├── .gitignore ├── AUTHORS ├── LICENSE ├── Makefile.am ├── README.md ├── autogen.sh ├── ax_bam.m4 ├── ax_boost_base.m4 ├── ax_boost_filesystem.m4 ├── ax_boost_serialization.m4 ├── ax_boost_system.m4 ├── ax_boost_thread.m4 ├── ax_check_eigen.m4 ├── ax_check_zlib.m4 ├── ax_openmp.m4 ├── boost.m4 ├── configure.ac ├── cufflinks.xcodeproj ├── cole.pbxuser ├── cole.perspectivev3 └── project.pbxproj ├── doc ├── CL_figure_scratch.doc ├── CL_main_text.doc ├── CL_supplement.tex ├── CL_versions.tex ├── Cartoons.pptx ├── Paper Outline.doc ├── algorithm │ ├── algorithm.bib │ ├── algorithm.pdf │ ├── algorithm.tex │ └── homework.cls ├── cufflinks.bib ├── html │ ├── css │ │ └── style.css │ ├── downloads │ │ └── test_data.sam │ ├── faq.html │ ├── gff.html │ ├── howitworks.html │ ├── igenome │ │ └── igenome_table.py │ ├── igenomes.html │ ├── images │ │ ├── ABC.png │ │ ├── JHU-seal.gif │ │ ├── JS.png │ │ ├── UCBerkeley-seal.gif │ │ ├── UCBerkeley-seal.scaled.gif │ │ ├── X_g.png │ │ ├── bg.jpg │ │ ├── bluec_l.gif │ │ ├── bluec_r.gif │ │ ├── cbcb_logo.gif │ │ ├── cbcblogo.gif │ │ ├── cbcblogo.jpg │ │ ├── cbcblogoandtext.gif │ │ ├── cbcbstrip.jpg │ │ ├── count_var_system.png │ │ ├── csail-logo-2C-full.svg │ │ ├── csail-logo-2C-notext.png │ │ ├── csail-logo-2C-notext.svg │ │ ├── entropy.png │ │ ├── est_trans_count.png │ │ ├── footer.jpg │ │ ├── fpkm_ratio.png │ │ ├── fpkm_var.png │ │ ├── gamma_t.png │ │ ├── greyc.gif │ │ ├── head.gif │ │ ├── log_norm_ratio.png │ │ ├── log_norm_ratio_approx.png │ │ ├── menu.jpg │ │ ├── menul.jpg │ │ ├── menur.jpg │ │ ├── osi-certified.gif │ │ ├── p_alpha_beta.png │ │ ├── psi_cost.png │ │ ├── psi_t_t.png │ │ ├── sep.gif │ │ ├── top.jpg │ │ ├── topl.jpg │ │ ├── topr.jpg │ │ ├── tuxedo_workflow.png │ │ ├── tuxedo_workflow.svg │ │ ├── ucsc-track.jpg │ │ ├── ucsc-track.tiff │ │ ├── var_gene_count.png │ │ └── var_transcript_count.png │ ├── index.html │ ├── manual.html │ ├── site.tmproj │ └── tutorial.html ├── illustrator │ └── Fig 2 - Tuxedo Workflow.ai └── pdfs │ ├── Actn.pdf │ ├── Additional_RT-PCR.pdf │ ├── Compatibility.pdf │ ├── Ddx.pdf │ ├── Dilworth_Konig.pdf │ ├── FHL3_RT-PCR.pdf │ ├── FHL3_RT-PCR.svg │ ├── Fhl3_RTN4.pdf │ ├── Mef2.pdf │ ├── Myf6_Myf5.pdf │ ├── Myl1.pdf │ ├── MyoD_Myog.pdf │ ├── Tpm1_Tpm2.pdf │ ├── categories.pdf │ ├── implied_length.pdf │ ├── library_frags.pdf │ ├── nomogram.pdf │ ├── promoter_overloaded.pdf │ ├── sim.pdf │ ├── sim_small.pdf │ ├── spikes.pdf │ ├── splice_overloaded.pdf │ ├── vs_no_discovery.pdf │ └── vs_no_discovery_small.pdf ├── external_tests └── tiny_tests │ └── 2x75 │ ├── accepted_hits.sam │ └── test_ref.fa ├── index.md ├── make_bin.sh ├── src ├── GArgs.cpp ├── GArgs.h ├── GBase.cpp ├── GBase.h ├── GFaSeqGet.cpp ├── GFaSeqGet.h ├── GFastaIndex.cpp ├── GFastaIndex.h ├── GHash.hh ├── GList.hh ├── GStr.cpp ├── GStr.h ├── GVec.hh ├── LICENSE ├── Makefile.am ├── abundances.cpp ├── abundances.h ├── assemble.cpp ├── assemble.h ├── biascorrection.cpp ├── biascorrection.h ├── bundles.cpp ├── bundles.h ├── clustering.cpp ├── clustering.h ├── codons.cpp ├── codons.h ├── common.cpp ├── common.h ├── compress_gtf.cpp ├── cuffcluster.cpp ├── cuffcompare.cpp ├── cuffdiff.cpp ├── cuffdiff_to_gct.py ├── cufflinks.cpp ├── cufflinks.xcodeproj │ ├── cole.pbxuser │ ├── cole.perspectivev3 │ └── project.pbxproj ├── cuffmerge ├── cuffnorm.cpp ├── cuffquant.cpp ├── differential.cpp ├── differential.h ├── filters.cpp ├── filters.h ├── gdna.cpp ├── gdna.h ├── genes.cpp ├── genes.h ├── gff.cpp ├── gff.h ├── gff_utils.cpp ├── gff_utils.h ├── gffread.cpp ├── graph_optimize.cpp ├── graph_optimize.h ├── gtf_reads.cpp ├── gtf_to_sam.cpp ├── gtf_tracking.cpp ├── gtf_tracking.h ├── hits.cpp ├── hits.h ├── jensen_shannon.cpp ├── jensen_shannon.h ├── lemon │ ├── bfs.h │ ├── bin_heap.h │ ├── bipartite_matching.h │ ├── bits │ │ ├── alteration_notifier.h │ │ ├── array_map.h │ │ ├── base_extender.h │ │ ├── debug_map.h │ │ ├── default_map.h │ │ ├── graph_adaptor_extender.h │ │ ├── graph_extender.h │ │ ├── invalid.h │ │ ├── map_extender.h │ │ ├── path_dump.h │ │ ├── traits.h │ │ ├── utility.h │ │ ├── variant.h │ │ └── vector_map.h │ ├── bucket_heap.h │ ├── concept_check.h │ ├── concepts │ │ ├── bpugraph.h │ │ ├── graph.h │ │ ├── graph_components.h │ │ ├── heap.h │ │ ├── maps.h │ │ ├── matrix_maps.h │ │ ├── path.h │ │ └── ugraph.h │ ├── dfs.h │ ├── error.h │ ├── fib_heap.h │ ├── graph_adaptor.h │ ├── graph_utils.h │ ├── list_graph.h │ ├── maps.h │ ├── math.h │ ├── smart_graph.h │ ├── tolerance.h │ └── topology.h ├── locfit │ ├── adap.c │ ├── ar_funs.c │ ├── arith.c │ ├── band.c │ ├── c_args.c │ ├── c_plot.c │ ├── cmd.c │ ├── dens_haz.c │ ├── dens_int.c │ ├── dens_odi.c │ ├── density.c │ ├── design.h │ ├── dist.c │ ├── ev_atree.c │ ├── ev_interp.c │ ├── ev_kdtre.c │ ├── ev_main.c │ ├── ev_trian.c │ ├── family.c │ ├── fitted.c │ ├── frend.c │ ├── help.c │ ├── imatlb.h │ ├── lf_dercor.c │ ├── lf_fitfun.c │ ├── lf_robust.c │ ├── lf_vari.c │ ├── lfcons.h │ ├── lfd.c │ ├── lffuns.h │ ├── lfstr.c │ ├── lfstruc.h │ ├── lfwin.h │ ├── linalg.c │ ├── local.h │ ├── locfit.c │ ├── m_chol.c │ ├── m_eigen.c │ ├── m_jacob.c │ ├── m_max.c │ ├── makecmd.c │ ├── math.c │ ├── minmax.c │ ├── mutil.h │ ├── nbhd.c │ ├── pcomp.c │ ├── pout.c │ ├── preplot.c │ ├── random.c │ ├── readfile.c │ ├── scb.c │ ├── scb_cons.c │ ├── simul.c │ ├── solve.c │ ├── startlf.c │ ├── strings.c │ ├── vari.cpp │ ├── vari.hpp │ ├── wdiag.c │ └── weight.c ├── matching_merge.cpp ├── matching_merge.h ├── multireads.cpp ├── multireads.h ├── negative_binomial_distribution.h ├── progressbar.h ├── replicates.cpp ├── replicates.h ├── rounding.h ├── sampling.cpp ├── sampling.h ├── scaffold_graph.cpp ├── scaffold_graph.h ├── scaffolds.cpp ├── scaffolds.h ├── tokenize.cpp ├── tokenize.h ├── tracking.cpp ├── tracking.h ├── transitive_closure.h ├── transitive_reduction.h └── update_check.h ├── tests └── unit_tests │ ├── test_abundances.cpp │ ├── test_main.cpp │ └── test_scaffolds.cpp └── version.m4 /.gitignore: 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