Commit 970ccb1a authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.3

parent ebec6624

Makefile

0 → 100644
+49 −0
Original line number Diff line number Diff line 
CC?=gcc

LD=${CC}

CFLAGS=  -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools

CFLAGS += `pkg-config --cflags htslib`

INC := -I include

CTAGS = ctags > tags

LIB = -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/

LIB += `pkg-config --libs htslib`

LIB += "-Wl,-rpath,`pkg-config --variable=libdir htslib`"





PRGTARGETS := segemehl haarz



LIBDIR := libs

BUILDDIR:= build

TARGETDIR := .

TARGETEXT := .x

SRCEXT := c





SOURCES := $(shell find $(LIBDIR) -type f -name *.$(SRCEXT))

SOURCES := $(filter-out $(EXCLUDE), $(SOURCES)) 



PRGSOURCES := $(patsubst %,$(LIBDIR)/%.c,$(PRGTARGETS))

LIBSOURCES := $(filter-out $(PRGSOURCES), $(SOURCES)) 



OBJECTS := $(patsubst $(LIBDIR)/%,$(BUILDDIR)/%,$(SOURCES:.$(SRCEXT)=.o))

LIBOBJECTS :=  $(patsubst $(LIBDIR)/%,$(BUILDDIR)/%,$(LIBSOURCES:.$(SRCEXT)=.o))





$(PRGTARGETS): $(OBJECTS)

	@echo "Linking $@";	

	$(LD) $(LIBOBJECTS) $(BUILDDIR)/$@.o -o $(TARGETDIR)/$@$(TARGETEXT) $(LIB)





$(BUILDDIR)/%.o: $(LIBDIR)/%.c

	@echo "Building... library for source $@";

	@mkdir -p $(BUILDDIR)	

	$(CC) $(CFLAGS) $(INC) -c -o $@ $<



all: $(PRGTARGETS)



clean:

	@echo " Cleaning...";

	@echo " $(RM) -r $(BUILDDIR) $(PRGTARGETS)"; $(RM) -r $(BUILDDIR) $(PRGTARGETS)





.PHONY: clean

Makefile.bak

0 → 100644
+49 −0
Original line number Diff line number Diff line 
CC?=gcc

LD=${CC}

CFLAGS=  -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools

CFLAGS += `pkg-config --cflags htslib`

INC := -I include

CTAGS = ctags > tags

LIB = -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/

LIB += `pkg-config --libs htslib`

LIB += "-Wl,-rpath,`pkg-config --variable=libdir htslib`"





ENTERTHETARGETSHERE



LIBDIR := libs

BUILDDIR:= build

TARGETDIR := .

TARGETEXT := .x

SRCEXT := c





SOURCES := $(shell find $(LIBDIR) -type f -name *.$(SRCEXT))

SOURCES := $(filter-out $(EXCLUDE), $(SOURCES)) 



PRGSOURCES := $(patsubst %,$(LIBDIR)/%.c,$(PRGTARGETS))

LIBSOURCES := $(filter-out $(PRGSOURCES), $(SOURCES)) 



OBJECTS := $(patsubst $(LIBDIR)/%,$(BUILDDIR)/%,$(SOURCES:.$(SRCEXT)=.o))

LIBOBJECTS :=  $(patsubst $(LIBDIR)/%,$(BUILDDIR)/%,$(LIBSOURCES:.$(SRCEXT)=.o))





$(PRGTARGETS): $(OBJECTS)

	@echo "Linking $@";	

	$(LD) $(LIBOBJECTS) $(BUILDDIR)/$@.o -o $(TARGETDIR)/$@$(TARGETEXT) $(LIB)





$(BUILDDIR)/%.o: $(LIBDIR)/%.c

	@echo "Building... library for source $@";

	@mkdir -p $(BUILDDIR)	

	$(CC) $(CFLAGS) $(INC) -c -o $@ $<



all: $(PRGTARGETS)



clean:

	@echo " Cleaning...";

	@echo " $(RM) -r $(BUILDDIR) $(PRGTARGETS)"; $(RM) -r $(BUILDDIR) $(PRGTARGETS)





.PHONY: clean

segemehl/libs/alignment.h→include/alignment.h

+112 −0
Original line number Diff line number Diff line 
/*

 *   segemehl - a read aligner

 *   Copyright (C) 2008-2017  Steve Hoffmann and Christian Otto

 *

 *   This program is free software: you can redistribute it and/or modify

 *   it under the terms of the GNU General Public License as published by

 *   the Free Software Foundation, either version 3 of the License, or

 *   (at your option) any later version.

 *

 *   This program is distributed in the hope that it will be useful,

 *   but WITHOUT ANY WARRANTY; without even the implied warranty of

 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

 *   GNU General Public License for more details.

 *

 *   You should have received a copy of the GNU General Public License

 *   along with this program.  If not, see <http://www.gnu.org/licenses/>.

 */





#ifndef ALIGNMENT_H

#define ALIGNMENT_H
@@ -16,10 +35,11 @@ 
 */



#include "basic-types.h"

#include "biofiles.h"



typedef enum 

{

  Replacement, Deletion, Insertion

  Replacement, Deletion, Insertion, Skipped, Softclip, Match, Mismatch

} Eoptype;



typedef struct
@@ -39,10 +59,12 @@ typedef struct { 
  Uint voff;

  Multieop *meops;

  Uint numofmeops;



  unsigned char rmvseq;

  unsigned char rmuseq;

} Alignment;







void copyAlignment(Alignment *to, Alignment *from);

void showmultieoplist(FILE *dev, Alignment *al);

void showDynmultieoplist(Alignment* al, int size);
@@ -55,17 +77,36 @@ void wrapAlignment(Alignment *al); 
Uint getEdist(Alignment *al);

Uint getBisulfiteMismatches(Alignment *al, Uint bisulfite);

Uint getWrongStrandBisulfiteMismatches(Alignment *al, Uint bisulfite);

void countEops(Alignment *al, Uint *mat, Uint *mis, Uint *ins, Uint *del);

void countEops(Alignment *al, Uint *mat, Uint *mis, Uint *ins, Uint *del, Uint *lmat);

char * multieopstring(Alignment *al, Uint leftpad, Uint rightpad, unsigned char rev);

Uint getUalignlen(Alignment *al);

Uint getValignlen(Alignment *al);

Uint getValignlenAndSkipped(Alignment *al);

int getSubstringEdist(Alignment *al, Uint u, Uint v);

int getAlignScore(Alignment *al, int *scores, int indel);

char* cigarstring(Alignment *al, Uint leftpad, Uint rightpad, char clipch, unsigned char rev);

char* cigarstring(Alignment *al, Uint leftpad, Uint rightpad, char clipch, unsigned char rev, char brief);

char* mdstring(Alignment *al, unsigned char rev);

Uint bl_cigarGetAlignLen(char *cigar);

char* bl_cigarGetAlignString(char *cigar);

char* bl_mdGetDiffString(char *MD);

char* getNTcodekey(void *space);

void getSoftClipScores(Alignment *al, int polyAlen, int *scores, int indel, int *pAscr, int *adscr, int *adlen) ;

char* mdstrings(Alignment **al, Uint noofaligns, unsigned char rev);

char* bl_cigarGetAlignString(char *cigar, uint64_t **, uint64_t **, Uint *nsplits);

Uint* getSplitEdist(Alignment *al, Uint *noofsplits);

Uint* getUPartialAlignlen(Alignment *al, Uint *noofparts);

char* getEopString (Alignment *al);

char isMatch (Alignment *al, Uint i, Uint j);

void  showAlignModel(Alignment* al, FILE *dev, gene_t *model);

Alignment* getSubAlignment (Alignment *al, Uint l, Uint r);

Uint bl_alignGet5PrimeV (Alignment *al, char rc);

Uint bl_alignGet3PrimeU (Alignment *al, char rc);

Uint bl_alignGet5PrimeU (Alignment *al, char rc);

void insertMeop(Alignment *al, Eoptype eop, Uint steps);

Alignment* expandAlignment(Alignment *al, Uint* expandpos, Uint *expandlen);

Uint getPartialAlignNumber(Alignment *al);

int getUalignlenNoClip(Alignment *al);

Alignment* bl_getPartialAlignments (Alignment *al, char *vseq, Uint *noofparts);

char* getAlignString(Alignment* al, char lf);

Alignment* reevalAlignment(Alignment *al);

char predictStrand(Alignment *al, char *vseq); 

#endif

segemehl/libs/aluruSort.h→include/aluruSort.h

+19 −0
Original line number Diff line number Diff line 
/*

 *   segemehl - a read aligner

 *   Copyright (C) 2008-2017  Steve Hoffmann and Christian Otto

 *

 *   This program is free software: you can redistribute it and/or modify

 *   it under the terms of the GNU General Public License as published by

 *   the Free Software Foundation, either version 3 of the License, or

 *   (at your option) any later version.

 *

 *   This program is distributed in the hope that it will be useful,

 *   but WITHOUT ANY WARRANTY; without even the implied warranty of

 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

 *   GNU General Public License for more details.

 *

 *   You should have received a copy of the GNU General Public License

 *   along with this program.  If not, see <http://www.gnu.org/licenses/>.

 */





#ifndef ALURUSORT_H

#define ALURUSORT_H

include/annotation.h

0 → 100644
+166 −0
Original line number Diff line number Diff line 
/*

 *   segemehl - a read aligner

 *   Copyright (C) 2008-2017  Steve Hoffmann and Christian Otto

 *

 *   This program is free software: you can redistribute it and/or modify

 *   it under the terms of the GNU General Public License as published by

 *   the Free Software Foundation, either version 3 of the License, or

 *   (at your option) any later version.

 *

 *   This program is distributed in the hope that it will be useful,

 *   but WITHOUT ANY WARRANTY; without even the implied warranty of

 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

 *   GNU General Public License for more details.

 *

 *   You should have received a copy of the GNU General Public License

 *   along with this program.  If not, see <http://www.gnu.org/licenses/>.

 */





#ifndef _ANNOTATION_

#define _ANNOTATION_



#include <stdio.h>

#include <stdlib.h>

#include <string.h>

#include "stringutils.h"

#include "basic-types.h"

#include "charsequence.h"

#include "gzidx.h"



typedef struct {

  int64_t dir5prime;

  int64_t dir3prime; 

  int64_t left;

  int64_t right;

  int8_t select;

} annotationoffs_t;





typedef struct {



  unsigned char type;

  Uint trackid;

  /*

   *

   * chromname is gff seqname

   *

   */

  char *chromname; 

  Uint chromnamelen;



  /*

   * BED und GFF: 1-offset

   * for personalSNP: start with 0-offset

   * end base is not part of the feature ie. if 

   * end = 100 last feature base is 99. see below.

   *

   */



  uint64_t start;

  uint64_t end;



  /* 

   * GFF: name is the feature key

   * BED: name is the name of the acutal feature

   * for personalSNP track name is alleles A,C,T,G separated by '/'. 

   * Leading '-' is indel: insertion if start-end=0 

   *

   * */

  

  char *name;     

  Uint namelen;

  double score;

  unsigned char strand;



  /*GFF fields*/

  unsigned char frame; 

  char *source; 

  Uint sourcelen;

  Uint noofattributes;

  char **attributes;

  Uint *attributelen;



  /*BED fields*/

  uint64_t thickStart;

  uint64_t thickEnd;

  Uint *itemRgb;

  Uint blockCount;

  uint64_t* blockSizes;

  uint64_t* blockStarts;

  Uint noofovl;

  Uint firstovl;

  Uint level;

  /*extension*/

  char **blockRefseqs;

  char *blockStrands;



  /*SNPitem*/

  Uint alleleCount;//number of alleles in name

  Uint *alleleFreq;//from comma separated list of number of observed alleles - if unkowns 0

  Uint *alleleScores;//from a comma separated list - if unkown 0



} annotationitem_t;



typedef struct {

    uint64_t noofchr;

    char **chrname;

    Uint *chrnamelen;

    Uint sz;

    uint64_t *noofbins;

    uint64_t **last; //stores the last interval strictly left of indexed interval [i*sz,i+1*sz];



} annotationindex_t;



typedef struct {

 

  uint64_t init;

  char sorted;

  char *trackname;

  Uint tracknamelen;

  char *description;

  Uint descriptionlen;

  Uint noofitems;

  annotationitem_t *items;

  char *filename;

  Uint filenamelen;

} annotationtrack_t;





typedef struct {

    uint64_t init;

    char sorted;

    Uint nooftracks;

    char **trackname;

    Uint *tracknamelen;

    char **description;

    Uint *descriptionlen;

    char **filename;

    Uint *filenamelen;

    Uint noofitems;

    annotationitem_t *items;

} annotationmultitrack_t;



void bl_annotationtrackDestruct (void *space, annotationtrack_t *track);

Uint bl_annotationtrackGetStats (void *space, annotationtrack_t *track);

void bl_annotationitemInit (annotationitem_t *item, unsigned char type);

void bl_annotationtrackInit (annotationtrack_t *track);

void bl_annotationitemDestruct (void *space, annotationitem_t *item);

Uint bl_annotationitem_cmp_track (Uint item, void *track, void *elem, void *nfo);

int bl_annotationitem_nostrand_cmp (void const *a, void const *b);

int bl_annotationitem_cmp (void const *a, void const *b);

void bl_annotationtrackDestruct (void *space, annotationtrack_t *track);

void bl_annotationtrackAssignTrackLevel(annotationtrack_t *track);

annotationmultitrack_t* bl_annotationtrackJoin(void *space, annotationmultitrack_t *dest, annotationtrack_t *src);

annotationitem_t* bl_annotationitemCopy(annotationitem_t *dest, annotationitem_t *src);

void bl_annotationmultitrackInit (annotationmultitrack_t *track);

Uint bl_annotationitem_cmp_multitrack (Uint item, void *track, void *elem, void *nfo);

void bl_annotationtrackSetItems(annotationtrack_t* track, annotationitem_t* items, Uint n);

annotationindex_t* bl_annotationIndex(annotationtrack_t *t);

void bl_annotationtrackDumpIndex(annotationindex_t *idx,annotationtrack_t *track); 

void bl_annotationmultitrackDestruct (void *space, annotationmultitrack_t *track);

void bl_annotationitemApplyOffset(annotationitem_t *item, int64_t off3, int64_t off5, int64_t left, int64_t right, int8_t select);

void  bl_annotationitemDump(FILE *dev, annotationitem_t *item);

void bl_annotationmultitrackApplyOffset(annotationmultitrack_t *mtrack, annotationoffs_t *off);

#endif