Commit ea4ce368 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.3.4

parent c43e3da4

include/fileio.h

+1 −1
Original line number Diff line number Diff line
@@ -45,7 +45,7 @@ 
#include "stringutils.h"

char * bl_getTempFile(char *path, char *tmp);

int bl_UnixSort(void *space, char *filename, const char *fieldstring, const char delim);

char* readfile(void *, char *, Uint*);

char* readfile(void *, char *, size_t*);

stringset_t **readcsv(void *, char *, char*, Uint *);

void writeY(char *, double  *, Uint, Uint, Uint);

void writeXYUint(char *filename, Uint *X, Uint *Y, Uint len);

include/segemehl.h

+2 −1
Original line number Diff line number Diff line
@@ -230,7 +230,7 @@ typedef struct segemehl_s { 
    */

    merge_t *merge;

    char orientation;

 

    char fullname;

} segemehl_t;



typedef struct checkthread_s {
@@ -387,6 +387,7 @@ se_setdefault(segemehl_t *info) { 
  info->bamhdr = NULL;

  info->head = NULL;

  info->orientation = 1;

  info->fullname = 0;

}



inline static void

include/version.h

+3 −3
Original line number Diff line number Diff line
@@ -24,11 +24,11 @@ 






#define VERSION "0.3.2"

#define VERSION "0.3.4"



#define REVISION "g664b3dd"

#define REVISION "ge5dee47"



#define TIME "2018-11-11 17:18:49 +0100"

#define TIME "2018-12-25 20:39:07 +0100"

include/version.h.bak

+2 −2
Original line number Diff line number Diff line
@@ -12,6 +12,6 @@ 




#define VERSION "v0.3.0"

#define REVISION "g664b3dd"

#define TIME "2018-11-11 17:18:49 +0100"

#define REVISION "ge5dee47"

#define TIME "2018-12-25 20:39:07 +0100"

libs/alignment.c

+27 −12
Original line number Diff line number Diff line
@@ -1252,7 +1252,7 @@ bl_mdGetDiffString(char *MD) { 


char*

cigarstring(Alignment *al, Uint leftclip, Uint rightclip, char clipch, unsigned char rev, char brief) {

  Uint i, j, k, q=0, p=0, cur=0, strsize, steps, msteps;

  Uint i, j, k, q=0, p=0, cur=0, strsize, steps=0, msteps;

  char *cigarstr;

  char eopc=0;
@@ -1266,10 +1266,9 @@ cigarstring(Alignment *al, Uint leftclip, Uint rightclip, char clipch, unsigned 
    cur+=strsize;

  }



  for(k=0; k < al->numofmeops; k++) {

  for(steps=0, k=0; k < al->numofmeops; k++) {

    i = (rev) ? al->numofmeops - k - 1 : k;

    //if Replacement occured 

    steps=0;

    if (al->meops[i].eop == Replacement) {

      //iter over all steps

      msteps=0;
@@ -1299,7 +1298,7 @@ cigarstring(Alignment *al, Uint leftclip, Uint rightclip, char clipch, unsigned 
        msteps++;

      }



      steps = msteps;

      steps += msteps;

      //set string ptrs

      p+=j;

      q+=j;
@@ -1311,7 +1310,8 @@ cigarstring(Alignment *al, Uint leftclip, Uint rightclip, char clipch, unsigned 
      else

        eopc = '=';

      //set ptrs

      steps = al->meops[i].steps;

      //steps = al->meops[i].steps;

      steps += al->meops[i].steps;

      p+=steps;

      q+=steps;

    }
@@ -1322,11 +1322,22 @@ cigarstring(Alignment *al, Uint leftclip, Uint rightclip, char clipch, unsigned 
      else

        eopc = 'X';

      //set ptrs

      steps = al->meops[i].steps;

      //steps = al->meops[i].steps;

      steps += al->meops[i].steps;

      p+=steps;

      q+=steps;

    }



    //dump previous matches and mismatches if in brief mode

    //if a different operation is coming

    if(brief && steps && eopc == 'M' && 

        al->meops[i].eop != Match && al->meops[i].eop != Mismatch) {

      

      strsize = snprintf(NULL, 0, "%d", steps)+1;

      sprintf(&cigarstr[cur], "%d%c", steps, eopc);

      cur+=strsize;

      steps = 0;

    }



    //if deletion occured

    if (al->meops[i].eop == Deletion) {
@@ -1355,11 +1366,15 @@ cigarstring(Alignment *al, Uint leftclip, Uint rightclip, char clipch, unsigned 
      //     p+=steps; no moves!

    }





    //dump everything except "M"s in the brief mode

    //unless we are at the end

    if(eopc != 'M' || k+1 == al->numofmeops) {

      //strsize = floor(log(steps)/log(10))+2;

      strsize = snprintf(NULL, 0, "%d", steps)+1;

      sprintf(&cigarstr[cur], "%d%c", steps, eopc);

      cur+=strsize;

      steps = 0;

    }

  }



  if(rightclip || (leftclip && rev)) {