repo_name stringlengths 6 97 | path stringlengths 3 341 | text stringlengths 8 1.02M |
|---|---|---|
bravegnu/mzero | src/clock.h | #ifndef CLOCK_H
#define CLOCK_H
#include <vector>
class ClockedIf
{
public:
virtual void execute(void) = 0;
};
class Clock
{
private:
std::vector<ClockedIf *> m_clocked_list;
public:
Clock();
void add_clocked(ClockedIf *clocked);
void tick();
};
#endif
|
bravegnu/mzero | src/alu.h | <reponame>bravegnu/mzero
// -*- mode: c++ -*-
#ifndef ALU_H
#define ALU_H
#include "decoder.h"
#include <cstdint>
class ALU;
typedef void (ALU::*ALUOp)();
enum class ShiftType {
LSL,
LSR,
ASR,
RRX,
ROR,
};
class ALU
{
private:
uint32_t *m_regs;
bool *m_c;
bool *m_v;
bool *m_n;
bool *m_z;
ui... |
bravegnu/mzero | src/utils.h | <reponame>bravegnu/mzero<filename>src/utils.h
#ifndef UTILS_H
#define UTILS_H
#include <stdexcept>
#include <cstring>
#include <string>
class IOError: public std::runtime_error {
public:
IOError(int err, std::string message): std::runtime_error(message + strerror(err)) {}
};
#endif
|
bravegnu/mzero | src/sysbus.h | #ifndef SYSBUS_H
#define SYSBUS_H
#include <vector>
#include <cstdint>
#include "device.h"
struct SysDevice {
uint32_t base_addr;
DeviceIf *device;
};
class SystemBus: public DeviceIf
{
private:
std::vector<SysDevice> m_devs;
public:
SystemBus();
void register_device(uint32_t base_addr, DeviceIf *dev);
... |
bravegnu/mzero | src/arm.h | <reponame>bravegnu/mzero
#ifndef ARM_H
#define ARM_H
#include <cstdint>
#include "clock.h"
#include "sysbus.h"
#include "decoder.h"
#include "alu.h"
#include "debug.h"
class CortexM0: public ClockedIf
{
private:
static const int MAX_REGS = 16;
uint32_t m_regs[MAX_REGS];
bool m_c;
bool m_o;
bool m_n;
bool... |
bravegnu/mzero | src/device.h | <filename>src/device.h
#ifndef DEVICE_H
#define DEVICE_H
#include <cstdint>
class DeviceIf
{
public:
virtual uint32_t read32(uint32_t addr) = 0;
virtual void write32(uint32_t addr, uint32_t data) = 0;
virtual uint32_t get_size() = 0;
};
#endif
|
bravegnu/mzero | src/memory.h | #ifndef MEMORY_H
#define MEMORY_H
#include "device.h"
#include <string>
#include <cstdint>
class Memory: public DeviceIf
{
private:
uint8_t *m_memory;
unsigned int m_size_kb;
uint32_t m_base_addr;
public:
Memory(unsigned int size_kb);
void load_bin(std::string filename, uint32_t offset);
uint32_t read32... |
AUAC-Technologies/AUAC-Core-Telemetry | Pipeline/PACKAGE_JSON.h | <reponame>AUAC-Technologies/AUAC-Core-Telemetry<filename>Pipeline/PACKAGE_JSON.h
/*MIT License
Copyright (c) 2020 <NAME>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, inclu... |
UMM-CSci-3403-Fall-2018/lab-3-memory-management-and-multi-dimensional-arrays-in-c-megabittronmini | mergesort/mergesort.c | #include<stdlib.h>
#include<stdio.h>
#include"mergesort.h"
//There's no need to sort an array less than size 2
bool needsSorting(int rangeSize) {
return rangeSize >= 2;
}
void mergeRanges(int *values, int start, int midPoint, int end) {
int rangeSize = end - start;
int *destination = (int*) calloc(rangeSi... |
UMM-CSci-3403-Fall-2018/lab-3-memory-management-and-multi-dimensional-arrays-in-c-megabittronmini | array_merge/array_merge.c | #include<stdlib.h>
#include<stdio.h>
#include"array_merge.h"
#include"../mergesort/mergesort.c"
int* array_merge(int num_arrays, int* sizes, int** values) {
// Count how many elements are in all arrays
int total_values = 0;
for (int i = 0; i < num_arrays; i++) {
total_values += sizes[i];
}
// If there ... |
Jakobimatrix/warning_guards | test/third_party_headers/register.h | void f(int x) {
//register int y = 2 * x;
}
|
Jakobimatrix/warning_guards | include/warning_guards/warning_guards.h | #ifndef COMMON_MACROS_H
#define COMMON_MACROS_H
// clang-format off
/*! Suppresses warnings in third party header files.
* Works with
* - GCC (https://gcc.gnu.org/onlinedocs/gcc/Diagnostic-Pragmas.html)
* - clang (http://clang.llvm.org/docs/UsersManual.html#controlling-diagnostics-via-pragmas)
*
* For reasons ... |
Jakobimatrix/warning_guards | test/third_party_headers/oldstyle_cast.h | <reponame>Jakobimatrix/warning_guards
int f(double x) {
return (int)x;
}
|
HPTears/TimeSeparateHelper | XKTimeSeparateHelper/Classes/XKTimeSeparateHelper.h | <reponame>HPTears/TimeSeparateHelper
//
// XKTimeSeparateHelper.h
// TimeSeparate
//
// Created by hupan on 2018/8/2.
// Copyright © 2018年 Tears. All rights reserved.
//
#import <Foundation/Foundation.h>
@interface XKTimeSeparateHelper : NSObject
/**
根据NSDate 返回年月 字符串 通过汉字分割
@param date date
@return 返回年月，通... |
HPTears/TimeSeparateHelper | XKTimeSeparateHelper/Classes/XKTimeManager.h | <gh_stars>0
//
// XKTimeManager.h
// TimeSeparate
//
// Created by hupan on 2018/8/2.
// Copyright © 2018年 Tears. All rights reserved.
//
#import <Foundation/Foundation.h>
@interface XKTimeManager : NSObject
@property (nonatomic, strong) NSDateFormatter *dateFormatter;
+ (instancetype)timeShareManager;
@end
|
MartinPippel/DAmar | msa/realigner.c | <filename>msa/realigner.c
/*****************************************************************************************\
* * *
* * These routines improve a multi-alignment of DNA sequences *
* * ... |
MartinPippel/DAmar | utils/LAcheck.c | <filename>utils/LAcheck.c
/*******************************************************************************************
*
* performs basic sanity checks on the overlaps
*
* Author: <NAME>
*
* Date : December 2014
*
*******************************************************************************************/
#in... |
MartinPippel/DAmar | db/fileUtils.c | #include "fileUtils.h"
#include "DB.h"
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
int isPacBioHeader(char* header)
{
char* c = header;
char* nameEnd;
char *pch;
// check if pacbio header is available
{
nameEnd = strchr(c, ' ');
if (nameEnd == NULL)
... |
MartinPippel/DAmar | utils/LAmergeUtils.h | <reponame>MartinPippel/DAmar<filename>utils/LAmergeUtils.h
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <assert.h>
#include <errno.h>
#include <getopt.h>
#include <sys/stat.h>
#include "db/DB.h"
#include "lib/pass.h"
#include "dalign/align.h"
#include "dalign/filter.h"
#define... |
MartinPippel/DAmar | lib/lasidx.h |
#pragma once
#include <stdio.h>
#include <db/DB.h>
typedef off_t lasidx;
lasidx* lasidx_create(HITS_DB* db, const char* pathLas);
lasidx* lasidx_load(HITS_DB* db, const char* pathLas, int create);
void lasidx_close(lasidx* idx);
|
MartinPippel/DAmar | utils/CTtrim.h | #include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <assert.h>
#include <errno.h>
#include <getopt.h>
#include <sys/stat.h>
#include "db/DB.h"
#include "lib/pass.h"
#include "dalign/align.h"
#include "dalign/filter.h"
#define TRIM_BIONANO_SINGLETON (1 << 0) // was not inc... |
MartinPippel/DAmar | lib/dmask.c | <filename>lib/dmask.c<gh_stars>10-100
#include <string.h>
#include <stdlib.h>
#include <assert.h>
#include <netdb.h>
#include <errno.h>
#include "dmask.h"
#include "dmask_proto.h"
static int hostname_to_ip(const char* hostname, char* ip)
{
struct hostent *he;
struct in_addr **addr_list;
if ((he = getho... |
MartinPippel/DAmar | lib/laz.h | <reponame>MartinPippel/DAmar
#pragma once
#include <stdio.h>
#include <stdlib.h>
#include <inttypes.h>
#include "dalign/align.h"
#define LAZ_MAGIC 0x254c415a
typedef struct
{
uint32_t magic;
uint16_t version;
uint16_t twidth;
uint64_t novl;
uint64_t reserved1;
uint64_t ... |
MartinPippel/DAmar | dalign/daligner.c | /************************************************************************************\
* *
* Copyright (c) 2014, Dr. <NAME> (EWM). All rights reserved. *
* ... |
MartinPippel/DAmar | lib/borders.c | /*******************************************************************************************
*
* Date : January 2014
*
*******************************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sys/param.h>
#include <assert.h... |
MartinPippel/DAmar | dalign/align.h | <gh_stars>10-100
/************************************************************************************\
* *
* Copyright (c) 2014, Dr. <NAME> (EWM). All rights reserved. *
* ... |
MartinPippel/DAmar | lib.ext/bitarr.h | /* bitarr.h */
/*
Prototypes for bitarr.c
IMPORTANT NOTE: A version of this code appeared in
Dr. Dobb's Journal issue #233 (August 1995)
Volume 20 Issue 8
in an article entitled `Implementing Bit Vectors in C'
by <NAME>
... |
MartinPippel/DAmar | scrub/qsort_r.h |
#ifndef __QSORTR_HEADER
#define __QSORTR_HEADER
// qsort_r is not part of the POSIX standard and the various incarnations of the
// function have different argument orders for the qsort_r call itself and the
// comparison function
#if defined (__APPLE__) || defined (__FreeBSD__)
#define QSORT_R(A,B,C,D,E) qsort... |
MartinPippel/DAmar | lib/trim.h |
#pragma once
#include "db/DB.h"
#include "dalign/align.h"
#include "lib/tracks.h"
#include "lib/pass.h"
#include "lib/read_loader.h"
typedef struct
{
HITS_DB* db;
HITS_TRACK* track;
Read_Loader* rl;
ovl_header_twidth twidth; // trace point spacing
Work_Data* align_work; // worki... |
MartinPippel/DAmar | db/FA2db.c | <reponame>MartinPippel/DAmar<filename>db/FA2db.c
/************************************************************************************\
* *
* Copyright (c) 2014, Dr. <NAME> (EWM). All rights reserved. *
* ... |
MartinPippel/DAmar | scrub/LAgap.c | /*******************************************************************************************
*
* Author : <NAME>
*
* Date : February 2016
*
*******************************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sys... |
MartinPippel/DAmar | scrub/LAlocal.c | <filename>scrub/LAlocal.c
/*******************************************************************************************
*
* creates a repeat annotation track (named -t) based on local alignments
*
* Date : February 2016
*
* Author : <NAME>
*
****************************************************************... |
MartinPippel/DAmar | utils/gff2track.c |
#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#include <string.h>
#include <ctype.h>
#include <unistd.h>
#include <assert.h>
#include <sys/param.h>
#include "lib/colors.h"
#include "lib/oflags.h"
#include "lib/pass.h"
#include "lib/tracks.h"
#include "lib/utils.h"
#include "lib/lasidx.h"
#include "db/D... |
MartinPippel/DAmar | scrub/Catrack.c | <filename>scrub/Catrack.c
/************************************************************************************\
* *
* Copyright (c) 2014, Dr. <NAME> (EWM). All rights reserved. *
* ... |
MartinPippel/DAmar | utils/txt2track.c | /*
* txt2track.c
*
* Created on: 11 Jan 2017
* Author: pippelmn
*/
#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#include <string.h>
#include <ctype.h>
#include <unistd.h>
#include <assert.h>
#include <sys/param.h>
#include "lib/colors.h"
#include "lib/oflags.h"
#include "lib/pass.h"
#include... |
MartinPippel/DAmar | scrub/TKmerge.c | /*******************************************************************************************
*
* merge multiple tracks of the same type into one
*
* Date : October 2016
*
* Author : <NAME>
*
*******************************************************************************************/
#include <stdio.h>
#in... |
MartinPippel/DAmar | msa/msa_main.c |
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <pthread.h>
#include <sys/stat.h>
#include <sys/param.h>
#include <assert.h>
#include <unistd.h>
#include "lib/oflags.h"
#include "lib/tracks.h"
#include "lib/pass.h"
#include "lib/colors.h"
#include "lib/utils.h"
#include "msa.h"
#include "db/DB.h"... |
MartinPippel/DAmar | utils/LAneighbors.c | <reponame>MartinPippel/DAmar<gh_stars>10-100
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <unistd.h>
#include <sys/types.h>
#include <sys/stat.h>
#include "lib/pass.h"
#include "db/DB.h"
#include "lib/utils.h"
#include "lib/tracks.h"
#include "dalign/align.h"
#include "lib/of... |
MartinPippel/DAmar | utils/TKshow.c | <filename>utils/TKshow.c
/*******************************************************************************************
*
* Date : February 2015
*
*******************************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unist... |
MartinPippel/DAmar | lib/pass.c | <reponame>MartinPippel/DAmar
#include <stdio.h>
#include <stdlib.h>
#include <assert.h>
#include "pass.h"
#include "oflags.h"
PassContext* pass_init(FILE* fileOvlIn, FILE* fileOvlOut)
{
PassContext* ctx = malloc(sizeof(PassContext));
ctx->fileOvlIn = fileOvlIn;
ctx->trace = NULL;
ctx->tmax = 0;
... |
MartinPippel/DAmar | db/FA2dam.c | /************************************************************************************\
* *
* Copyright (c) 2014, Dr. <NAME> (EWM). All rights reserved. *
* ... |
MartinPippel/DAmar | touring/OGlayout.c | /*******************************************************************************************
*
* Creates a Yifan Hu Layout from a given graph file.
*
* input : dot, graphml
* output: dot, svg
* parameter: adopted from Gephi (https://gephi.org/)
* -R ... remove reverse edges from... |
MartinPippel/DAmar | lib/lasidx.c |
#include <stdio.h>
#include <string.h>
#include <strings.h>
#include <stdlib.h>
#include <sys/stat.h>
#include <limits.h>
#include <sys/param.h>
#include <unistd.h>
#include "lasidx.h"
#include "pass.h"
static char* lasidx_filename(const char* pathLas)
{
char* pathIdx = strdup(pathLas);
char* pathDot = rind... |
MartinPippel/DAmar | dalign/filter.c | /************************************************************************************\
* *
* Copyright (c) 2014, Dr. <NAME> (EWM). All rights reserved. *
* ... |
MartinPippel/DAmar | touring/OGtour.c |
/*******************************************************************************************
*
* Tours the overlap graph
* (C implementation of touring_v2.py)
*
* Date : February 2016
*
* Author : <NAME>
*
*******************************************************************************************/
#i... |
MartinPippel/DAmar | utils/LAfilterMito.c | /*******************************************************************************************
*
* filters overlaps by various criteria
*
* Author : Martin
*
* Date : December 2018
*
*******************************************************************************************/
#include <assert.h>
#include <... |
MartinPippel/DAmar | lib/tracks.c | <reponame>MartinPippel/DAmar
#include "tracks.h"
#include "pass.h"
#include "tracks.h"
#include "lib/compression.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <assert.h>
#if defined(__APPLE__)
#include <sys/syslimits.h>
#else
#include <linux/limits.h>
#endif
HITS_TRACK*... |
MartinPippel/DAmar | db/DBsplit.c | <filename>db/DBsplit.c
/************************************************************************************\
* *
* Copyright (c) 2014, Dr. <NAME> (EWM). All rights reserved. *
* ... |
MartinPippel/DAmar | utils/CTanalyze.c | <filename>utils/CTanalyze.c
/*
* analyzeContigs.c
*
* assign contigs into following sets: haploid, alternative, repeat
*
* use:
* self alignment information from contigs
* union of fixed reads that map to the contigs (derived from fixedReadOverlaps)
*
*
* Created on: 3 Aug 2017
* Author: pippel... |
MartinPippel/DAmar | corrector/consensus.c | <reponame>MartinPippel/DAmar
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include "consensus.h"
#include "lib/colors.h"
#define CONS_MIN_COV_FRACTION 0.5 // base calling threshold
#undef DEBUG_SHOW_ADD
typedef struct
{
char* B; // sequence that gets a... |
MartinPippel/DAmar | utils/TKhist.c | /*
* TKhist.c
*
* Created on: 30 Nov 2016
* Author: pippelmn
*/
#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#include <string.h>
#include <ctype.h>
#include <assert.h>
#include <unistd.h>
#include <math.h>
#include <sys/param.h>
#include "lib/colors.h"
#include "lib/oflags.h"
#include "lib/ut... |
MartinPippel/DAmar | lib/stats.h |
void ln_estimate(int* data, int n, double* mu, double* sig);
double ln_invcdf(double p, double mu, double sig);
double ln_p(double x, double mu, double sig);
void n_estimate(int* data, int n, double* mu, double* sig);
void n_estimate_double(double* data, int n, double* mu, double* sig);
|
MartinPippel/DAmar | utils/H5dextractUtils.h | #ifndef DEXTRACT_UTILS_H_
#define DEXTRACT_UTILS_H_
#include "stdio.h"
#include <math.h>
#include <sys/stat.h>
#include <ctype.h>
#include <hdf5.h>
typedef unsigned long long uint64;
typedef unsigned int uint32;
typedef unsigned short uint16;
typedef unsigned char uint8;
typedef signed long long int6... |
MartinPippel/DAmar | lib/oflags.c | <filename>lib/oflags.c
#include <stdlib.h>
#include "oflags.h"
OverlapFlag2Label oflag2label[] = {
{OVL_COMP, "complement", '<'},
{OVL_DISCARD, "discarded", 'x'},
{OVL_REPEAT, "r... |
MartinPippel/DAmar | corrector/consensus.h | <filename>corrector/consensus.h
#pragma once
typedef struct
{
unsigned char counts[5]; // A C G T -
} profile_entry;
typedef struct
{
int* vector;
int vecmax;
int* trace;
int ntrace;
int* Stop; // Ongoing stack of alignment indels
char* Babs; // Absolute base... |
MartinPippel/DAmar | touring/OGlayout.h | <reponame>MartinPippel/DAmar<gh_stars>10-100
/*
* OGLayout.h
*
* Created on: Jul 14, 2016
* Author: pippelmn
*/
#ifndef TOURING_OGLAYOUT_H_
#define TOURING_OGLAYOUT_H_
#define max(a,b) \
({ __typeof__ (a) _a = (a); \
__typeof__ (b) _b = (b); \
_a > _b ? _a : _b; })
#define min(a,b) \
({ ... |
MartinPippel/DAmar | utils/LAfilterChains.c | /*******************************************************************************************
*
* filters overlaps by various criteria
*
* Author : <NAME>
*
* Date : May 2015
*
*******************************************************************************************/
#include <assert.h>
#include <limit... |
MartinPippel/DAmar | utils/TKtrim.c | <gh_stars>10-100
/*******************************************************************************************
*
* Date : November 2016
*
*******************************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#i... |
MartinPippel/DAmar | utils/LAindex.c | <gh_stars>10-100
/**
* Index an overlap file.
* - index is used in LAexplorer
*/
/**
* Idea: add repeats track to contig database
*
* Input:
* 1. Contig-db with reads track (readID,beg,end)
* 2. database with interval track that should be added to Contig-db
* 3. interval track
*/
#include <stdio.h>
#incl... |
MartinPippel/DAmar | dalign/align.c | <filename>dalign/align.c
/************************************************************************************\
* *
* Copyright (c) 2014, Dr. <NAME> (EWM). All rights reserved. *
* ... |
MartinPippel/DAmar | db/TKcat.c | <filename>db/TKcat.c
/************************************************************************************\
* *
* Copyright (c) 2014, Dr. <NAME> (EWM). All rights reserved. *
* ... |
MartinPippel/DAmar | lib/trim.c | <filename>lib/trim.c<gh_stars>10-100
#include <stdlib.h>
#include <sys/param.h>
#include <assert.h>
#include <string.h>
#include "trim.h"
#include "lib/oflags.h"
#include "lib/utils.h"
#include "lib/colors.h"
#undef DEBUG_VALIDATE
#undef DEBUG_TRIM
static void align(TRIM* trim, Overlap* ovl, int ab, int ae, int bb, ... |
MartinPippel/DAmar | lib/anno.h |
#pragma once
#define ANNO_TYPE_FLIP 1
#define ANNO_TYPE_WEAK 2
#define ANNO_TYPE_GAP 3
|
MartinPippel/DAmar | scrub/datander.c | /*********************************************************************************************\
*
* Find all local self-alignment between long, noisy DNA reads:
* Compare sequences in each supplied blocks against themselves search for local alignments
* of MIN_OVERLAP or more above the diagonal (A start coor... |
MartinPippel/DAmar | db/fileUtils.h | <reponame>MartinPippel/DAmar<gh_stars>10-100
#ifndef _FASTA_UTILS
#define _FASTA_UTILS
#include <stdio.h>
// checks if fasta header has pacbio format
int isPacBioHeader(char* header);
typedef struct
{ int argc;
char **argv;
FILE *input;
int count;
char *name;
} File_Iterator;
File_Itera... |
MartinPippel/DAmar | lib/colors.h |
#ifndef __COLOR_H
#define __COLOR_H
#define COLORIZE
#ifdef COLORIZE
#define ANSI_COLOR_RED "\x1b[31m"
#define ANSI_COLOR_GREEN "\x1b[32m"
#define ANSI_COLOR_YELLOW "\x1b[33m"
#define ANSI_COLOR_BLUE "\x1b[34m"
#define ANSI_COLOR_MAGENTA "\x1b[35m"
#define ANSI_COLOR_CYAN "\x1b[36m"
#define ANSI_COLOR_... |
MartinPippel/DAmar | msa/msa.c |
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sys/param.h>
#include "lib/colors.h"
#include "msa.h"
#define CONS_MIN_COV_FRACTION 0.5 // base calling threshold
typedef struct
{
char* B; // sequence that gets aligned to
msa_profile_entry* A; // the prof... |
MartinPippel/DAmar | db/DB2fa.c | /************************************************************************************\
* *
* Copyright (c) 2014, Dr. <NAME> (EWM). All rights reserved. *
* ... |
MartinPippel/DAmar | db/QV2db.c | <reponame>MartinPippel/DAmar
/************************************************************************************\
* *
* Copyright (c) 2014, Dr. <NAME> (EWM). All rights reserved. *
* ... |
MartinPippel/DAmar | utils/LAshow.c | /*******************************************************************************************
*
* Displays the contents of a .las file
*
* Date : May 2015
*
* Author : <NAME>
*
*******************************************************************************************/
#include <stdio.h>
#include <stdlib... |
MartinPippel/DAmar | utils/H5dextractUtils.c | #include "H5dextractUtils.h"
#include <string.h>
#include <getopt.h>
#include <stdio.h>
#include <stdlib.h>
#include <errno.h>
#include <limits.h>
static char *Usage = " [options] -F file | <input:bax_h5> ...";
static void printUsage(char *prog, FILE* out)
{
fprintf(out, "\nUsage:\t%s\t%s\n\n", prog, Usage);
... |
MartinPippel/DAmar | scrub/LArepeat.c | /*******************************************************************************************
*
* creates a repeat annotation track (named -t) based on coverage statistics
*
* intervals are tagged as repetitive when the -h coverage threshold is reached
* and terminated when the coverage drops below -l
*
* -n ... |
MartinPippel/DAmar | utils/LAstats.c | /*******************************************************************************************
*
* display basic stats on the overlaps contained in a .las file
*
* Author : <NAME>
*
* Date : May 2015
*
*******************************************************************************************/
#include <a... |
MartinPippel/DAmar | utils/LAcartoons.c | <reponame>MartinPippel/DAmar<filename>utils/LAcartoons.c<gh_stars>10-100
/*******************************************************************************************
*
* Prints an ASCII representation of the overlaps. Uses ANSI color codes.
* Best used jointly with 'less -SR'
*
* Date : October 2014
*
* A... |
MartinPippel/DAmar | utils/CTanalyze.h | /*
* analyzeContigs.h
*
* Created on: 3 Aug 2017
* Author: pippel
*/
#ifndef UTILS_LAANALYZE_H_
#define UTILS_LAANALYZE_H_
#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#include <string.h>
#include "db/DB.h"
#include "dalign/align.h"
// if abs(beg) > abs(end), i.e. overlap is in complement o... |
MartinPippel/DAmar | msa/redriver.c | <reponame>MartinPippel/DAmar
/*****************************************************************************************\
* *
* This program improves a multi-alignment of DNA sequences *
* ... |
MartinPippel/DAmar | corrector/LAcorrect.c | /*******************************************************************************************
*
* Consensus based read correction
*
* Date : revisited April 2017
*
* Author : <NAME>
*
*******************************************************************************************/
#include <assert.h>
#include <... |
MartinPippel/DAmar | dalign/DMserver.c | <filename>dalign/DMserver.c<gh_stars>10-100
/*
maintains coverage statistics for all reads based on .las files produced by daligner and serves mask track
Author: <NAME>
Date: September 2016
overall usage:
- create initial mask track with DBdust and split database into blocks with D... |
MartinPippel/DAmar | corrector/LAconvert.c | <filename>corrector/LAconvert.c
/*******************************************************************************************
*
* conversion from unccorected db to corrected db and las
*
* Author: <NAME>
*
* Date : March 2017
*
************************************************************************************... |
MartinPippel/DAmar | scrub/LAq.c | /*******************************************************************************************
*
* calculate the quality and trim track
*
* Date : October 2015
*
* Author : <NAME>
*
*******************************************************************************************/
#include <stdio.h>
#include <std... |
MartinPippel/DAmar | lib.ext/bitarr.c |
/* bitarr.c */
/**************************************************************************
Bit Vectors in C
FILENAME: bitarr.c
LANGUAGE: ANSI C
REQUIRES: "types.h" (see below for minimal contents)
AUTHOR: <NAME> <<EMAIL>>
CREATED: 22 March 1995
MODIFIED: 20 July 1996
(see http://www.cs... |
MartinPippel/DAmar | scrub/LAfilter.c | <reponame>MartinPippel/DAmar
/*******************************************************************************************
*
* filters overlaps by various criteria
*
* Author : <NAME>
*
* Date : May 2015
*
*******************************************************************************************/
#inclu... |
MartinPippel/DAmar | utils/LAmerge.c | #include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <unistd.h>
#include <math.h>
#include "lib/pass.h"
#include "dalign/align.h"
#include "dalign/filter.h"
#include "LAmergeUtils.h"
#undef DEBUG
// is only called once, and if the sort flag is enabled
void sortFile(char* fout, char*... |
MartinPippel/DAmar | utils/TKcombine.c | <gh_stars>10-100
/*
takes two tracks containing intervals and merges them
into a single track, removing contained/duplicate intervals
in the process and merging overlapping ones.
Source tracks and result track can be trimmed and/or untrimmed
Date: March 2015
*/
#include <assert.h>
#include <stdio.h>
#include <... |
MartinPippel/DAmar | scrub/LAstitch.c | /*******************************************************************************************
*
* A->B overlaps can be split into multiple A->B records due to bad regions in either one
* of the reads, causing the overlapper to stop aligning. Here we look for those records
* (with a maximum gap of -f), join the tw... |
MartinPippel/DAmar | lib/oflags.h |
#pragma once
#define OVL_COMP (1 << 0) // B on reverse strand
#define OVL_DISCARD (1 << 1) // overlap tagged for removal
#define OVL_REPEAT (1 << 3) // repeat induced overlap
#define OVL_LOCAL (1 << 4) // local alignment
#define OVL_DIFF (1 << 5) // too many ... |
MartinPippel/DAmar | lib/utils.c | <gh_stars>10-100
#include <assert.h>
#include <stdlib.h>
#include <sys/param.h>
#include <ctype.h>
#include <string.h>
#include "tracks.h"
#include "lib/pass.h"
/*
fgetln is only available on bsd derived systems.
getline on the other hand is only in gnu libc derived systems.
if fgetln is miss... |
MartinPippel/DAmar | utils/LAextract.c | <filename>utils/LAextract.c
/*******************************************************************************************
*
* extract overlaps for specific a-read ids
*
* Author : <NAME>
*
* Date : September 2014
*
*******************************************************************************************/... |
MartinPippel/DAmar | msa/realigner.h | /*****************************************************************************************\
* *
* This is the interface library for a restructured version of realigner *
* ... |
MartinPippel/DAmar | utils/LAexplorer.c |
#include <gtk/gtk.h>
#include <stdlib.h>
#include <strings.h>
#include <math.h>
#include <string.h>
#include "lib/oflags.h"
#include "lib/utils.h"
#include "lib/pass.h"
#include "lib/tracks.h"
#include "lib/lasidx.h"
#include "db/DB.h"
#include "dalign/align.h"
// drawing area padding
#define PADDING 20
#define H... |
MartinPippel/DAmar | db/FA2x.c |
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "DB.h"
#include "lib/tracks.h"
#include "FA2x.h"
#ifdef HIDE_FILES
#define PATHSEP "/."
#else
#define PATHSEP "/"
#endif
int find_track(CreateContext* ctx, const char* name)
{
int i;
for (i = 0; i < ctx->t_cur; i++)
{
if (strcm... |
MartinPippel/DAmar | lib/laz.c | <reponame>MartinPippel/DAmar
#include "laz.h"
#include <zlib.h>
LAZ* laz_open(char* fpath, int create)
{
FILE* fin = NULL;
LAZ* laz = NULL;
if (create)
{
laz->file = fopen(fpath, "wb");
}
else
{
laz->file = fopen(fpath, "rb");
}
if (laz->file == NULL)
{
... |
MartinPippel/DAmar | utils/LAcount.c | /*******************************************************************************************
*
* validates the overlaps prior to sorting and merging
*
* Author: <NAME>
*
* Date : January 2015
*
*******************************************************************************************/
#include <stdio.h>
#inc... |
MartinPippel/DAmar | msa/msa.h | <filename>msa/msa.h
#pragma once
#include "lib/pass.h"
#include "dalign/align.h"
typedef struct
{
unsigned long counts[5]; // A C G T -
} msa_profile_entry;
typedef struct
{
int* vector;
int vecmax;
int* trace;
int ntrace;
int* Stop; // Ongoing stack of alignment indels
... |
MartinPippel/DAmar | utils/LAZtest.c | /*******************************************************************************************
*
* Displays the contents of a .las file
*
* Date : May 2015
*
* Author : <NAME>
*
*******************************************************************************************/
#include <assert.h>
#include <ctype... |
MartinPippel/DAmar | scrub/tandem.c | /************************************************************************************\
* *
* Copyright (c) 2014, Dr. <NAME> (EWM). All rights reserved. *
* ... |
MartinPippel/DAmar | scrub/TKhomogenize.c | <gh_stars>10-100
/*******************************************************************************************
*
* Reassign repeat intervals based on overlaps and an existing repeat annotation
*
* Date : January 2016
*
* Author : <NAME>
*
*******************************************************************... |
MartinPippel/DAmar | scrub/tandem.h | /************************************************************************************\
* *
* Copyright (c) 2014, Dr. <NAME> (EWM). All rights reserved. *
* ... |
MartinPippel/DAmar | lib/read_loader.c |
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include "read_loader.h"
#define BLOCK_BUFFER (10*1024*1024)
Read_Loader* rl_init(HITS_DB* db, size_t max_mem)
{
Read_Loader* rl = malloc(sizeof(Read_Loader));
rl->db = db;
rl->max_mem = max_mem;
rl->index = (char**)malloc(sizeof(char*) *... |
MartinPippel/DAmar | db/FA2x.h |
typedef struct
{
int well;
int beg;
int end;
int len;
int hasPacbioHeader;
int seqIDinFasta;
int maxPrologLen;
char *prolog;
int maxSequenceLen;
char *seq;
int maxtracks;
int ntracks;
int maxName;
char **trackName;
int **trackfields;
} pacbio_read;
// used in fasta2DB and fasta2DAM... |
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