Commit b3c9819f authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 0.7.4

parent 74101643

Dockerfile

+11 −5
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@@ -3,11 +3,17 @@ MAINTAINER Matei David <matei.david.at.oicr.on.ca> 
ARG DEBIAN_FRONTEND=noninteractive



# install prerequisites

RUN apt-get update && \

RUN for i in 1 2 3; do \

        apt-get update \

        && break; sleep 1; \

    done && \

    for i in 1 2 3; do \

        apt-get install -y \

             build-essential \

             cmake \

        libhdf5-dev

             libhdf5-dev \

        && break; sleep 1; \

    done



# if necessary, specify compiler

#RUN apt-get install -y g++-4.9 g++-5 g++-6

README.org

+1 −1
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@@ -2,7 +2,7 @@ 


*** Nanocall: An Oxford Nanopore Basecaller



[[http://travis-ci.org/mateidavid/nanocall][http://travis-ci.org/mateidavid/nanocall.svg?branch=master]]

[[http://travis-ci.org/mateidavid/nanocall][http://travis-ci.org/mateidavid/nanocall.svg?branch=master]] [[https://tldrlegal.com/license/mit-license][http://img.shields.io/:license-mit-blue.svg]]



**** Installation

VERSION

+1 −1
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0.6.14
 
0.7.4

src/Makefile

deleted100644 → 0
+0 −35
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SHELL := /bin/bash



HDF_ROOT = /usr



OPT_FLAG = -O0

CXXFLAGS = -Wall -Wextra -pedantic -g3 -ggdb -fno-eliminate-unused-debug-types ${OPT_FLAG}

M_CXXFLAGS = -std=c++11 -pthread

CPPFLAGS = -isystem ${HDF_ROOT}/include -I fast5/src -I tclap/include -I hpptools/include



TARGETS = compute-state-transitions compute-scaled-pore-model run-fwbw run-viterbi nanocall



.PHONY: all test clean



all: ${TARGETS}



clean:

	rm -rf ${TARGETS}



compute-state-transitions: compute-state-transitions.cpp

	${CXX} ${M_CXXFLAGS} ${CXXFLAGS} ${CPPFLAGS} $^ -o $@ ${LDFLAGS}



compute-scaled-pore-model: compute-scaled-pore-model.cpp

	${CXX} ${M_CXXFLAGS} ${CXXFLAGS} ${CPPFLAGS} $^ -o $@ ${LDFLAGS} -L ${HDF_ROOT}/lib -lhdf5



run-fwbw: run-fwbw.cpp

	${CXX} ${M_CXXFLAGS} ${CXXFLAGS} ${CPPFLAGS} $^ -o $@ ${LDFLAGS} -lz



run-viterbi: run-viterbi.cpp

	${CXX} ${M_CXXFLAGS} ${CXXFLAGS} ${CPPFLAGS} $^ -o $@ ${LDFLAGS} -lz



nanocall: nanocall.cpp Builtin_Model.cpp

	${CXX} ${M_CXXFLAGS} ${CXXFLAGS} ${CPPFLAGS} $^ -o $@ ${LDFLAGS} -L ${HDF_ROOT}/lib -lhdf5 -lz



list-directory: list-directory.cpp

	${CXX} ${M_CXXFLAGS} ${CXXFLAGS} ${CPPFLAGS} $^ -o $@ ${LDFLAGS}

src/nanocall/Event.hpp

+8 −2
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@@ -22,7 +22,7 @@ public: 
    Float_Type log_mean;

    Float_Type log_corrected_mean;

    Float_Type log_stdv;

    Float_Type log_start;

    //Float_Type log_start;

    //

    Float_Type orig_mean;

    Float_Type p_model_state;
@@ -32,10 +32,16 @@ public: 
    //

    void update_logs()

    {

        assert(mean > 0);

        log_mean = std::log(mean);

        assert(corrected_mean > 0);

        log_corrected_mean = std::log(corrected_mean);

        if (stdv == 0.0)

        {

            stdv = 0.01;

        }

        log_stdv = std::log(stdv);

        log_start = std::log(start);

        //log_start = std::log(start);

    }

    void set_model_state(const std::string& s)

    {