├── .travis.yml ├── CHANGELOG.md ├── README.md ├── contributors.txt ├── delly_docker ├── DELLY │ ├── links │ │ ├── README │ │ └── input.txt │ ├── pom.xml │ ├── src │ │ └── main │ │ │ └── java │ │ │ └── io │ │ │ └── seqware │ │ │ └── DELLYWorkflow.java │ ├── workflow.properties │ └── workflow │ │ ├── config │ │ └── DELLYWorkflow.ini │ │ └── metadata.xml ├── Dockerfile ├── Dockerfile-2.0.4 ├── Dockerfile-2.2.0 ├── Dockerfile-feature_gosu_and_icgc_portal ├── Dockstore.cwl ├── Dockstore.json ├── Dockstore.wdl ├── Dockstore_wdl.json ├── inventory └── scripts │ ├── DNAcopy_1.38.1.tar.gz │ ├── DellySomaticFreqFilter.py │ ├── cleanup.sh │ ├── cov │ ├── cov_plot.pl │ ├── cov_v0.5.6_linux_x86_64bit │ ├── cov_v0.5.6_parallel_linux_x86_64bit │ ├── delly │ ├── dellyVcf2Tsv.py │ ├── delly_pcawg_qc_json.py │ ├── delly_pcawg_timing_json.py │ ├── delly_pe_dump.sh │ ├── delly_prepare_uploader.sh │ ├── delly_v0.6.3_parallel_linux_x86_64bit │ ├── delly_v0.6.6_parallel_linux_x86_64bit │ ├── gcNormCov.R │ ├── gcNormCov_extended.R │ ├── read_depth_ratio_plusCovSigSeg.R │ ├── run_seqware_workflow.pl │ ├── start.sh │ ├── vcf-sort │ ├── vcf_index.sh │ └── vcfcombine ├── deprecated ├── bin │ ├── DNAcopy_1.38.1.tar.gz │ ├── DellySomaticFreqFilter.py │ ├── cleanup.sh │ ├── cov │ ├── cov_plot.pl │ ├── cov_v0.0.11 │ ├── cov_v0.5.6_linux_x86_64bit │ ├── cov_v0.5.6_parallel_linux_x86_64bit │ ├── delly │ ├── dellyVcf2Tsv.py │ ├── delly_pe_dump.sh │ ├── delly_prepare_uploader.sh │ ├── delly_uploader.pl │ ├── delly_v0.5.9_parallel_linux_x86_64bit │ ├── delly_v0.6.3_parallel_linux_x86_64bit │ ├── gcNormCov.R │ ├── gcNormCov_extended.R │ ├── gencode.v19.gene.minimal.bed.gz │ ├── gencode.v19.gene.minimal_noChr.bed.gz │ ├── gnos_upload_vcf.pl │ ├── py │ │ ├── docopt.py │ │ ├── docopt.pyc │ │ ├── numpy │ │ │ ├── __config__.py │ │ │ ├── __config__.pyc │ │ │ ├── __init__.py │ │ │ ├── __init__.pyc │ │ │ ├── _import_tools.py │ │ │ ├── _import_tools.pyc │ │ │ ├── add_newdocs.py │ │ │ ├── add_newdocs.pyc │ │ │ ├── compat │ │ │ │ ├── __init__.py │ │ │ │ ├── __init__.pyc │ │ │ │ ├── _inspect.py │ │ │ │ ├── _inspect.pyc │ │ │ │ ├── py3k.py │ │ │ │ ├── py3k.pyc │ │ │ │ └── setup.py │ │ │ ├── core │ │ │ │ ├── __init__.py │ │ │ │ ├── __init__.pyc │ │ │ │ ├── _dummy.so │ │ │ │ ├── _internal.py │ │ │ │ ├── _internal.pyc │ │ │ │ ├── _methods.py │ │ │ │ ├── _methods.pyc │ │ │ │ ├── arrayprint.py │ │ │ │ ├── arrayprint.pyc │ │ │ │ ├── defchararray.py │ │ │ │ ├── defchararray.pyc │ │ │ │ ├── fromnumeric.py │ │ │ │ ├── fromnumeric.pyc │ │ │ │ ├── function_base.py │ │ │ │ ├── function_base.pyc │ │ │ │ ├── generate_numpy_api.py │ │ │ │ ├── getlimits.py │ │ │ │ ├── getlimits.pyc │ │ │ │ ├── info.py │ │ │ │ ├── info.pyc │ │ │ │ ├── machar.py │ │ │ │ ├── machar.pyc │ │ │ │ ├── memmap.py │ │ │ │ ├── memmap.pyc │ │ │ │ ├── multiarray.so │ │ │ │ ├── multiarray_tests.so │ │ │ │ ├── numeric.py │ │ │ │ ├── numeric.pyc │ │ │ │ ├── numerictypes.py │ │ │ │ ├── numerictypes.pyc │ │ │ │ ├── operand_flag_tests.so │ │ │ │ ├── records.py │ │ │ │ ├── records.pyc │ │ │ │ ├── scalarmath.so │ │ │ │ ├── setup.py │ │ │ │ ├── setup_common.py │ │ │ │ ├── shape_base.py │ │ │ │ ├── shape_base.pyc │ │ │ │ ├── struct_ufunc_test.so │ │ │ │ ├── test_rational.so │ │ │ │ ├── umath.so │ │ │ │ └── umath_tests.so │ │ │ ├── ctypeslib.py │ │ │ ├── ctypeslib.pyc │ │ │ ├── distutils │ │ │ │ ├── __config__.py │ │ │ │ ├── __init__.py │ │ │ │ ├── __version__.py │ │ │ │ ├── ccompiler.py │ │ │ │ ├── command │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── autodist.py │ │ │ │ │ ├── bdist_rpm.py │ │ │ │ │ ├── build.py │ │ │ │ │ ├── build_clib.py │ │ │ │ │ ├── build_ext.py │ │ │ │ │ ├── build_py.py │ │ │ │ │ ├── build_scripts.py │ │ │ │ │ ├── build_src.py │ │ │ │ │ ├── config.py │ │ │ │ │ ├── config_compiler.py │ │ │ │ │ ├── develop.py │ │ │ │ │ ├── egg_info.py │ │ │ │ │ ├── install.py │ │ │ │ │ ├── install_clib.py │ │ │ │ │ ├── install_data.py │ │ │ │ │ ├── install_headers.py │ │ │ │ │ └── sdist.py │ │ │ │ ├── compat.py │ │ │ │ ├── conv_template.py │ │ │ │ ├── core.py │ │ │ │ ├── cpuinfo.py │ │ │ │ ├── environment.py │ │ │ │ ├── exec_command.py │ │ │ │ ├── extension.py │ │ │ │ ├── fcompiler │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── absoft.py │ │ │ │ │ ├── compaq.py │ │ │ │ │ ├── g95.py │ │ │ │ │ ├── gnu.py │ │ │ │ │ ├── hpux.py │ │ │ │ │ ├── ibm.py │ │ │ │ │ ├── intel.py │ │ │ │ │ ├── lahey.py │ │ │ │ │ ├── mips.py │ │ │ │ │ ├── nag.py │ │ │ │ │ ├── none.py │ │ │ │ │ ├── pathf95.py │ │ │ │ │ ├── pg.py │ │ │ │ │ ├── sun.py │ │ │ │ │ └── vast.py │ │ │ │ ├── from_template.py │ │ │ │ ├── info.py │ │ │ │ ├── intelccompiler.py │ │ │ │ ├── lib2def.py │ │ │ │ ├── line_endings.py │ │ │ │ ├── log.py │ │ │ │ ├── mingw32ccompiler.py │ │ │ │ ├── misc_util.py │ │ │ │ ├── npy_pkg_config.py │ │ │ │ ├── numpy_distribution.py │ │ │ │ ├── pathccompiler.py │ │ │ │ ├── setup.py │ │ │ │ ├── system_info.py │ │ │ │ └── unixccompiler.py │ │ │ ├── doc │ │ │ │ ├── __init__.py │ │ │ │ ├── basics.py │ │ │ │ ├── broadcasting.py │ │ │ │ ├── byteswapping.py │ │ │ │ ├── constants.py │ │ │ │ ├── creation.py │ │ │ │ ├── glossary.py │ │ │ │ ├── howtofind.py │ │ │ │ ├── indexing.py │ │ │ │ ├── internals.py │ │ │ │ ├── io.py │ │ │ │ ├── jargon.py │ │ │ │ ├── methods_vs_functions.py │ │ │ │ ├── misc.py │ │ │ │ ├── performance.py │ │ │ │ ├── structured_arrays.py │ │ │ │ ├── subclassing.py │ │ │ │ └── ufuncs.py │ │ │ ├── dual.py │ │ │ ├── f2py │ │ │ │ ├── __init__.py │ │ │ │ ├── __version__.py │ │ │ │ ├── auxfuncs.py │ │ │ │ ├── capi_maps.py │ │ │ │ ├── cb_rules.py │ │ │ │ ├── cfuncs.py │ │ │ │ ├── common_rules.py │ │ │ │ ├── crackfortran.py │ │ │ │ ├── diagnose.py │ │ │ │ ├── f2py2e.py │ │ │ │ ├── f2py_testing.py │ │ │ │ ├── f90mod_rules.py │ │ │ │ ├── func2subr.py │ │ │ │ ├── info.py │ │ │ │ ├── rules.py │ │ │ │ ├── setup.py │ │ │ │ └── use_rules.py │ │ │ ├── fft │ │ │ │ ├── __init__.py │ │ │ │ ├── __init__.pyc │ │ │ │ ├── fftpack.py │ │ │ │ ├── fftpack.pyc │ │ │ │ ├── fftpack_lite.so │ │ │ │ ├── helper.py │ │ │ │ ├── helper.pyc │ │ │ │ ├── info.py │ │ │ │ ├── info.pyc │ │ │ │ └── setup.py │ │ │ ├── lib │ │ │ │ ├── __init__.py │ │ │ │ ├── __init__.pyc │ │ │ │ ├── _compiled_base.so │ │ │ │ ├── _datasource.py │ │ │ │ ├── _datasource.pyc │ │ │ │ ├── _iotools.py │ │ │ │ ├── _iotools.pyc │ │ │ │ ├── arraypad.py │ │ │ │ ├── arraypad.pyc │ │ │ │ ├── arraysetops.py │ │ │ │ ├── arraysetops.pyc │ │ │ │ ├── arrayterator.py │ │ │ │ ├── arrayterator.pyc │ │ │ │ ├── financial.py │ │ │ │ ├── financial.pyc │ │ │ │ ├── format.py │ │ │ │ ├── format.pyc │ │ │ │ ├── function_base.py │ │ │ │ ├── function_base.pyc │ │ │ │ ├── index_tricks.py │ │ │ │ ├── index_tricks.pyc │ │ │ │ ├── info.py │ │ │ │ ├── info.pyc │ │ │ │ ├── nanfunctions.py │ │ │ │ ├── nanfunctions.pyc │ │ │ │ ├── npyio.py │ │ │ │ ├── npyio.pyc │ │ │ │ ├── polynomial.py │ │ │ │ ├── polynomial.pyc │ │ │ │ ├── recfunctions.py │ │ │ │ ├── scimath.py │ │ │ │ ├── scimath.pyc │ │ │ │ ├── setup.py │ │ │ │ ├── shape_base.py │ │ │ │ ├── shape_base.pyc │ │ │ │ ├── stride_tricks.py │ │ │ │ ├── stride_tricks.pyc │ │ │ │ ├── twodim_base.py │ │ │ │ ├── twodim_base.pyc │ │ │ │ ├── type_check.py │ │ │ │ ├── type_check.pyc │ │ │ │ ├── ufunclike.py │ │ │ │ ├── ufunclike.pyc │ │ │ │ ├── user_array.py │ │ │ │ ├── utils.py │ │ │ │ └── utils.pyc │ │ │ ├── linalg │ │ │ │ ├── __init__.py │ │ │ │ ├── __init__.pyc │ │ │ │ ├── _umath_linalg.so │ │ │ │ ├── info.py │ │ │ │ ├── info.pyc │ │ │ │ ├── lapack_lite.so │ │ │ │ ├── linalg.py │ │ │ │ ├── linalg.pyc │ │ │ │ └── setup.py │ │ │ ├── ma │ │ │ │ ├── __init__.py │ │ │ │ ├── __init__.pyc │ │ │ │ ├── bench.py │ │ │ │ ├── core.py │ │ │ │ ├── core.pyc │ │ │ │ ├── extras.py │ │ │ │ ├── extras.pyc │ │ │ │ ├── mrecords.py │ │ │ │ ├── setup.py │ │ │ │ ├── testutils.py │ │ │ │ ├── timer_comparison.py │ │ │ │ └── version.py │ │ │ ├── matlib.py │ │ │ ├── matrixlib │ │ │ │ ├── __init__.py │ │ │ │ ├── __init__.pyc │ │ │ │ ├── defmatrix.py │ │ │ │ ├── defmatrix.pyc │ │ │ │ └── setup.py │ │ │ ├── numarray │ │ │ │ ├── __init__.py │ │ │ │ ├── _capi.so │ │ │ │ ├── alter_code1.py │ │ │ │ ├── alter_code2.py │ │ │ │ ├── compat.py │ │ │ │ ├── convolve.py │ │ │ │ ├── fft.py │ │ │ │ ├── functions.py │ │ │ │ ├── image.py │ │ │ │ ├── linear_algebra.py │ │ │ │ ├── ma.py │ │ │ │ ├── matrix.py │ │ │ │ ├── mlab.py │ │ │ │ ├── nd_image.py │ │ │ │ ├── numerictypes.py │ │ │ │ ├── random_array.py │ │ │ │ ├── session.py │ │ │ │ ├── setup.py │ │ │ │ ├── ufuncs.py │ │ │ │ └── util.py │ │ │ ├── oldnumeric │ │ │ │ ├── __init__.py │ │ │ │ ├── alter_code1.py │ │ │ │ ├── alter_code2.py │ │ │ │ ├── array_printer.py │ │ │ │ ├── arrayfns.py │ │ │ │ ├── compat.py │ │ │ │ ├── fft.py │ │ │ │ ├── fix_default_axis.py │ │ │ │ ├── functions.py │ │ │ │ ├── linear_algebra.py │ │ │ │ ├── ma.py │ │ │ │ ├── matrix.py │ │ │ │ ├── misc.py │ │ │ │ ├── mlab.py │ │ │ │ ├── precision.py │ │ │ │ ├── random_array.py │ │ │ │ ├── rng.py │ │ │ │ ├── rng_stats.py │ │ │ │ ├── setup.py │ │ │ │ ├── typeconv.py │ │ │ │ ├── ufuncs.py │ │ │ │ └── user_array.py │ │ │ ├── polynomial │ │ │ │ ├── __init__.py │ │ │ │ ├── __init__.pyc │ │ │ │ ├── chebyshev.py │ │ │ │ ├── chebyshev.pyc │ │ │ │ ├── hermite.py │ │ │ │ ├── hermite.pyc │ │ │ │ ├── hermite_e.py │ │ │ │ ├── hermite_e.pyc │ │ │ │ ├── laguerre.py │ │ │ │ ├── laguerre.pyc │ │ │ │ ├── legendre.py │ │ │ │ ├── legendre.pyc │ │ │ │ ├── polynomial.py │ │ │ │ ├── polynomial.pyc │ │ │ │ ├── polytemplate.py │ │ │ │ ├── polytemplate.pyc │ │ │ │ ├── polyutils.py │ │ │ │ ├── polyutils.pyc │ │ │ │ └── setup.py │ │ │ ├── random │ │ │ │ ├── __init__.py │ │ │ │ ├── __init__.pyc │ │ │ │ ├── info.py │ │ │ │ ├── info.pyc │ │ │ │ ├── mtrand.so │ │ │ │ └── setup.py │ │ │ ├── setup.py │ │ │ ├── testing │ │ │ │ ├── __init__.py │ │ │ │ ├── __init__.pyc │ │ │ │ ├── decorators.py │ │ │ │ ├── decorators.pyc │ │ │ │ ├── noseclasses.py │ │ │ │ ├── nosetester.py │ │ │ │ ├── nosetester.pyc │ │ │ │ ├── numpytest.py │ │ │ │ ├── numpytest.pyc │ │ │ │ ├── print_coercion_tables.py │ │ │ │ ├── setup.py │ │ │ │ ├── utils.py │ │ │ │ └── utils.pyc │ │ │ ├── version.py │ │ │ └── version.pyc │ │ ├── pybedtools │ │ │ ├── _Window.c │ │ │ ├── _Window.pyx │ │ │ ├── _Window.so │ │ │ ├── __init__.py │ │ │ ├── __main__.py │ │ │ ├── bedtool.py │ │ │ ├── cbedtools.cpp │ │ │ ├── cbedtools.pxd │ │ │ ├── cbedtools.pyx │ │ │ ├── cbedtools.so │ │ │ ├── colorize.py │ │ │ ├── contrib │ │ │ │ ├── __init__.py │ │ │ │ ├── bigbed.py │ │ │ │ ├── bigwig.py │ │ │ │ ├── classifier.py │ │ │ │ ├── intersection_matrix.py │ │ │ │ ├── plotting.py │ │ │ │ └── venn_maker.py │ │ │ ├── featurefuncs.cpp │ │ │ ├── featurefuncs.pyx │ │ │ ├── featurefuncs.so │ │ │ ├── genome_registry.py │ │ │ ├── handlers.py │ │ │ ├── helpers.py │ │ │ ├── parallel.py │ │ │ ├── scripts │ │ │ │ ├── __init__.py │ │ │ │ ├── annotate.py │ │ │ │ ├── examples │ │ │ │ │ └── pbt_plotting_example.py │ │ │ │ ├── intersection_matrix.py │ │ │ │ ├── intron_exon_reads.py │ │ │ │ ├── peak_pie.py │ │ │ │ ├── py_ms_example.py │ │ │ │ ├── pybedtools │ │ │ │ ├── pybedtools_demo.py │ │ │ │ ├── venn_gchart.py │ │ │ │ └── venn_mpl.py │ │ │ ├── seqtest.py │ │ │ ├── settings.py │ │ │ ├── stats.py │ │ │ ├── tempfiles.py │ │ │ └── version.py │ │ └── vcf │ │ │ ├── __init__.py │ │ │ ├── __init__.pyc │ │ │ ├── cparse.pyx │ │ │ ├── filters.py │ │ │ ├── filters.pyc │ │ │ ├── model.py │ │ │ ├── model.pyc │ │ │ ├── parser.py │ │ │ ├── parser.pyc │ │ │ ├── test │ │ │ ├── __init__.py │ │ │ ├── prof.py │ │ │ └── test_vcf.py │ │ │ └── utils.py │ ├── read_depth_ratio_plusCovSigSeg.R │ ├── sv_calling_vcf_pawg_dkfz.sh │ ├── vcf-sort │ ├── vcf_index.sh │ └── vcfcombine ├── config │ ├── DELLYWorkflow.ini │ └── pom.xml ├── docker │ ├── config │ │ ├── DELLYWorkflow.ini │ │ ├── Dockerfile │ │ └── pom.xml │ └── src │ │ └── DELLYWorkflow.java ├── links │ └── REFGENOME_AND_REFGENOME_GC_GO_HERE ├── src │ └── DELLYWorkflow.java └── usr │ └── bin │ ├── annotateSvCalls_delly_vcf.sh │ ├── svAnnotation_delly_vcf.sh │ └── update_SVs.sh ├── full_workflow └── img └── 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