) | def get_output_args():
  function binRelEntropy (line 183) | def binRelEntropy(p, q):
  function getCHANCE (line 196) | def getCHANCE(args, idx, mat):
  function getSyntheticJSD (line 237) | def getSyntheticJSD(vec):
  function getJSD (line 259) | def getJSD(args, idx, mat):
  function getJSDcommon (line 307) | def getJSDcommon(chip, input):
  function getExpected (line 351) | def getExpected(mu):
  function main (line 367) | def main(args=None):

FILE: deeptools/plotHeatmap.py
  function parse_arguments (line 34) | def parse_arguments(args=None):
  function process_args (line 52) | def process_args(args=None):
  function prepare_layout (line 65) | def prepare_layout(hm_matrix, heatmapsize, showSummaryPlot, showColorbar...
  function addProfilePlot (line 121) | def addProfilePlot(hm, plt, fig, grids, iterNum, iterNum2, perGroup, ave...
  function plotlyMatrix (line 206) | def plotlyMatrix(hm,
  function plotMatrix (line 381) | def plotMatrix(hm, outFileName,
  function mergeSmallGroups (line 772) | def mergeSmallGroups(matrixDict):
  function main (line 808) | def main(args=None):

FILE: deeptools/plotPCA.py
  function parse_arguments (line 16) | def parse_arguments(args=None):
  function plotCorrelationArgs (line 38) | def plotCorrelationArgs():
  function main (line 158) | def main(args=None):

FILE: deeptools/plotProfile.py
  function parse_arguments (line 35) | def parse_arguments(args=None):
  function process_args (line 55) | def process_args(args=None):
  class Profile (line 90) | class Profile(object):
    method __init__ (line 92) | def __init__(self, hm, out_file_name,
    method getTicks (line 196) | def getTicks(self, idx):
    method cm2inch (line 204) | def cm2inch(*tupl):
    method plot_hexbin (line 211) | def plot_hexbin(self):
    method plotly_hexbin (line 337) | def plotly_hexbin(self):
    method plot_heatmap (line 463) | def plot_heatmap(self):
    method plotly_heatmap (line 582) | def plotly_heatmap(self):
    method plot_profile (line 677) | def plot_profile(self):
    method plotly_profile (line 809) | def plotly_profile(self):
  function main (line 911) | def main(args=None):

FILE: deeptools/sumCoveragePerBin.py
  class SumCoveragePerBin (line 10) | class SumCoveragePerBin(countReadsPerBin.CountReadsPerBin):
    method get_coverage_of_region (line 14) | def get_coverage_of_region(self, bamHandle, chrom, regions,
  class Tester (line 217) | class Tester(object):
    method __init__ (line 219) | def __init__(self):

FILE: deeptools/test/skiptest_heatmapper_images.py
  function test_plotHeatmap_simple_plot (line 18) | def test_plotHeatmap_simple_plot():
  function test_plotHeatmap_rename_labels (line 35) | def test_plotHeatmap_rename_labels():
  function test_plotHeatmap_scale_regions (line 45) | def test_plotHeatmap_scale_regions():
  function test_plotHeatmap_multi_bigwig_pergroup (line 54) | def test_plotHeatmap_multi_bigwig_pergroup():
  function test_plotHeatmap_multiple_colors_muti_scales (line 64) | def test_plotHeatmap_multiple_colors_muti_scales():
  function test_plotHeatmap_multiple_colormap_no_boxes (line 74) | def test_plotHeatmap_multiple_colormap_no_boxes():
  function test_plotHeatmap_interpolation (line 84) | def test_plotHeatmap_interpolation():
  function test_plotProfiler (line 94) | def test_plotProfiler():
  function test_plotProfiler_heatmap (line 104) | def test_plotProfiler_heatmap():
  function test_plotProfiler_overlapped_lines (line 113) | def test_plotProfiler_overlapped_lines():
  function test_plotProfiler_multibigwig (line 123) | def test_plotProfiler_multibigwig():
  function test_plotProfiler_multibigwig_pergroup (line 133) | def test_plotProfiler_multibigwig_pergroup():

FILE: deeptools/test/test_bamCoverage_and_bamCompare.py
  function test_bam_coverage_arguments (line 35) | def test_bam_coverage_arguments():
  function test_bam_coverage_extend (line 52) | def test_bam_coverage_extend():
  function test_bam_coverage_extend_and_normalizeUsingRPGC (line 65) | def test_bam_coverage_extend_and_normalizeUsingRPGC():
  function test_bam_coverage_skipnas (line 82) | def test_bam_coverage_skipnas():
  function test_bam_coverage_filtering (line 96) | def test_bam_coverage_filtering():
  function test_bam_compare_arguments (line 110) | def test_bam_compare_arguments():
  function test_bam_compare_diff_files (line 130) | def test_bam_compare_diff_files():
  function test_bam_compare_pseudocounts (line 148) | def test_bam_compare_pseudocounts():
  function test_bam_compare_ZoverZ (line 165) | def test_bam_compare_ZoverZ():
  function test_get_num_kept_reads (line 182) | def test_get_num_kept_reads():
  function test_bam_compare_diff_files_skipnas (line 214) | def test_bam_compare_diff_files_skipnas():
  function test_bam_compare_extend (line 234) | def test_bam_compare_extend():
  function test_bam_compare_scale_factors_ratio (line 252) | def test_bam_compare_scale_factors_ratio():
  function test_bam_compare_scale_factors_subtract (line 292) | def test_bam_compare_scale_factors_subtract():
  function test_bam_coverage_filter_blacklist (line 334) | def test_bam_coverage_filter_blacklist():
  function test_bam_coverage_offset1 (line 364) | def test_bam_coverage_offset1():
  function test_bam_coverage_offset1_10 (line 382) | def test_bam_coverage_offset1_10():
  function test_bam_coverage_offset_minus1 (line 400) | def test_bam_coverage_offset_minus1():
  function test_bam_coverage_offset20_minus4 (line 418) | def test_bam_coverage_offset20_minus4():
  function test_bam_compare_filter_blacklist (line 436) | def test_bam_compare_filter_blacklist():

FILE: deeptools/test/test_bigwigAverage.py
  function test_bigwigAverage (line 37) | def test_bigwigAverage():
  function test_bigwigAverage_skipnas (line 49) | def test_bigwigAverage_skipnas():
  function test_bigwigAverageWithScale (line 62) | def test_bigwigAverageWithScale():
  function test_bigwigAverageThree (line 74) | def test_bigwigAverageThree():

FILE: deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py
  function test_bigwigCompare (line 40) | def test_bigwigCompare():
  function test_bigwigCompare_skipnas (line 52) | def test_bigwigCompare_skipnas():
  function test_bigwigCompare_skipZeroOverZero (line 65) | def test_bigwigCompare_skipZeroOverZero():
  function test_multiBigwigSummary (line 77) | def test_multiBigwigSummary():
  function test_multiBigwigSummary_outrawcounts (line 92) | def test_multiBigwigSummary_outrawcounts():
  function test_multiBigwigSummary_gtf (line 113) | def test_multiBigwigSummary_gtf():
  function test_multiBigwigSummary_metagene (line 126) | def test_multiBigwigSummary_metagene():

FILE: deeptools/test/test_computeMatrixOperations.py
  function getHeader (line 12) | def getHeader(fp):
  class TestComputeMatrixOperations (line 20) | class TestComputeMatrixOperations(object):
    method testSubset (line 27) | def testSubset(self):
    method testRelabel (line 46) | def testRelabel(self):
    method testfilterStrand (line 63) | def testfilterStrand(self):
    method testrbind (line 95) | def testrbind(self):
    method testrbind2 (line 113) | def testrbind2(self):
    method testcbind (line 131) | def testcbind(self):
    method testsort (line 149) | def testsort(self):

FILE: deeptools/test/test_countReadsPerBin.py
  class TestCountReadsPerBin (line 13) | class TestCountReadsPerBin():
    method ifiles (line 15) | def ifiles(self, ext='bam'):
    method test_count_reads_in_region (line 45) | def test_count_reads_in_region(self, bc):
    method test_count_reads_in_region_extension_1 (line 55) | def test_count_reads_in_region_extension_1(self, bc):
    method test_count_reads_in_region_total (line 75) | def test_count_reads_in_region_total(self, bc):
    method test_countReadsInRegions_min_mapping_quality (line 86) | def test_countReadsInRegions_min_mapping_quality(self, bc):
    method test_count_reads_in_region_ignore_duplicates (line 96) | def test_count_reads_in_region_ignore_duplicates(self, bc):
    method test_count_reads_in_region_ignore_bed_regions (line 106) | def test_count_reads_in_region_ignore_bed_regions(self, bc):
    method test_get_coverage_of_region_sam_flag_include (line 116) | def test_get_coverage_of_region_sam_flag_include(self, bc):
    method test_get_coverage_of_region_sam_flag_exclude (line 123) | def test_get_coverage_of_region_sam_flag_exclude(self, bc):
    method test_get_coverage_of_region_large_bin (line 130) | def test_get_coverage_of_region_large_bin(self, bc):
    method test_get_coverage_of_region_ignore_duplicates (line 138) | def test_get_coverage_of_region_ignore_duplicates(self, bc):
    method test_get_coverage_of_region_split_read (line 156) | def test_get_coverage_of_region_split_read(self, bc):
    method test_get_coverage_of_region_zeros_to_nan (line 180) | def test_get_coverage_of_region_zeros_to_nan(self, bc):
    method test_bed_file (line 190) | def test_bed_file(self, bc):

FILE: deeptools/test/test_heatmapper.py
  function cmpMatrices (line 15) | def cmpMatrices(f1, f2):
  function test_computeMatrix_reference_point (line 51) | def test_computeMatrix_reference_point():
  function test_computeMatrix_reference_point_center (line 60) | def test_computeMatrix_reference_point_center():
  function test_computeMatrix_reference_point_tes (line 69) | def test_computeMatrix_reference_point_tes():
  function test_computeMatrix_reference_point_missing_data_as_zero (line 78) | def test_computeMatrix_reference_point_missing_data_as_zero():
  function test_computeMatrix_scale_regions (line 87) | def test_computeMatrix_scale_regions():
  function test_computeMatrix_multiple_bed (line 97) | def test_computeMatrix_multiple_bed():
  function test_computeMatrix_region_extend_over_chr_end (line 106) | def test_computeMatrix_region_extend_over_chr_end():
  function test_computeMatrix_unscaled (line 115) | def test_computeMatrix_unscaled():
  function test_computeMatrix_gtf (line 124) | def test_computeMatrix_gtf():
  function test_computeMatrix_metagene (line 133) | def test_computeMatrix_metagene():
  function test_chopRegions_body (line 142) | def test_chopRegions_body():
  function test_chopRegions_TSS (line 168) | def test_chopRegions_TSS():
  function test_chopRegions_TES (line 218) | def test_chopRegions_TES():
  function test_chopRegionsFromMiddle (line 268) | def test_chopRegionsFromMiddle():

FILE: deeptools/test/test_multiBamSummary.py
  function test_multiBamSummary_gtf (line 16) | def test_multiBamSummary_gtf():
  function test_multiBamSummary_metagene (line 33) | def test_multiBamSummary_metagene():
  function test_multiBamSummary_scalingFactors (line 50) | def test_multiBamSummary_scalingFactors():

FILE: deeptools/test/test_plotCoverage.py
  function test_plotCoverage_default (line 16) | def test_plotCoverage_default():

FILE: deeptools/test/test_readFiltering.py
  function test_estimate_read_filtering_minimal (line 15) | def test_estimate_read_filtering_minimal():
  function test_estimate_read_filtering_params (line 36) | def test_estimate_read_filtering_params():
  function test_sieve (line 57) | def test_sieve():
  function test_sieve_BED (line 87) | def test_sieve_BED():
  function test_sieve_BED_shift (line 129) | def test_sieve_BED_shift():

FILE: deeptools/test/test_tools.py
  function test_tools (line 11) | def test_tools():

FILE: deeptools/test/test_writeBedGraph.py
  class TestWriteBedGraph (line 8) | class TestWriteBedGraph():
    method ifiles (line 9) | def ifiles(self, ext='bam'):
    method test_writeBedGraph_worker (line 25) | def test_writeBedGraph_worker(self, bc):
    method test_writeBedGraph_worker_zerotonan (line 38) | def test_writeBedGraph_worker_zerotonan(self, bc):
    method test_writeBedGraph_worker_scaling (line 50) | def test_writeBedGraph_worker_scaling(self, bc):
    method test_writeBedGraph_worker_ignore_duplicates (line 61) | def test_writeBedGraph_worker_ignore_duplicates(self, bc):
    method test_writeBedGraph_worker_smoothing (line 79) | def test_writeBedGraph_worker_smoothing(self, bc):
    method test_writeBedGraph_cigar (line 92) | def test_writeBedGraph_cigar(self, bc):

FILE: deeptools/utilities.py
  function smartLabel (line 14) | def smartLabel(label):
  function smartLabels (line 28) | def smartLabels(labels):
  function convertCmap (line 32) | def convertCmap(c, vmin=0, vmax=1):
  function getTLen (line 50) | def getTLen(read, notAbs=False):
  function getGC_content (line 79) | def getGC_content(tb, chrom, fragStart, fragEnd, fraction=True):
  function tbitToBamChrName (line 92) | def tbitToBamChrName(tbitNames, bamNames):
  function getCommonChrNames (line 161) | def getCommonChrNames(bamFileHandles, verbose=True):
  function copyFileInMemory (line 232) | def copyFileInMemory(filePath, suffix=''):
  function getTempFileName (line 250) | def getTempFileName(suffix=''):
  function gtfOptions (line 265) | def gtfOptions(allArgs=None):
  function toString (line 282) | def toString(s):
  function toBytes (line 297) | def toBytes(s):
  function mungeChromosome (line 312) | def mungeChromosome(chrom, chromList):
  function bam_total_reads (line 335) | def bam_total_reads(bam_handle, chroms_to_ignore, stats):
  function bam_blacklisted_worker (line 346) | def bam_blacklisted_worker(args):
  function bam_blacklisted_reads (line 359) | def bam_blacklisted_reads(bam_handle, chroms_to_ignore, blackListFileNam...

FILE: deeptools/writeBedGraph.py
  function writeBedGraph_wrapper (line 18) | def writeBedGraph_wrapper(args):
  class WriteBedGraph (line 30) | class WriteBedGraph(cr.CountReadsPerBin):
    method run (line 93) | def run(self, func_to_call, func_args, out_file_name, blackListFileNam...
    method writeBedGraph_worker (line 173) | def writeBedGraph_worker(self, chrom, start, end,
  function bedGraphToBigWig (line 286) | def bedGraphToBigWig(chromSizes, bedGraphFiles, bigWigPath):
  function getGenomeChunkLength (line 322) | def getGenomeChunkLength(bamHandles, tile_size, mappedList):
  function scaleCoverage (line 343) | def scaleCoverage(tile_coverage, args):
  function ratio (line 350) | def ratio(tile_coverage, args):

FILE: deeptools/writeBedGraph_bam_and_bw.py
  function getCoverageFromBigwig (line 22) | def getCoverageFromBigwig(bigwigHandle, chrom, start, end, tileSize,
  function writeBedGraph_wrapper (line 41) | def writeBedGraph_wrapper(args):
  function writeBedGraph_worker (line 45) | def writeBedGraph_worker(
  function writeBedGraph (line 145) | def writeBedGraph(

FILE: docs/conf.py
  function get_version (line 84) | def get_version():

FILE: scripts/convertChromsBigWig.py
  function parse_arguments (line 12) | def parse_arguments(defaults):
  function get_chromosome_mapping (line 69) | def get_chromosome_mapping(genome="GRCm38", from_format="ensembl", to_fo...
  function convert_bigwig (line 118) | def convert_bigwig(mapping_table, bw_in_filename, bw_out_filename, verbo...
  function main (line 159) | def main(args=None):