[med-svn] [nanopolish] branch master updated (fbe48f9 -> e3ac028)
Andreas Tille
tille at debian.org
Fri Sep 1 06:39:31 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository nanopolish.
from fbe48f9 Make sure abs() gets int arguments
new 1d012e1 More abs() replacements
adds 7f34bba New upstream version 0.7.2
new 000c04e Updated version 0.7.2 from 'upstream/0.7.2'
new 428a685 New upstream version
new e3ac028 Refresh patches
The 4 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
Dockerfile | 4 +-
Makefile | 50 +-
README.md | 97 +-
debian/changelog | 3 +-
debian/patches/adjust-include-path.patch | 39 +-
debian/patches/compiler-flags.patch | 20 +-
debian/patches/external-libs.patch | 40 +-
debian/patches/fast5-0.5.6.patch | 33 -
debian/patches/fix-ftbfs-with-gcc6.patch | 14 -
debian/patches/gcc-7.patch | 16 -
debian/patches/reproducible.patch | 6 +-
debian/patches/series | 3 -
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 +-
102 files changed, 133790 insertions(+), 3638 deletions(-)
delete mode 100644 debian/patches/fast5-0.5.6.patch
delete mode 100644 debian/patches/fix-ftbfs-with-gcc6.patch
delete mode 100644 debian/patches/gcc-7.patch
delete mode 100644 etc/r9-models/nanopolish_models.fofn
create mode 100644 etc/r9-models/r9.4_450bps.cpg.6mer.template.model
create mode 100644 etc/r9-models/r9.4_450bps.nucleotide.5mer.template.model
create mode 100644 etc/r9-models/r9.4_450bps.nucleotide.6mer.template.model
create mode 100644 etc/r9-models/r9_250bps.cpg.6mer.template.model
create mode 100644 etc/r9-models/r9_250bps.nucleotide.5mer.complement.pop1.model
create mode 100644 etc/r9-models/r9_250bps.nucleotide.5mer.complement.pop2.model
create mode 100644 etc/r9-models/r9_250bps.nucleotide.5mer.template.model
copy etc/r9-models/{template_median68pA.model => r9_250bps.nucleotide.6mer.complement.pop1.model} (99%)
create mode 100644 etc/r9-models/r9_250bps.nucleotide.6mer.complement.pop2.model
rename etc/r9-models/{template_median68pA.model => r9_250bps.nucleotide.6mer.template.model} (99%)
delete mode 100644 etc/r9-models/template_median68pA.5mers.model
create mode 100644 scripts/calculate_methylation_frequency.py
create mode 100644 scripts/convert_all_models.py
create mode 100644 scripts/convert_model_to_header.py
create mode 100644 scripts/import_ont_model.py
create mode 100755 scripts/import_ont_models_from_dir.sh
create mode 100644 src/builtin_models/r9_250bps_cpg_6mer_complement_pop1_model.inl
create mode 100644 src/builtin_models/r9_250bps_cpg_6mer_complement_pop2_model.inl
create mode 100644 src/builtin_models/r9_250bps_cpg_6mer_template_model.inl
create mode 100644 src/builtin_models/r9_250bps_nucleotide_5mer_complement_pop1_model.inl
create mode 100644 src/builtin_models/r9_250bps_nucleotide_5mer_complement_pop2_model.inl
create mode 100644 src/builtin_models/r9_250bps_nucleotide_5mer_template_model.inl
create mode 100644 src/builtin_models/r9_250bps_nucleotide_6mer_complement_pop1_model.inl
create mode 100644 src/builtin_models/r9_250bps_nucleotide_6mer_complement_pop2_model.inl
create mode 100644 src/builtin_models/r9_250bps_nucleotide_6mer_template_model.inl
create mode 100644 src/builtin_models/r9_4_450bps_cpg_6mer_template_model.inl
create mode 100644 src/builtin_models/r9_4_450bps_nucleotide_5mer_template_model.inl
create mode 100644 src/builtin_models/r9_4_450bps_nucleotide_6mer_template_model.inl
create mode 100644 src/common/alg.hpp
create mode 100644 src/common/fs_support.hpp
create mode 100644 src/common/nanopolish_bam_processor.cpp
create mode 100644 src/common/nanopolish_bam_processor.h
create mode 100644 src/common/nanopolish_bam_utils.cpp
create mode 100644 src/common/nanopolish_bam_utils.h
create mode 100644 src/hmm/nanopolish_builtin_models.h
create mode 100644 src/hmm/nanopolish_profile_hmm_r7.cpp
create mode 100644 src/hmm/nanopolish_profile_hmm_r7.h
copy src/hmm/{nanopolish_profile_hmm.inl => nanopolish_profile_hmm_r7.inl} (55%)
create mode 100644 src/hmm/nanopolish_profile_hmm_r9.cpp
copy src/hmm/{nanopolish_profile_hmm.h => nanopolish_profile_hmm_r9.h} (50%)
rename src/hmm/{nanopolish_profile_hmm.inl => nanopolish_profile_hmm_r9.inl} (71%)
create mode 100644 src/nanopolish_call_methylation.cpp
rename src/{nanopolish_methyltest.h => nanopolish_call_methylation.h} (56%)
create mode 100644 src/nanopolish_extract.cpp
create mode 100644 src/nanopolish_extract.h
delete mode 100644 src/nanopolish_methyltest.cpp
create mode 100644 src/nanopolish_phase_reads.cpp
create mode 100644 src/nanopolish_phase_reads.h
create mode 100644 src/nanopolish_variant_db.cpp
create mode 100644 src/nanopolish_variant_db.h
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