Makefile

+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

+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
+

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: segemehl
 Upstream-Contact: steve@bioinf.uni-leipzig.de
 Source: http://www.bioinf.uni-leipzig.de/Software/segemehl/
-Files-Excluded: */cscope.out
-                *.o
-                *~
-                *.SUNOS
 
 Files: *
-Copyright: 2008-2015 Bioinformatik Leipzig
-License: non-commercial
- SEGEMEHL is free software for non-commercial use 
+Copyright: 2008-2018 Bioinformatik Leipzig
+License: GPL-3+
 
 Files: debian/*
-Copyright: 2016 Andreas Tille <tille@debian.org>
-License: to_be_clarified
- Ask upstream for free license and choose the same for
- the packaging.
+Copyright: 2016-2018 Andreas Tille <tille@debian.org>
+License: GPL-3+
+
+License: GPL-3+
+    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.
+ .
+ On Debian systems you can find the full text of the GNU General Public
+ License at /usr/share/common-licenses/GPL-3+.

debian/watch

-version=3
+version=4
 
 opts="uversionmangle=s/_/./g,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
   http://www.bioinf.uni-leipzig.de/Software/segemehl/ .*/segemehl_(\d[_.\d]+)\.tar\.gz
 
+# opts="searchmode=plain,uversionmangle=s/_/./g,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+# May be we can use searchmode=plain to fetch "<a href="downloads/segemehl.tar.gz">Download segemehl version 0.3</a>"
+

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

+/*
+ *   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

+/*
+ *   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

+/*
+ *   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
+

include/bamio.h

+#ifndef BAMITER_H
+#define BAMITER_H
+
+/*
+ *
+ *	bamiter.h
+ *  alignment representation
+ *  
+ *
+ */
+
+#include <stdint.h>
+#include <inttypes.h>
+#include <pthread.h>
+
+#include "filebuffer.h"
+#include "htslib/sam.h"
+#include "htslib/faidx.h"
+#include "htslib/kstring.h"
+#include "htslib/khash.h"
+#include "samio.h"
+#include "intervaltree.h"
+#define BAM_ITR_BUFSZ 1000
+
+
+typedef struct{
+    uint32_t n;
+    uint32_t c; //massive padding for better alignment 
+    uint64_t *d;
+} bam_cs_data_t;
+
+typedef struct{
+    uint8_t prev;
+    uint8_t next;
+    uint32_t tid;
+    uint32_t beg;
+    uint32_t n;
+    bam_cs_data_t *x;
+} bam_cs_t;
+
+/*
+ * lower -> higher bits
+ *  0:  4-bit : char encoding
+ *  4:  1-bit : rc 
+ *  5:  8-bit : nucleotide qual (64)
+ *  13: 8-bit : mapping qual (64)
+ *  21: 8-bit : mm/nh
+ *  29: 2-bit : paired
+ *  31: 2-bit : conversion protocol
+ *  33: 16-bit: query position 
+ *  49: 15-bit: number mismatches/nm 
+ 
+ */
+
+#define BAM_CS_NT_MASK ((uint64_t)((1<<4)-1))
+#define BAM_CS_RC_MASK ((uint64_t)((1<<1)-1))
+#define BAM_CS_NQ_MASK ((uint64_t)((1<<8)-1))
+#define BAM_CS_MQ_MASK (((uint64_t)(1<<8)-1))
+#define BAM_CS_MM_MASK (((uint64_t)(1<<8)-1))
+#define BAM_CS_PP_MASK (((uint64_t)(1<<2)-1))
+#define BAM_CS_CP_MASK (((uint64_t)(1<<2)-1))
+#define BAM_CS_QP_MASK (((uint64_t)(1<<16)-1)) 
+#define BAM_CS_NM_MASK (((uint64_t)(1<<15)-1)) 
+//#define BAM_CS_RS_MASK (1<<2)-1 
+
+#define BAM_CS_NT_LBIT 0
+#define BAM_CS_RC_LBIT 4
+#define BAM_CS_NQ_LBIT 5
+#define BAM_CS_MQ_LBIT 13
+#define BAM_CS_MM_LBIT 21
+#define BAM_CS_PP_LBIT 29
+#define BAM_CS_CP_LBIT 31
+#define BAM_CS_QP_LBIT 33 
+#define BAM_CS_NM_LBIT 49
+//#define BAM_CS_RS_LBIT 62
+
+/*
+ *  encoding of common nucleotides
+ */
+
+#define BAM_CS_NT_A 0x1
+#define BAM_CS_NT_C 0x2
+#define BAM_CS_NT_G 0x4
+#define BAM_CS_NT_T 0x8
+#define BAM_CS_NT_N 0xF
+#define BAM_CS_NT_D 0x0
+
+#define BAM_CS_DEFAULT_REG 1000000
+#define BAM_CS_DEFAULT_COVERAGE 30 
+#define BAM_CS_DEFAULT_MAX_COVERAGE 10000
+#define BAM_CS_DEFAULT_CIRCBUF_SZ 10000000
+
+#define METHYL_FWD_STRAND 1
+#define METHYL_REV_STRAND 2
+#define METHYL_BTH_STRAND 0
+
+//char cop = (char) bam_cigar_opchr(cigar[i]);
+//fprintf(stderr, "%c",  "=ACMGRSVTWYHKDBN"[bam_seqi(seq, qpos+j)]);
+
+#define BAM_CS_GET_NT(val) (((val) & BAM_CS_NT_MASK) )
+#define BAM_CS_GET_RC(val) (((val) >> BAM_CS_RC_LBIT) & BAM_CS_RC_MASK)
+#define BAM_CS_GET_NQ(val) (((val) >> BAM_CS_NQ_LBIT) & BAM_CS_NQ_MASK)
+#define BAM_CS_GET_MQ(val) (((val) >> BAM_CS_MQ_LBIT) & BAM_CS_MQ_MASK)
+#define BAM_CS_GET_MM(val) (((val) >> BAM_CS_MM_LBIT) & BAM_CS_MM_MASK)
+#define BAM_CS_GET_PP(val) (((val) >> BAM_CS_PP_LBIT) & BAM_CS_PP_MASK)
+#define BAM_CS_GET_CP(val) (((val) >> BAM_CS_CP_LBIT) & BAM_CS_CP_MASK)
+#define BAM_CS_GET_QP(val) (((val) >> BAM_CS_QP_LBIT) & BAM_CS_QP_MASK)
+#define BAM_CS_GET_NM(val) (((val) >> BAM_CS_NM_LBIT) & BAM_CS_NM_MASK)
+#define BAM_CS_GET_RS(val) (((val) >> BAM_CS_RS_LBIT) & BAM_CS_RS_MASK)
+
+
+typedef struct{
+
+    bam_hdr_t *hdr;
+    uint32_t last_tid;
+    uint32_t last_beg;
+    uint32_t last_len;
+
+    uint8_t isthreaded;
+    pthread_mutex_t *mtx;
+
+} bl_bam_methyl_master_t;
+
+typedef struct {
+    FILE *out;
+
+    hts_idx_t *idx;
+    bam_hdr_t *hdr;
+    samFile *in;   
+    faidx_t *fai;
+    intervalforest_t *forest;
+    uint8_t uniqueonly;
+    uint8_t isthreaded;
+    bl_bam_methyl_master_t *ms;
+    pthread_mutex_t *devmtx; 
+    pthread_mutex_t *faimtx; 
+    pthread_mutex_t *bammtx; 
+    circbuffer_t *cb; 
+
+} bl_bam_methyl_worker_t;
+
+
+
+typedef struct {
+    samFile *in;
+    faidx_t *fai;
+    hts_idx_t *idx;
+    bam_hdr_t *hdr;
+} bam_info_t;
+
+
+typedef struct {
+    uint16_t n;
+    uint16_t i;
+    uint16_t maxn;
+    uint8_t next;
+    bam1_t *d;
+    uint8_t isthreaded;
+    pthread_mutex_t *mtx;
+} bl_bam1_buffer_t;
+
+bam_info_t* bl_bamLoadInfo(bam_info_t *nfo, char *bamfn,  char *fafn);
+
+bl_bam_methyl_master_t* bl_bamInitMaster(bl_bam_methyl_master_t *ms, 
+        bam_hdr_t *hdr, uint8_t isthreaded, pthread_mutex_t *mtx);
+
+bl_bam_methyl_worker_t* bl_bamInitWorker(bl_bam_methyl_worker_t *wk, 
+        bl_bam_methyl_master_t *ms, FILE *out, bam_info_t *nfo, uint8_t uniqueonly, 
+        uint8_t isthreaded, pthread_mutex_t* devmtx, pthread_mutex_t *bammtx, 
+        circbuffer_t *cb, intervalforest_t *forest);
+void* bl_bamCrossSectioMethylWorker(void *args);
+void* bl_bamMethylStringWorker(void *args);
+
+void bl_bamDestructInfo(bam_info_t *nfo);
+void bl_bamPrintBamrec (htsFile *fp, samrec_t *rec, bam_hdr_t *hdr, pthread_mutex_t *mtx) ;
+htsFile* bl_bamOpenFile(char *fn); 
+bam_hdr_t* bl_bamGetHeader (samheader_t *head, Uint binno);
+#endif

segemehl/libs/basic-types.h → include/basic-types.h

+/*
+ *   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 BASIC_TYPES_H
 #define BASIC_TYPES_H
 
@@ -14,6 +33,8 @@
 #define MAXBUFFERSIZE 10000
 #define BASEINC 10000
 #define MAX_INT_LENGTH 50
+#define MAGIC_INIT 0x0BADF00D
+
 typedef unsigned char Uchar;
 typedef unsigned int Uint;
 typedef signed long long Lint;
@@ -69,6 +90,12 @@ typedef struct {
 } QuadSint;
 
 
+typedef struct {
+  Uint a,
+      b,
+      c,
+      d;
+} QuadUint;
 
 
 #endif

include/bedfiles.h

+/*
+ *   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 _BEDFILES_
+#define _BEDFILES_
+
+/*
+ *
+ *	bedfiles.h
+ *  
+ * 
+ *  @author Steve Hoffmann, steve@bioinf.uni-leipzig.de
+ *  @company Bioinformatics, University of Leipzig 
+ *  @date 10/30/16 17:41:47 CET  
+ *
+ */
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "stringutils.h"
+#include "basic-types.h"
+#include "charsequence.h"
+#include "gzidx.h"
+#include "biofiles.h"
+
+annotationtrack_t* bl_BEDread (void *space, char *filename);
+void bl_annotationitemDump(FILE *dev, annotationitem_t *item);
+void bl_BEDwrite (annotationitem_t *items, Uint n, FILE *dev);
+
+#endif

include/bgzip.h

+#ifndef BGZIP_H
+#define BGZIP_H
+
+#include <inttypes.h>
+#include "gzip.h"
+typedef struct {
+    uint32_t lenCompressedData;
+} bgzip_Header ;
+
+
+bgzip_Header bgzip_Header_default();
+
+int bgzip_extractBgzHeader(gzip_Header* gzipHeader, bgzip_Header *bgzipHeader);
+
+int64_t bgzip_findLenUncompressedData(FILE* f, gzip_Header* gzipHeader,
+                                   bgzip_Header *bgzipHeader);
+
+
+#endif // BGZIP_H

segemehl/libs/biofiles.h → include/biofiles.h

+/*
+ *   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 _BIOFILES_
 #define _BIOFILES_
 
@@ -21,11 +40,11 @@
 
 #include <stdio.h>
 #include <stdlib.h>
-#include <string.h>
 #include "stringutils.h"
 #include "basic-types.h"
 #include "charsequence.h"
-#include "zran.h"
+#include "gzidx.h"
+#include "annotation.h"
 
 #define ID 1
 #define IDEND 2
@@ -81,6 +100,7 @@ typedef struct fasta_s {
   unsigned char hasMates;
   unsigned char hasIndex;
   unsigned char chunkIsActive;
+  unsigned char checkid;
  
   Uint nooffiles;
   Uint *filetotal; 
@@ -96,87 +116,9 @@ typedef struct fasta_s {
   struct access **gzindex;
   struct access **mategzindex;
 
-} fasta_t;
-
-
-
-
-typedef struct {
-
-  unsigned char type;
-  /*
-   *
-   * chromname is gff seqname
-   *
-   */
-  char *chromname; 
-  Uint chromnamelen;
+  Uint nextindex;
 
-  /*
-   * 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.
-   *
-   */
-
-  Uint start;
-  Uint 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*/
-  Uint thickStart;
-  Uint thickEnd;
-  Uint *itemRgb;
-  Uint blockCount;
-  Uint* blockSizes;
-  Uint* 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 {
-
-  char *trackname;
-  Uint tracknamelen;
-  char *description;
-  Uint descriptionlen;
-  Uint noofitems;
-  annotationitem_t *items;
-
-} annotationtrack_t;
+} fasta_t;
 
 
 typedef struct {
@@ -279,14 +221,34 @@ void bl_fastaSetMateClip (fasta_t *f, Uint elem, Uint p5, Uint p3);
 void bl_fastaSetClip (fasta_t *f, Uint elem, Uint p5, Uint p3);
 int bl_rm(void *space, char *filename);
 Uint bl_fastxFindIDIdx (char *id, fasta_t *set);
-annotationtrack_t* bl_BEDread (void *space, char *filename);
-void bl_BEDwrite (annotationtrack_t *track, FILE *dev);
-void bl_annotationtrackDestruct (void *space, annotationtrack_t *track);
+
 annotationtrack_t* bl_GFFread (void *space, char *filename);
 Uint bl_annotationitem_cmp_track (Uint item, void *track, void *elem, void *nfo);
 int bl_fastxIDcmp (char *a, char *b);
 void bl_GFFAddAttribute (void *space, annotationitem_t *item, char *attr, Uint len);
 void bl_GFFwrite(char *filename, annotationtrack_t *set);
-Uint bl_annotationtrackGetStats (void *space, annotationtrack_t *track);
 
+char* bl_fastaGetLeftClip(fasta_t *f, Uint elem) ;
+char* bl_fastaGetRightClip(fasta_t *f, Uint elem) ;
+char* bl_fastaGetLeftClipQual(fasta_t *f, Uint elem) ;
+char* bl_fastaGetRightClipQual(fasta_t *f, Uint elem) ;
+char* bl_fastaGetMateLeftClip(fasta_t *f, Uint elem) ;
+char* bl_fastaGetMateRightClip(fasta_t *f, Uint elem) ;
+char* bl_fastaGetMateLeftClipQual(fasta_t *f, Uint elem) ;
+char* bl_fastaGetMateRightClipQual(fasta_t *f, Uint elem) ;
+char* bl_fastaGetMateNoClip(fasta_t *f, Uint elem);
+char* bl_fastaGetSequenceNoClip(fasta_t *f, Uint elem);
+char* bl_fastaGetQualityNoClip(fasta_t* f, Uint elem);
+char* bl_fastaGetMateQualityNoClip(fasta_t *f, Uint elem);
+void bl_addExon (gene_t *gene, Uint start, Uint end, char strand, char *refchr);
+void bl_dumpGene(gene_t *gene);
+gene_t* bl_initGene (char *identifier, char strand);
+char bl_isExon(gene_t *gene, Uint pos);
+void bl_wrapGene(gene_t *gene);
+Uint bl_getExonNumber (gene_t *model);
+Uint bl_getExonStart (gene_t *model, Uint id);
+Uint bl_getExonEnd (gene_t *model, Uint id);
+fasta_t* bl_fastxCopyIndex (void *space, fasta_t *f, Uint offset, Uint size);
+fasta_t* bl_fastxCopy (void *space, fasta_t *f, Uint offset, Uint size);
+annotationtrack_t* bl_annotationRead (void *space, char *fn) ;
 #endif

segemehl/libs/bitArray.h → include/bitArray.h

+/*
+ *   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 BITARRAY_H
 #define BITARRAY_H
 

segemehl/libs/bitVector.h → include/bitVector.h

+/*
+ *   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 BITVECTOR_H
 #define BITVECTOR_H
 

segemehl/libs/bitvectoralg.h → include/bitvectoralg.h

+/*
+ *   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/>.
+ */
+
+
 
 /*
  *
@@ -71,5 +90,7 @@ char*
 getstringalphabet (void *space, char *string, Uint len, Uint *asize);
 
 Alignment*
-bitvectorbacktrack(Alignment *al, bitvector *D, Uint dim, Uint k, Uint l);
+bitvectorbacktrack(Alignment *al, bitvector *D, Uint dim, Uint k, 
+    Uint l, 
+    char *subject, Uint *enctab, bitvector *peq); //patch
 

include/brendel.h

+/*
+ *   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/>.
+ */
+
+
+
+/*
+ *
+ *	brendel.h
+ *  
+ * 
+ *  @author Steve Hoffmann, steve@bioinf.uni-leipzig.de
+ *  @company Bioinformatics, University of Leipzig 
+ *  @date 07/01/2016 03:25:21 PM CEST  
+ *
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <assert.h>
+#include <ctype.h>
+#include <math.h>
+#include "basic-types.h"
+#include "alignment.h"
+#include "memory.h"
+#include "mathematics.h"
+#include "iupac.h"
+#include "biofiles.h"
+
+Alignment* splicedaligndp (char *read, unsigned int m, char *genome, unsigned int n, gene_t **model);
+mapping_t* bl_dpsplicealign2map(Alignment *al, gene_t *model, MultiCharSeq *mseq, Uint vpos, Uint vlen, char strand, char *querydesc, char *query, char *qual, Uint ulen, char ismate) ;
+char bl_checkSpliceAlign(mapping_t *m);
+Alignment* splicedaligndpopt (char *read, unsigned int m, char *genome, unsigned int n, gene_t **model, Uint a, Uint b, Uint l, Uint r);
+

segemehl/libs/sufarray/charsequence.h → include/charsequence.h

+/*
+ *   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 INTSEQUENCE_H
  #define INTSEQUENCE_H
 

segemehl/libs/citation.h → include/citation.h

+/*
+ *   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/>.
+ */
+
+
 
 /*
  *
@@ -34,10 +53,12 @@
                  "\"Stefan Kurtz uses suffix arrays to fix his bike.\" (A. Torda)\0",
                  "\"Ich hol' jetzt die Hilti!\" (Ein verzweifelter Bauarbeiter)\0",
                  "\"Kaeff'chen?\" (Lars)\0",
-                 "\"Wir sind hier nicht in Seattle Dirk!\" (Tocotronic)\0"}; 
+                 "\"Wir sind hier nicht in Seattle Dirk!\" (Tocotronic)\0", 
+                 "\"Boooooring!\" (David S.)\0"
+                 }; 
 
 
- unsigned citenumber = 15;
+ unsigned citenumber = 16;
 
  char* citerand() { 
    Uint r;

segemehl/libs/container.h → include/container.h

+/*
+ *   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/>.
+ */
+
+
 /**
  * container.h
  * implementation of a simple container for objects of defined size

segemehl/libs/debug.h → include/debug.h

+/*
+ *   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 DEBUG_H
  #define DEBUG_H