--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mrcanavar-0.34/utils.c	Tue Feb 21 10:44:13 2012 -0500
@@ -0,0 +1,319 @@
+
+#include "utils.h"
+
+
+
+void print_error(char *msg){
+  fprintf(stderr, "\nmrCaNaVaR version %s.\nLast update: %s.\n", VERSION, LAST_UPDATE);
+  fprintf(stderr, "\n%s\n", msg);
+  fprintf(stderr, "Invoke parameter -h for help.\n");
+  exit (0);
+}
+
+void set_runmode(enum MODETYPE NEWMODE){
+  if (RUNMODE != NONE && RUNMODE != NEWMODE){
+    print_error("Select one run mode only.\n"); 
+  }
+  RUNMODE = NEWMODE;
+}
+
+void set_gender(enum GENDERTYPE SET){
+  if (GENDER != AUTODETECT && RUNMODE != SET){
+    print_error("Select only one of --xx or --xy.\n"); 
+  }
+  GENDER= SET;
+}
+
+void set_str(char **target, char *source){
+
+  if (*target != NULL) free((*target));
+
+  (*target) = (char *) malloc(sizeof(char) * (strlen(source)+1));
+
+  strncpy((*target), source, (strlen(source)+1));
+
+}
+
+
+void init_globals(void){
+  GENOME_FASTA = NULL;
+  GENOME_CONF  = NULL;
+  GENOME_GAPS  = NULL;
+  RUNMODE      = NONE;
+  GENDER       = AUTODETECT;
+  MULTGC       = 0;
+  MAX_GC_CORR  = 20.0;
+  MIN_GC_CORR  = 0.05;
+  VERBOSE      = 0;
+  
+  num_chrom    = 0;
+
+  CHECKSAM     = 1;
+
+  /* set window size defaults */
+
+  LW_SIZE  = 5000;
+  SW_SIZE  = 1000;
+  CW_SIZE  = 1000;
+  LW_SLIDE = 1000;
+  SW_SLIDE = 1000;
+
+  LW_MEAN  = 0.0;
+  SW_MEAN  = 0.0;
+  CW_MEAN  = 0.0;
+
+  LW_STD   = 0.0;
+  SW_STD   = 0.0;
+  CW_STD   = 0.0;
+
+  CONT_WINDOW = 7;
+  CUT_WINDOW  = 6;
+
+}
+
+
+FILE *my_fopen(char *fname, char *mode, char GZ){
+  FILE *fp;
+  
+
+  if (!GZ)
+    fp = fopen(fname, mode);
+  else
+    fp = gzopen(fname, mode);
+  
+  if (fp == NULL){
+    fprintf(stderr, "Unable to open file %s in %s mode.", fname, mode[0]=='w' ? "write" : "read");
+    exit (0);
+  }
+
+  return fp;
+}
+
+
+void saveRefConfig(char *configFile){
+  
+  int i;
+  int wcnt;
+  char chrom_name_len;
+  int retVal;
+  FILE *config;
+  
+  config = my_fopen(configFile, "w", 0);
+
+  /* sort the chromosomes pointer array */
+
+  qsort(chromosomes, num_chrom, sizeof (struct chrom *), compChr);
+
+
+  /* start with the magicNum, I will use this as a format check when loading */
+  retVal = fwrite(&magicNum, sizeof(magicNum), 1, config);
+
+  /* window sizes / slides */
+  
+  retVal = fwrite(&LW_SIZE,  sizeof(LW_SIZE),  1, config);
+  retVal = fwrite(&SW_SIZE,  sizeof(SW_SIZE),  1, config);
+  retVal = fwrite(&CW_SIZE,  sizeof(CW_SIZE),  1, config);
+  retVal = fwrite(&LW_SLIDE, sizeof(LW_SLIDE), 1, config);
+  retVal = fwrite(&SW_SLIDE, sizeof(SW_SLIDE), 1, config);
+
+  
+  /* reference genome numbers */
+  
+  /* number of chromosomes */
+  retVal = fwrite(&num_chrom, sizeof(num_chrom), 1, config);
+  
+  /* iterate through chromosomes, write their names, and window counts */
+
+  for (i=0; i<num_chrom; i++){
+    chrom_name_len = (char) strlen(chromosomes[i]->name);
+    retVal = fwrite(&chrom_name_len, sizeof(chrom_name_len), 1, config);
+    retVal = fwrite(chromosomes[i]->name, chrom_name_len * sizeof(char), 1, config);
+
+    retVal = fwrite(&(chromosomes[i]->length), sizeof(chromosomes[i]->length), 1, config);
+    retVal = fwrite(&(chromosomes[i]->lw_cnt), sizeof(chromosomes[i]->lw_cnt), 1, config);
+    retVal = fwrite(&(chromosomes[i]->sw_cnt), sizeof(chromosomes[i]->sw_cnt), 1, config);
+    retVal = fwrite(&(chromosomes[i]->cw_cnt), sizeof(chromosomes[i]->cw_cnt), 1, config);    
+
+    /* long windows */
+    for (wcnt=0; wcnt<chromosomes[i]->lw_cnt; wcnt++){
+      retVal = fwrite(&(chromosomes[i]->lw[wcnt].start), sizeof(chromosomes[i]->lw[wcnt].start), 1, config);
+      retVal = fwrite(&(chromosomes[i]->lw[wcnt].end),   sizeof(chromosomes[i]->lw[wcnt].end),   1, config);
+      retVal = fwrite(&(chromosomes[i]->lw[wcnt].gc),    sizeof(chromosomes[i]->lw[wcnt].gc),    1, config);
+    }
+
+    /* short windows */
+    for (wcnt=0; wcnt<chromosomes[i]->sw_cnt; wcnt++){
+      retVal = fwrite(&(chromosomes[i]->sw[wcnt].start), sizeof(chromosomes[i]->sw[wcnt].start), 1, config);
+      retVal = fwrite(&(chromosomes[i]->sw[wcnt].end),   sizeof(chromosomes[i]->sw[wcnt].end),   1, config);
+      retVal = fwrite(&(chromosomes[i]->sw[wcnt].gc),    sizeof(chromosomes[i]->sw[wcnt].gc),    1, config);
+    }
+
+    /* copy windows */
+    for (wcnt=0; wcnt<chromosomes[i]->cw_cnt; wcnt++){
+      retVal = fwrite(&(chromosomes[i]->cw[wcnt].start), sizeof(chromosomes[i]->cw[wcnt].start), 1, config);
+      retVal = fwrite(&(chromosomes[i]->cw[wcnt].end),   sizeof(chromosomes[i]->cw[wcnt].end),   1, config);
+      retVal = fwrite(&(chromosomes[i]->cw[wcnt].gc),    sizeof(chromosomes[i]->cw[wcnt].gc),    1, config);
+    }
+
+  }
+
+  fclose(config);
+
+}
+
+
+
+
+void loadRefConfig(char *configFile){
+  
+  int i;
+  int wcnt;
+  char chrom_name_len;
+  char readString[MAX_STR];
+  int retVal;
+
+  int isMagicNum;
+
+  FILE *config;
+
+  config = my_fopen(configFile, "r", 0);
+
+  /* start with the magicNum,  use this as a format check when loading */
+  retVal = fread(&isMagicNum, sizeof(isMagicNum), 1, config);
+
+  if (isMagicNum != magicNum)
+    print_error("Reference configuration file seems to be invalid or corrupt.\n");
+
+
+  fprintf(stdout, "Loading reference configuration, hold on ... ");
+  fflush(stdout);
+
+  /* window sizes / slides */
+  
+  retVal = fread(&LW_SIZE,  sizeof(LW_SIZE),  1, config);
+  retVal = fread(&SW_SIZE,  sizeof(SW_SIZE),  1, config);
+  retVal = fread(&CW_SIZE,  sizeof(CW_SIZE),  1, config);
+  retVal = fread(&LW_SLIDE, sizeof(LW_SLIDE), 1, config);
+  retVal = fread(&SW_SLIDE, sizeof(SW_SLIDE), 1, config);
+
+  
+  /* reference genome numbers */
+  
+  /* number of chromosomes */
+  retVal = fread(&num_chrom, sizeof(num_chrom), 1, config);
+
+  /* create chromosomes data structure */
+
+  chromosomes = (struct chrom **) malloc(sizeof(struct chrom *) * num_chrom);
+  for (i=0; i<num_chrom; i++)
+    chromosomes[i] = (struct chrom *) malloc(sizeof(struct chrom) * num_chrom);
+
+  /* iterate through chromosomes, write their names, and window counts */
+
+  for (i=0; i<num_chrom; i++){
+
+    retVal = fread(&chrom_name_len, sizeof(chrom_name_len), 1, config);
+
+    retVal = fread(readString, chrom_name_len * sizeof(char), 1, config);
+    readString[chrom_name_len] = 0;
+    trimspace(readString);
+
+    set_str(&(chromosomes[i]->name), readString);
+
+    retVal = fread(&(chromosomes[i]->length), sizeof(chromosomes[i]->length), 1, config);
+    retVal = fread(&(chromosomes[i]->lw_cnt), sizeof(chromosomes[i]->lw_cnt), 1, config);
+    retVal = fread(&(chromosomes[i]->sw_cnt), sizeof(chromosomes[i]->sw_cnt), 1, config);
+    retVal = fread(&(chromosomes[i]->cw_cnt), sizeof(chromosomes[i]->cw_cnt), 1, config);    
+
+    /* create windows structures */
+
+
+    chromosomes[i]->lw = (struct window *) malloc (sizeof(struct window) * chromosomes[i]->lw_cnt);
+    chromosomes[i]->sw = (struct window *) malloc (sizeof(struct window) * chromosomes[i]->sw_cnt);
+    chromosomes[i]->cw = (struct window *) malloc (sizeof(struct window) * chromosomes[i]->cw_cnt);
+
+
+    
+    /* long windows */
+    for (wcnt=0; wcnt<chromosomes[i]->lw_cnt; wcnt++){
+      retVal = fread(&(chromosomes[i]->lw[wcnt].start), sizeof(chromosomes[i]->lw[wcnt].start), 1, config);
+      retVal = fread(&(chromosomes[i]->lw[wcnt].end),   sizeof(chromosomes[i]->lw[wcnt].end),   1, config);
+      retVal = fread(&(chromosomes[i]->lw[wcnt].gc),    sizeof(chromosomes[i]->lw[wcnt].gc),    1, config);
+      // this is the default, auto-control-picker will fix this
+      chromosomes[i]->lw[wcnt].isControl = 1;
+      chromosomes[i]->lw[wcnt].depth = 0.0;
+    }
+
+    /* short windows */
+    for (wcnt=0; wcnt<chromosomes[i]->sw_cnt; wcnt++){
+      retVal = fread(&(chromosomes[i]->sw[wcnt].start), sizeof(chromosomes[i]->sw[wcnt].start), 1, config);
+      retVal = fread(&(chromosomes[i]->sw[wcnt].end),   sizeof(chromosomes[i]->sw[wcnt].end),   1, config);
+      retVal = fread(&(chromosomes[i]->sw[wcnt].gc),    sizeof(chromosomes[i]->sw[wcnt].gc),    1, config);
+      chromosomes[i]->sw[wcnt].isControl = 1;
+      chromosomes[i]->sw[wcnt].depth = 0.0;
+    }
+
+    /* copy windows */
+    for (wcnt=0; wcnt<chromosomes[i]->cw_cnt; wcnt++){
+      retVal = fread(&(chromosomes[i]->cw[wcnt].start), sizeof(chromosomes[i]->cw[wcnt].start), 1, config);
+      retVal = fread(&(chromosomes[i]->cw[wcnt].end),   sizeof(chromosomes[i]->cw[wcnt].end),   1, config);
+      retVal = fread(&(chromosomes[i]->cw[wcnt].gc),    sizeof(chromosomes[i]->cw[wcnt].gc),    1, config);
+      chromosomes[i]->cw[wcnt].isControl = 1;
+      chromosomes[i]->cw[wcnt].depth = 0.0;
+    }
+
+    /* fill in the rest of the chromosomes structure */
+    
+  }
+
+  fprintf(stdout, "[OK]. %d chromosomes loaded.\n", num_chrom);
+
+  fclose(config);
+}
+
+
+
+static int compChr(const void *p1, const void *p2){
+  /* compare function to sort the chromosome pointer array */
+  struct chrom *a, *b;
+
+  a = *((struct chrom **)p1);
+  b = *((struct chrom **)p2);
+
+
+  return (strcmp ( a->name, b->name) );
+
+}
+
+
+int endswith(char *src, char *end){
+  
+
+  int endlen = strlen(end);
+  int srclen = strlen(src);
+  int copyindex;
+
+
+  if (endlen > srclen)
+    return 0;
+
+  copyindex = srclen - endlen;
+
+  if (memcmp(src+copyindex, end, endlen))
+    return 0;
+  else 
+    return 1;
+
+  
+}
+
+void trimspace(char *str){
+  int len;
+  len = strlen(str) - 1;
+  while(1){
+    if (isspace(str[len]))
+      str[len--]=0;
+    else 
+      break;
+  }
+}