[med-svn] [nanopolish] 02/04: Updated version 0.7.2 from 'upstream/0.7.2'
Andreas Tille
tille at debian.org
Fri Sep 1 06:39:32 UTC 2017
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tille pushed a commit to branch master
in repository nanopolish.
commit 000c04e5fc7f2190551f79c4ac7ecf76fcbeb2a4
Merge: 1d012e1 7f34bba
Author: Andreas Tille <tille at debian.org>
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(-)
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