Releases: UCSC-nanopore-cgl/signalAlign
Releases · UCSC-nanopore-cgl/signalAlign
Minor update
v1.0.0
v0.3.0
Docker (#31) * Add info about using local pip and remove python setup.py install from makefile so that users and install via pip * edited travis * make python3 install * added trusty as ubuntu box * maybe trusty this time * fix cparsers.c issue and modify setup.py as well as increase version to 0.2.1 * add cython to install before setting up * maybe this will work * install pysam from command line * update readme * Remove cparsers install * 2d_fix branch merge * revert to original nanoporeRead.py * Merged commits from embed_integration to soe_install * remove cythonize from ext_modules * Fix load_from_raw wrapper * Remove the NUM_OF_KMERS global variable * Fix finding signalMachine logic * probably fix segfault in signalMachine * Get kmer length from first kmer of npRead * Get kmer length from first kmer of npRead * uncomment tests * Throw error if data is empty * Fix variant calling to work with new variant ambiguous characters and lists of directories as input * get most of em working for rRNA * remove some output and correctly append when concat files * optional train transitions during EM * set lambda param along with event mean sd * re-define alpha if it is less than 1 * update for random read processing * real randomization... oops * add mod_only option * add mod_only to config * Update buildalignments to include stuff from embed * Remove redundant print statement * change CreateHdpTrainingData and bindings.generate_master_kmer_table to account for log file and change probability calculation for mean only descaling modeling * udpate travis with encrypted code, update setup with new py3helpers version, add nose option for creating new models * travis testing * add create_ambig_bases2 and test for loading positions model file * signalalign lib tests pass with create_ambig_chars2 * create ambig bases on fly with input file * update debug for multiprocess debug logic for signalalign and allow for passing in alphabet for hdp trainging * make it so signalalign sample can take ambig_model * fix entry points * fix logic error * fixed ambig_model issues * remove print statement * add mods to ambig dictionary * sort mods from model * Add plot_em_model_distributions * fix makefile * whoops * remove tree when destination exists for multiprocess signalalign samples, flush output after, add delete_alignments option and set write_hdp_training_file verbose option to debug * remove assignment output logic error * udpate plot_em_model_distributions to visualize assignments as well * fix logic error which cut off last set of mods * go back to mean only calculations * fix high number of variants, scatter vs non scatter and overall figure size scaling issue * fix variable kmer plotting issue by sorting kmers on input * fix weird shape error on different np version * add plot_multiple_variant_accuracy.py script * add plot_multiple_variant_accuracy to makefile * print progress statements and only execute plot_confusion_matrix for two variants * fix minor bugs in plot_labelled_read.py * output full and add overwrite to load_from_raw2 * fix rna based tombo plotting * update remove_sa_analysis to have basecall and all analysis options * multithreaded remove_sa_analysis * plot calibration curve * update plot_calivration curve and confusion matrix to plot correctly * copy config file if it is not already in destination directory * write file and fix precision curve plot * udpate plot_labelled_read and fast5 embedding for eventalign table * remove todo comment * add more accuracy metrics for per position accuracy * update to produce and parse full builtAssignment files * add overwrite parameter to train models * add overwrite to optional arguments * edit plot_multiple_variant_accuracy * minor tweak to trainModels and plot_multiple_variant_accuracy * Test em (#30) * rename filter_reads_to_string_wrapper to filter_reads_to_string_wrapper_funct * Fix multiple identical alignments in bam error * Major update and transfer to cmake * Update Dockerfile and remove old CMakeLists.txt * Remove map alignment error and minor alignedsignal error * Remove map alignment error and minor alignedsignal error * repack after running * Include external tools headers * Fix plot labelled read and pass overwrite through to correct location * Include filter reads and remove_sa_analyses.py in scripts * include sonlib include for tests * remove run wrapper for dockerfile * udpate dockerfile * update docker * update docker and travis * add nucleotide_encodings.md * remove some print statements * change aligned signal tests * add log file to test * remove output from test_compare_trained_models and removed test_mixture_model * removed output from filter reads tests * silence output of mea_algorithm tests and fix a minor error in temporary direcotory handling * silence sequence tools output * silence variant call outputs * remove output from runSignalAlign tests * fix up some syntax bugs and cleanup some PEP errors * fix minor bugs * add pytest.ini * fix mostly cosmetic issues * update tests and fix bug in plot_variant_accuracy.py * update pytest.ini * updated Dockerfile with tests and travis to run dockerfile * less verbose docker and fix git pull error with embed * added sonLib commit and Dockerfile update to install pytest correctly * add back test data from dockerignore * pytest * pytest * pytest * fix diagonal expansion error and optimize imports for signalalignment.py * get version from CMakeFile.txt * add another test * fix minor bugs * fix pandas deprecated .ix and check config for hdp * remove aec library from hdf5 * update dockerignore and fix file finding in hiddenMarkovModel * update setup.py to deal with h5py and pysam updates which break SA * fix changing directory in tests * remove emtpy class * assume runsSignalAlign.py is in the path * update dockerfile * update travis to run test then push runtime image * drop high memory requirement test * no error on runSignalAlign.py with bad argument * Remove old info and update version to 0.3.0 * use embed_dependencies base image Co-authored-by: Andrew D Bailey IV <adbailey4@citrisdance.soe.ucsc.edu> Co-authored-by: Ubuntu <ubuntu@ip-172-31-42-184.us-west-2.compute.internal>