This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository nanopolish.
commit 000c04e5fc7f2190551f79c4ac7ecf76fcbeb2a4 Merge: 1d012e1 7f34bba Author: Andreas Tille <[email protected]> Date: Fri Sep 1 07:27:11 2017 +0200 Updated version 0.7.2 from 'upstream/0.7.2' with Debian dir 56b006e3e20382644e4806ea684659378e7b46bc Dockerfile | 4 +- Makefile | 50 +- README.md | 97 +- etc/r9-models/nanopolish_models.fofn | 2 - etc/r9-models/r9.4_450bps.cpg.6mer.template.model | 15630 ++++++++++++++++++ .../r9.4_450bps.nucleotide.5mer.template.model | 1030 ++ .../r9.4_450bps.nucleotide.6mer.template.model | 4102 +++++ etc/r9-models/r9_250bps.cpg.6mer.template.model | 15632 ++++++++++++++++++ ...r9_250bps.nucleotide.5mer.complement.pop1.model | 1031 ++ ...r9_250bps.nucleotide.5mer.complement.pop2.model | 1031 ++ .../r9_250bps.nucleotide.5mer.template.model | 1031 ++ ...9_250bps.nucleotide.6mer.complement.pop1.model} | 9 +- ...r9_250bps.nucleotide.6mer.complement.pop2.model | 4102 +++++ ...el => r9_250bps.nucleotide.6mer.template.model} | 7 +- etc/r9-models/template_median68pA.5mers.model | 1030 -- scripts/calculate_methylation_frequency.py | 83 + scripts/convert_all_models.py | 30 + scripts/convert_model_to_header.py | 103 + scripts/dropmodel.py | 23 +- scripts/import_ont_model.py | 65 + scripts/import_ont_models_from_dir.sh | 15 + scripts/nanopolish_makerange.py | 21 +- scripts/nanopolish_merge.py | 34 +- src/alignment/nanopolish_alignment_db.cpp | 256 +- src/alignment/nanopolish_alignment_db.h | 52 +- src/alignment/nanopolish_anchor.cpp | 6 +- src/alignment/nanopolish_anchor.h | 3 +- src/alignment/nanopolish_eventalign.cpp | 30 +- .../r9_250bps_cpg_6mer_complement_pop1_model.inl | 15658 +++++++++++++++++++ .../r9_250bps_cpg_6mer_complement_pop2_model.inl | 15658 +++++++++++++++++++ .../r9_250bps_cpg_6mer_template_model.inl | 15658 +++++++++++++++++++ ...50bps_nucleotide_5mer_complement_pop1_model.inl | 1057 ++ ...50bps_nucleotide_5mer_complement_pop2_model.inl | 1057 ++ .../r9_250bps_nucleotide_5mer_template_model.inl | 1057 ++ ...50bps_nucleotide_6mer_complement_pop1_model.inl | 4129 +++++ ...50bps_nucleotide_6mer_complement_pop2_model.inl | 4129 +++++ .../r9_250bps_nucleotide_6mer_template_model.inl | 4129 +++++ .../r9_4_450bps_cpg_6mer_template_model.inl | 15658 +++++++++++++++++++ .../r9_4_450bps_nucleotide_5mer_template_model.inl | 1057 ++ .../r9_4_450bps_nucleotide_6mer_template_model.inl | 4129 +++++ src/common/alg.hpp | 654 + src/common/fs_support.hpp | 43 + src/common/logger.hpp | 330 +- src/common/nanopolish_alphabet.h | 8 +- src/common/nanopolish_bam_processor.cpp | 127 + src/common/nanopolish_bam_processor.h | 53 + src/common/nanopolish_bam_utils.cpp | 81 + src/common/nanopolish_bam_utils.h | 29 + src/common/nanopolish_common.cpp | 38 + src/common/nanopolish_common.h | 27 +- src/common/nanopolish_fast5_map.cpp | 5 +- src/common/nanopolish_model_names.cpp | 14 +- src/common/nanopolish_model_names.h | 8 +- src/common/nanopolish_variant.cpp | 865 +- src/common/nanopolish_variant.h | 80 +- src/hmm/nanopolish_builtin_models.h | 41 + src/hmm/nanopolish_emissions.h | 67 +- src/hmm/nanopolish_pore_model_set.cpp | 129 +- src/hmm/nanopolish_pore_model_set.h | 53 +- src/hmm/nanopolish_profile_hmm.cpp | 290 +- src/hmm/nanopolish_profile_hmm.h | 84 - src/hmm/nanopolish_profile_hmm_r7.cpp | 194 + src/hmm/nanopolish_profile_hmm_r7.h | 84 + ...ofile_hmm.inl => nanopolish_profile_hmm_r7.inl} | 266 +- src/hmm/nanopolish_profile_hmm_r9.cpp | 197 + ...h_profile_hmm.h => nanopolish_profile_hmm_r9.h} | 59 +- ...ofile_hmm.inl => nanopolish_profile_hmm_r9.inl} | 164 +- src/hmm/nanopolish_transition_parameters.cpp | 2 +- src/main/nanopolish.cpp | 38 +- src/nanopolish_call_methylation.cpp | 442 + ..._methyltest.h => nanopolish_call_methylation.h} | 8 +- src/nanopolish_call_variants.cpp | 406 +- src/nanopolish_consensus.cpp | 16 +- src/nanopolish_extract.cpp | 382 + src/nanopolish_extract.h | 16 + src/nanopolish_getmodel.cpp | 31 +- src/nanopolish_haplotype.cpp | 10 + src/nanopolish_haplotype.h | 4 + src/nanopolish_methyltest.cpp | 522 - src/nanopolish_methyltrain.cpp | 411 +- src/nanopolish_phase_reads.cpp | 386 + src/nanopolish_phase_reads.h | 13 + src/nanopolish_poremodel.cpp | 131 +- src/nanopolish_poremodel.h | 33 +- src/nanopolish_scorereads.cpp | 2 +- src/nanopolish_squiggle_read.cpp | 923 +- src/nanopolish_squiggle_read.h | 71 +- src/nanopolish_train_poremodel_from_basecalls.cpp | 12 +- src/nanopolish_variant_db.cpp | 191 + src/nanopolish_variant_db.h | 147 + src/test/nanopolish_test.cpp | 129 +- src/training_core.cpp | 16 +- src/training_core.hpp | 37 +- 93 files changed, 133763 insertions(+), 3491 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/nanopolish.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
