├── .gitignore ├── Build ├── INSTALL ├── LICENSE ├── README.md ├── bin ├── cal_genome_enrichment.pl ├── convert2annovar.pl ├── secondary │ ├── addVCFHeader │ ├── checkSampleGT │ ├── checkupgrade │ ├── convertConfig │ ├── convertQCstat │ ├── download │ ├── filterByMapQ.pl │ ├── fixVarscanSample │ ├── genVarStat │ ├── getFastaSeq.pl │ ├── html_gen │ ├── interleave_fastq │ ├── mendelfix │ ├── mergeBAMOneRG │ ├── mergeBAMUnionRG │ ├── phred64to33 │ ├── pipeline │ ├── readFilter │ ├── rmDupAltVCF │ ├── run │ ├── runBOWTIE │ ├── runBOWTIE2 │ ├── runBWA │ ├── runBWA-MEM │ ├── runFREEBAYES │ ├── runGATKFULLCALL │ ├── runGATKFULLFILTER │ ├── runGATKFULLREALN │ ├── runGATKFULLRECAL │ ├── runGATKLITECALL │ ├── runGATKLITEFILTER │ ├── runGATKLITEREALN │ ├── runGATKLITERECAL │ ├── runSAMTOOLS │ ├── runSNAP │ ├── runSNVER │ ├── runSOAP │ ├── runSOAPSNP │ ├── runVARSCAN │ ├── sameBAMSQ │ ├── snver_code_in_pipeline │ ├── splitVCFbySample │ ├── split_bam │ ├── stats │ ├── stats_with_filter │ ├── test_suite │ ├── test_suite_bam │ ├── test_suite_exome │ ├── update │ ├── vcfsorter │ └── worker ├── seqmule ├── soap2sam.pl └── soapsnp2vcf ├── doc ├── Installation.md ├── Manuals │ ├── download.md │ ├── pipeline.md │ ├── run.md │ ├── stats.md │ └── update.md ├── Miscellaneous │ ├── Caveats.md │ ├── ChangeLog.md │ ├── FAQ.md │ └── TechNotes.md ├── Tutorials │ ├── Analysis.md │ ├── Execution.md │ └── Quick start.md ├── favicon.ico ├── img │ └── seqmule.png └── index.md ├── docker ├── Dockerfile ├── README.md └── build.sh ├── img └── seqmule.png ├── inc └── boost_lib │ └── boost │ ├── aligned_storage.hpp │ ├── assert.hpp │ ├── bind.hpp │ ├── bind │ ├── arg.hpp │ ├── bind.hpp │ ├── bind_cc.hpp │ ├── bind_mf2_cc.hpp │ ├── bind_mf_cc.hpp │ ├── bind_template.hpp │ ├── mem_fn.hpp │ ├── mem_fn_cc.hpp │ ├── mem_fn_template.hpp │ ├── placeholders.hpp │ └── storage.hpp │ ├── call_traits.hpp │ ├── checked_delete.hpp │ ├── concept │ ├── assert.hpp │ ├── detail │ │ ├── backward_compatibility.hpp │ │ ├── concept_def.hpp │ │ ├── concept_undef.hpp │ │ ├── general.hpp │ │ └── has_constraints.hpp │ └── usage.hpp │ ├── concept_check.hpp │ ├── config.hpp │ ├── config │ ├── abi_prefix.hpp │ ├── abi_suffix.hpp │ ├── auto_link.hpp │ ├── compiler │ │ └── gcc.hpp │ ├── no_tr1 │ │ ├── memory.hpp │ │ └── utility.hpp │ ├── platform │ │ └── linux.hpp │ ├── posix_features.hpp │ ├── select_compiler_config.hpp │ ├── select_platform_config.hpp │ ├── select_stdlib_config.hpp │ ├── stdlib │ │ └── libstdcpp3.hpp │ ├── suffix.hpp │ └── user.hpp │ ├── cstdint.hpp │ ├── current_function.hpp │ ├── detail │ ├── call_traits.hpp │ ├── indirect_traits.hpp │ ├── is_incrementable.hpp │ ├── iterator.hpp │ ├── sp_typeinfo.hpp │ └── workaround.hpp │ ├── exception │ ├── detail │ │ └── attribute_noreturn.hpp │ └── exception.hpp │ ├── get_pointer.hpp │ ├── integer_traits.hpp │ ├── iostreams │ ├── categories.hpp │ ├── chain.hpp │ ├── char_traits.hpp │ ├── checked_operations.hpp │ ├── close.hpp │ ├── concepts.hpp │ ├── constants.hpp │ ├── copy.hpp │ ├── detail │ │ ├── access_control.hpp │ │ ├── adapter │ │ │ ├── concept_adapter.hpp │ │ │ ├── mode_adapter.hpp │ │ │ ├── non_blocking_adapter.hpp │ │ │ ├── output_iterator_adapter.hpp │ │ │ └── range_adapter.hpp │ │ ├── bool_trait_def.hpp │ │ ├── buffer.hpp │ │ ├── call_traits.hpp │ │ ├── char_traits.hpp │ │ ├── config │ │ │ ├── auto_link.hpp │ │ │ ├── codecvt.hpp │ │ │ ├── disable_warnings.hpp │ │ │ ├── dyn_link.hpp │ │ │ ├── enable_warnings.hpp │ │ │ ├── fpos.hpp │ │ │ ├── gcc.hpp │ │ │ ├── limits.hpp │ │ │ ├── overload_resolution.hpp │ │ │ ├── unreachable_return.hpp │ │ │ ├── wide_streams.hpp │ │ │ └── zlib.hpp │ │ ├── default_arg.hpp │ │ ├── dispatch.hpp │ │ ├── double_object.hpp │ │ ├── enable_if_stream.hpp │ │ ├── error.hpp │ │ ├── execute.hpp │ │ ├── forward.hpp │ │ ├── functional.hpp │ │ ├── ios.hpp │ │ ├── is_dereferenceable.hpp │ │ ├── is_iterator_range.hpp │ │ ├── optional.hpp │ │ ├── push.hpp │ │ ├── push_params.hpp │ │ ├── resolve.hpp │ │ ├── select.hpp │ │ ├── select_by_size.hpp │ │ ├── streambuf.hpp │ │ ├── streambuf │ │ │ ├── chainbuf.hpp │ │ │ ├── direct_streambuf.hpp │ │ │ ├── indirect_streambuf.hpp │ │ │ └── linked_streambuf.hpp │ │ ├── template_params.hpp │ │ ├── translate_int_type.hpp │ │ └── wrap_unwrap.hpp │ ├── device │ │ ├── array.hpp │ │ ├── back_inserter.hpp │ │ └── null.hpp │ ├── filter │ │ ├── gzip.hpp │ │ ├── symmetric.hpp │ │ └── zlib.hpp │ ├── filtering_streambuf.hpp │ ├── flush.hpp │ ├── get.hpp │ ├── imbue.hpp │ ├── input_sequence.hpp │ ├── operations.hpp │ ├── operations_fwd.hpp │ ├── optimal_buffer_size.hpp │ ├── output_sequence.hpp │ ├── pipeline.hpp │ ├── positioning.hpp │ ├── put.hpp │ ├── putback.hpp │ ├── read.hpp │ ├── seek.hpp │ ├── stream_buffer.hpp │ ├── traits.hpp │ ├── traits_fwd.hpp │ └── write.hpp │ ├── is_placeholder.hpp │ ├── iterator.hpp │ ├── iterator │ ├── detail │ │ ├── config_def.hpp │ │ ├── config_undef.hpp │ │ ├── enable_if.hpp │ │ └── facade_iterator_category.hpp │ ├── interoperable.hpp │ ├── iterator_adaptor.hpp │ ├── iterator_categories.hpp │ ├── iterator_concepts.hpp │ ├── iterator_facade.hpp │ ├── iterator_traits.hpp │ └── reverse_iterator.hpp │ ├── limits.hpp │ ├── mem_fn.hpp │ ├── memory_order.hpp │ ├── mpl │ ├── always.hpp │ ├── and.hpp │ ├── apply.hpp │ ├── apply_fwd.hpp │ ├── apply_wrap.hpp │ ├── arg.hpp │ ├── arg_fwd.hpp │ ├── assert.hpp │ ├── aux_ │ │ ├── adl_barrier.hpp │ │ ├── arg_typedef.hpp │ │ ├── arity.hpp │ │ ├── arity_spec.hpp │ │ ├── common_name_wknd.hpp │ │ ├── config │ │ │ ├── adl.hpp │ │ │ ├── arrays.hpp │ │ │ ├── bcc.hpp │ │ │ ├── bind.hpp │ │ │ ├── compiler.hpp │ │ │ ├── ctps.hpp │ │ │ ├── dtp.hpp │ │ │ ├── eti.hpp │ │ │ ├── gcc.hpp │ │ │ ├── has_apply.hpp │ │ │ ├── has_xxx.hpp │ │ │ ├── integral.hpp │ │ │ ├── intel.hpp │ │ │ ├── lambda.hpp │ │ │ ├── msvc.hpp │ │ │ ├── msvc_typename.hpp │ │ │ ├── nttp.hpp │ │ │ ├── overload_resolution.hpp │ │ │ ├── pp_counter.hpp │ │ │ ├── preprocessor.hpp │ │ │ ├── static_constant.hpp │ │ │ ├── ttp.hpp │ │ │ ├── use_preprocessed.hpp │ │ │ └── workaround.hpp │ │ ├── full_lambda.hpp │ │ ├── has_apply.hpp │ │ ├── has_type.hpp │ │ ├── include_preprocessed.hpp │ │ ├── integral_wrapper.hpp │ │ ├── lambda_arity_param.hpp │ │ ├── lambda_support.hpp │ │ ├── msvc_never_true.hpp │ │ ├── na.hpp │ │ ├── na_assert.hpp │ │ ├── na_fwd.hpp │ │ ├── na_spec.hpp │ │ ├── nested_type_wknd.hpp │ │ ├── nttp_decl.hpp │ │ ├── preprocessed │ │ │ └── gcc │ │ │ │ ├── and.hpp │ │ │ │ ├── apply.hpp │ │ │ │ ├── apply_fwd.hpp │ │ │ │ ├── apply_wrap.hpp │ │ │ │ ├── arg.hpp │ │ │ │ ├── bind.hpp │ │ │ │ ├── bind_fwd.hpp │ │ │ │ ├── full_lambda.hpp │ │ │ │ ├── or.hpp │ │ │ │ ├── placeholders.hpp │ │ │ │ ├── quote.hpp │ │ │ │ └── template_arity.hpp │ │ ├── preprocessor │ │ │ ├── def_params_tail.hpp │ │ │ ├── enum.hpp │ │ │ └── params.hpp │ │ ├── static_cast.hpp │ │ ├── template_arity.hpp │ │ ├── template_arity_fwd.hpp │ │ ├── type_wrapper.hpp │ │ ├── value_wknd.hpp │ │ └── yes_no.hpp │ ├── bind.hpp │ ├── bind_fwd.hpp │ ├── bool.hpp │ ├── bool_fwd.hpp │ ├── eval_if.hpp │ ├── has_xxx.hpp │ ├── identity.hpp │ ├── if.hpp │ ├── int.hpp │ ├── int_fwd.hpp │ ├── integral_c.hpp │ ├── integral_c_fwd.hpp │ ├── integral_c_tag.hpp │ ├── lambda.hpp │ ├── lambda_fwd.hpp │ ├── limits │ │ └── arity.hpp │ ├── next.hpp │ ├── next_prior.hpp │ ├── not.hpp │ ├── or.hpp │ ├── placeholders.hpp │ ├── protect.hpp │ ├── quote.hpp │ ├── size_t.hpp │ ├── size_t_fwd.hpp │ ├── void.hpp │ └── void_fwd.hpp │ ├── next_prior.hpp │ ├── noncopyable.hpp │ ├── preprocessor │ ├── arithmetic │ │ ├── add.hpp │ │ ├── dec.hpp │ │ ├── detail │ │ │ └── div_base.hpp │ │ ├── inc.hpp │ │ ├── mod.hpp │ │ └── sub.hpp │ ├── array │ │ ├── data.hpp │ │ ├── elem.hpp │ │ └── size.hpp │ ├── cat.hpp │ ├── comma_if.hpp │ ├── comparison │ │ └── less_equal.hpp │ ├── config │ │ └── config.hpp │ ├── control │ │ ├── deduce_d.hpp │ │ ├── detail │ │ │ └── while.hpp │ │ ├── expr_if.hpp │ │ ├── expr_iif.hpp │ │ ├── if.hpp │ │ ├── iif.hpp │ │ └── while.hpp │ ├── debug │ │ └── error.hpp │ ├── detail │ │ ├── auto_rec.hpp │ │ ├── check.hpp │ │ └── is_binary.hpp │ ├── empty.hpp │ ├── facilities │ │ ├── empty.hpp │ │ ├── identity.hpp │ │ ├── intercept.hpp │ │ └── overload.hpp │ ├── identity.hpp │ ├── inc.hpp │ ├── iteration │ │ ├── detail │ │ │ ├── bounds │ │ │ │ ├── lower1.hpp │ │ │ │ └── upper1.hpp │ │ │ ├── iter │ │ │ │ └── forward1.hpp │ │ │ └── local.hpp │ │ ├── iterate.hpp │ │ └── local.hpp │ ├── list │ │ ├── adt.hpp │ │ ├── append.hpp │ │ ├── detail │ │ │ ├── fold_left.hpp │ │ │ └── fold_right.hpp │ │ ├── fold_left.hpp │ │ ├── fold_right.hpp │ │ ├── for_each_i.hpp │ │ ├── reverse.hpp │ │ └── transform.hpp │ ├── logical │ │ ├── and.hpp │ │ ├── bitand.hpp │ │ ├── bool.hpp │ │ ├── compl.hpp │ │ └── not.hpp │ ├── punctuation │ │ ├── comma.hpp │ │ └── comma_if.hpp │ ├── repeat.hpp │ ├── repetition │ │ ├── detail │ │ │ └── for.hpp │ │ ├── enum_binary_params.hpp │ │ ├── enum_params.hpp │ │ ├── enum_shifted_params.hpp │ │ ├── enum_trailing_params.hpp │ │ ├── for.hpp │ │ ├── repeat.hpp │ │ └── repeat_from_to.hpp │ ├── seq │ │ ├── cat.hpp │ │ ├── elem.hpp │ │ ├── enum.hpp │ │ ├── fold_left.hpp │ │ ├── for_each_i.hpp │ │ ├── seq.hpp │ │ ├── size.hpp │ │ └── transform.hpp │ ├── slot │ │ ├── detail │ │ │ ├── def.hpp │ │ │ └── shared.hpp │ │ └── slot.hpp │ ├── stringize.hpp │ ├── tuple │ │ ├── eat.hpp │ │ ├── elem.hpp │ │ ├── rem.hpp │ │ └── to_list.hpp │ └── variadic │ │ ├── elem.hpp │ │ └── size.hpp │ ├── range │ ├── algorithm │ │ └── equal.hpp │ ├── begin.hpp │ ├── concepts.hpp │ ├── config.hpp │ ├── const_iterator.hpp │ ├── detail │ │ ├── common.hpp │ │ ├── extract_optional_type.hpp │ │ ├── implementation_help.hpp │ │ ├── misc_concept.hpp │ │ ├── safe_bool.hpp │ │ └── sfinae.hpp │ ├── difference_type.hpp │ ├── distance.hpp │ ├── empty.hpp │ ├── end.hpp │ ├── functions.hpp │ ├── iterator.hpp │ ├── iterator_range.hpp │ ├── iterator_range_core.hpp │ ├── iterator_range_io.hpp │ ├── mutable_iterator.hpp │ ├── rbegin.hpp │ ├── rend.hpp │ ├── reverse_iterator.hpp │ ├── size.hpp │ ├── size_type.hpp │ └── value_type.hpp │ ├── ref.hpp │ ├── shared_ptr.hpp │ ├── smart_ptr │ ├── bad_weak_ptr.hpp │ ├── detail │ │ ├── operator_bool.hpp │ │ ├── shared_count.hpp │ │ ├── sp_convertible.hpp │ │ ├── sp_counted_base.hpp │ │ ├── sp_counted_base_gcc_x86.hpp │ │ ├── sp_counted_impl.hpp │ │ ├── sp_has_sync.hpp │ │ ├── spinlock.hpp │ │ ├── spinlock_pool.hpp │ │ ├── spinlock_sync.hpp │ │ └── yield_k.hpp │ └── shared_ptr.hpp │ ├── static_assert.hpp │ ├── throw_exception.hpp │ ├── type.hpp │ ├── type_traits │ ├── add_const.hpp │ ├── add_pointer.hpp │ ├── add_reference.hpp │ ├── add_rvalue_reference.hpp │ ├── add_volatile.hpp │ ├── aligned_storage.hpp │ ├── alignment_of.hpp │ ├── broken_compiler_spec.hpp │ ├── config.hpp │ ├── conversion_traits.hpp │ ├── detail │ │ ├── bool_trait_def.hpp │ │ ├── bool_trait_undef.hpp │ │ ├── cv_traits_impl.hpp │ │ ├── false_result.hpp │ │ ├── ice_and.hpp │ │ ├── ice_eq.hpp │ │ ├── ice_not.hpp │ │ ├── ice_or.hpp │ │ ├── is_function_ptr_helper.hpp │ │ ├── is_mem_fun_pointer_impl.hpp │ │ ├── size_t_trait_def.hpp │ │ ├── size_t_trait_undef.hpp │ │ ├── template_arity_spec.hpp │ │ ├── type_trait_def.hpp │ │ ├── type_trait_undef.hpp │ │ └── yes_no_type.hpp │ ├── function_traits.hpp │ ├── ice.hpp │ ├── integral_constant.hpp │ ├── intrinsics.hpp │ ├── is_abstract.hpp │ ├── is_arithmetic.hpp │ ├── is_array.hpp │ ├── is_base_and_derived.hpp │ ├── is_class.hpp │ ├── is_const.hpp │ ├── is_convertible.hpp │ ├── is_enum.hpp │ ├── is_float.hpp │ ├── is_function.hpp │ ├── is_integral.hpp │ ├── is_lvalue_reference.hpp │ ├── is_member_function_pointer.hpp │ ├── is_member_pointer.hpp │ ├── is_pod.hpp │ ├── is_pointer.hpp │ ├── is_reference.hpp │ ├── is_rvalue_reference.hpp │ ├── is_same.hpp │ ├── is_scalar.hpp │ ├── is_signed.hpp │ ├── is_union.hpp │ ├── is_unsigned.hpp │ ├── is_void.hpp │ ├── is_volatile.hpp │ ├── make_unsigned.hpp │ ├── remove_const.hpp │ ├── remove_cv.hpp │ ├── remove_pointer.hpp │ ├── remove_reference.hpp │ └── type_with_alignment.hpp │ ├── utility.hpp │ ├── utility │ ├── addressof.hpp │ ├── base_from_member.hpp │ ├── binary.hpp │ ├── declval.hpp │ ├── detail │ │ └── result_of_iterate.hpp │ ├── enable_if.hpp │ ├── identity_type.hpp │ └── result_of.hpp │ └── visit_each.hpp ├── lib ├── Config │ └── Tiny.pm ├── SeqMule │ ├── Install.pm │ ├── Parallel.pm │ ├── SeqUtils.pm │ └── Utils.pm ├── Sort │ └── Topological.pm └── VennDiagram_1.6.5.tar.gz ├── misc ├── advanced_config ├── db_locations ├── exe_locations ├── hg18.bed ├── hg18_exome.legacy.bed ├── hg18_exonPlus5bp_UCSCrefGene.bed ├── hg19.bed ├── hg19_exome.legacy.bed ├── hg19_exonPlus5bp_UCSCrefGene.bed ├── pipeline.jpg ├── predefined_config │ ├── bowtie1_samtools.config │ ├── bowtie2_freebayes.config │ ├── bowtie2_gatk.config │ ├── bowtie2_gatk_HaplotypeCaller.config │ ├── bowtie2_gatk_HaplotypeCaller_norealn_norecal.config │ ├── bowtie2_gatk_HaplotypeCaller_samtools.config │ ├── bowtie2_gatk_HaplotypeCaller_samtools_varscan.config │ ├── bowtie2_gatklite_norealn_norecal.config │ ├── bowtie2_gatklite_norecal.config │ ├── bowtie2_gatklite_samtools.config │ ├── bowtie2_gatklite_samtools_varscan.config │ ├── bowtie2_samtools.config │ ├── bwa_backtrack_gatk.config │ ├── bwa_backtrack_samtools.config │ ├── bwa_freebayes.config │ ├── bwa_gatk.config │ ├── bwa_gatk_HaplotypeCaller.config │ ├── bwa_gatk_HaplotypeCaller_norealn_norecal.config │ ├── bwa_gatk_HaplotypeCaller_samtools.config │ ├── bwa_gatk_HaplotypeCaller_samtools_varscan.config │ ├── bwa_gatklite_freebayes_varscan.config │ ├── bwa_gatklite_norealn_norecal.config │ ├── bwa_gatklite_norecal.config │ ├── bwa_gatklite_samtools.config │ ├── bwa_gatklite_samtools_freebayes.config │ ├── bwa_gatklite_samtools_varscan.config │ ├── bwa_samtools.config │ ├── forSomatic_bowtie2_samtools.config │ ├── forSomatic_bowtie2_varscan.config │ ├── forSomatic_bwa_samtools.config │ ├── forSomatic_bwa_varscan.config │ ├── forSomatic_snap_samtools.config │ ├── forSomatic_snap_samtools_varscan.config │ ├── forSomatic_snap_varscan.config │ ├── gen_predefined_config │ ├── snap_freebayes.config │ ├── snap_freebayes_samtools_varscan.config │ └── soap_soapsnp.config ├── script_for_internal_use │ ├── check_ref_capture_match │ ├── genManualMarkdown.pl │ ├── pkg_update.script │ ├── prepare_examples │ ├── prepare_freebayes_package │ │ └── prepare_freebayes_package │ ├── update_db_md5 │ ├── update_md5 │ └── whole_genome_consistency_eval_cmd └── template │ ├── css │ ├── ddsmoothmenu.css │ ├── lightbox.css │ ├── nivo-slider.css │ └── templatemo_style.css │ ├── images │ ├── seqmule_report.jpg │ ├── seqmule_workflow_bam.png │ ├── seqmule_workflow_fq.png │ ├── templatemo_body.jpg │ ├── templatemo_hbg.jpg │ ├── templatemo_header_nav.png │ ├── templatemo_hr_divider.png │ ├── templatemo_image_frame_160.png │ ├── templatemo_image_frame_215.png │ ├── templatemo_image_frame_300.png │ ├── templatemo_image_frame_430.png │ ├── 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