diff chromeister/src/commonFunctions.c @ 0:4616cc3476d4 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chromeister/src/commonFunctions.c	Sat Dec 15 18:06:48 2018 -0500
@@ -0,0 +1,218 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <sys/time.h>
+#include <inttypes.h>
+#include <ctype.h>
+#include <string.h>
+#include <pthread.h>
+#include <math.h>
+#include "structs.h"
+
+void terror(char *s) {
+    printf("ERR**** %s ****\n", s);
+    exit(-1);
+}
+
+char buffered_fgetc(char *buffer, uint64_t *pos, uint64_t *read, FILE *f) {
+    if (*pos >= READBUF) {
+        *pos = 0;
+        memset(buffer, 0, READBUF);
+        *read = fread(buffer, 1, READBUF, f);
+    }
+    *pos = *pos + 1;
+    return buffer[*pos-1];
+}
+
+Queue * generate_queue(Head * queue_head, uint64_t t_reads, uint64_t n_threads, uint64_t levels){
+    uint64_t i, j;
+    uint64_t reads_per_thread;
+    if(levels > t_reads) levels = t_reads;
+    uint64_t pieces = t_reads/levels;
+    uint64_t from, to, t_queues = 0, current_queue = 0;
+    for(i=0;i<levels;i++) t_queues += ((i+1)*n_threads);
+    Queue * queues = (Queue *) malloc(t_queues * sizeof(Queue));
+    if(queues == NULL) terror("Could not allocate queue tasks");
+    queue_head->head = &queues[0];
+    
+    for(i=0;i<levels;i++){
+
+        //reads_per_thread = (uint64_t) (floorl((long double) pieces / (long double) ((i+1)*n_threads)));
+        reads_per_thread = (uint64_t) (ceill((long double) pieces / (long double) ((i+1)*n_threads)));
+        
+
+        for(j=0;j<(i+1)*n_threads;j++){
+            from = j * reads_per_thread + (pieces*i);
+            to = (j + 1) * reads_per_thread + (pieces*i);
+            
+            if(j == (i+1)*n_threads - 1) to = pieces*(i+1);
+
+
+            if(i == levels - 1 && j == (i+1)*n_threads - 1){
+                //If its the last 
+                queues[current_queue].next = NULL;
+            }else{
+                //Else add it to the queue
+                queues[current_queue].next = &queues[current_queue+1];
+            }
+            
+
+            queues[current_queue].r1 = from;
+            queues[current_queue].r2 = to;
+            current_queue++;
+            //printf("current_piece: %"PRIu64"-%"PRIu64" diff: %"PRIu64"\n", from, to, to - from);
+
+        }
+
+    }
+    //printf("TREADS was %"PRIu64"\n", t_reads);    
+    return &queues[0];
+}
+
+void print_queue(Queue * q){
+    fprintf(stdout, "Task: %"PRIu64"-%"PRIu64"\n", q->r1, q->r2);
+}
+
+Queue * get_task_from_queue(Head * queue_head, pthread_mutex_t * lock){
+    pthread_mutex_lock(lock);
+
+    Queue * ptr = queue_head->head;
+    if(queue_head->head != NULL) queue_head->head = queue_head->head->next;
+    //if(ptr != NULL){ printf("Taking "); /*print_queue(ptr);*/ }
+
+    pthread_mutex_unlock(lock);
+
+
+    return ptr;
+}
+
+uint64_t quick_pow4(uint64_t n){
+    static uint64_t pow4[33]={1L, 4L, 16L, 64L, 256L, 1024L, 4096L, 16384L, 65536L, 
+    262144L, 1048576L, 4194304L, 16777216L, 67108864L, 268435456L, 1073741824L, 4294967296L, 
+    17179869184L, 68719476736L, 274877906944L, 1099511627776L, 4398046511104L, 17592186044416L, 
+    70368744177664L, 281474976710656L, 1125899906842624L, 4503599627370496L, 18014398509481984L, 
+    72057594037927936L, 288230376151711744L, 1152921504606846976L, 4611686018427387904L};
+    return pow4[n];
+}
+
+uint64_t quick_pow4byLetter(uint64_t n, const char c){
+    static uint64_t pow4_G[33]={2*1L, 2*4L, 2*16L, 2*64L, 2*256L, 2*1024L, 2*4096L, 2*16384L, 2*65536L, 
+    (uint64_t)2*262144L, (uint64_t)2*1048576L,(uint64_t)2*4194304L, (uint64_t)2*16777216L, (uint64_t)2*67108864L, (uint64_t)2*268435456L, (uint64_t)2*1073741824L, (uint64_t)2*4294967296L, 
+    (uint64_t)2*17179869184L, (uint64_t)2*68719476736L, (uint64_t)2*274877906944L, (uint64_t)2*1099511627776L, (uint64_t)2*4398046511104L, (uint64_t)2*17592186044416L, 
+    (uint64_t)2*70368744177664L, (uint64_t)2*281474976710656L, (uint64_t)2*1125899906842624L, (uint64_t)2*4503599627370496L, (uint64_t)2*18014398509481984L, 
+    (uint64_t)2*72057594037927936L, (uint64_t) 2*288230376151711744L, (uint64_t) 2*1152921504606846976L, (uint64_t) 2*4611686018427387904L};
+    
+    static uint64_t pow4_T[33]={3*1L, 3*4L, 3*16L, 3*64L, 3*256L, 3*1024L, 3*4096L, 3*16384L, 3*65536L, 
+    (uint64_t)3*262144L, (uint64_t) 3*1048576L, (uint64_t)3*4194304L, (uint64_t)3*16777216L, (uint64_t)3*67108864L, (uint64_t)3*268435456L, (uint64_t)3*1073741824L, (uint64_t)3*4294967296L, 
+    (uint64_t)3*17179869184L, (uint64_t)3*68719476736L, (uint64_t)3*274877906944L, (uint64_t)3*1099511627776L, (uint64_t)3*4398046511104L, (uint64_t)3*17592186044416L, 
+    (uint64_t)3*70368744177664L, (uint64_t)3*281474976710656L, (uint64_t)3*1125899906842624L, (uint64_t)3*4503599627370496L, (uint64_t)3*18014398509481984L, 
+    (uint64_t)3*72057594037927936L, (uint64_t) 3*288230376151711744L, (uint64_t) 3*1152921504606846976L, (uint64_t) 3*4611686018427387904L};
+    
+    if(c == 'A') return 0;
+    if(c == 'C') return quick_pow4(n);
+    if(c == 'G') return pow4_G[n];
+    if(c == 'T') return pow4_T[n];
+    return 0;
+}
+
+uint64_t hashOfWord(const unsigned char * word, uint32_t k, uint64_t offset){
+    
+    uint64_t value = 0, jIdx;
+    for(jIdx=0;jIdx<k-offset;jIdx++){
+        value += quick_pow4byLetter(k-(jIdx+1), (char) word[jIdx]);
+    }
+    return value;
+}
+
+void perfect_hash_to_word(unsigned char * word, uint64_t hash, uint32_t k){
+    uint64_t jIdx = (uint64_t) (k-1), upIdx = 0;
+    uint64_t v;
+    while(jIdx >= 0){
+        v = (uint64_t) floor(hash / (pow(4, jIdx)));
+        if(v == 0){ word[upIdx++] = (unsigned char) 'A'; hash -= ((uint64_t) pow(4, jIdx) * 0); }
+        if(v == 1){ word[upIdx++] = (unsigned char) 'C'; hash -= ((uint64_t) pow(4, jIdx) * 1); }
+        if(v == 2){ word[upIdx++] = (unsigned char) 'G'; hash -= ((uint64_t) pow(4, jIdx) * 2); }
+        if(v == 3){ word[upIdx++] = (unsigned char) 'T'; hash -= ((uint64_t) pow(4, jIdx) * 3); }
+        
+        if(jIdx == 0) break;
+        --jIdx;
+    }
+}
+
+uint64_t collisioned_hash(const unsigned char * word, uint32_t k){
+    uint64_t jIdx, value = 0;
+    for(jIdx=0;jIdx<k;jIdx+=diffuse_z){
+        value += quick_pow4byLetter(k - (jIdx+1), (char) word[jIdx]);
+    }
+    return value;
+}
+
+void decomposed_hash_of_word(const unsigned char * word, unsigned char * vector, uint32_t k){
+    uint64_t jIdx;
+    for(jIdx=0;jIdx<k/BYTES_IN_MER;jIdx++){
+        vector[jIdx] = (unsigned char) quick_pow4byLetter(0, (char) word[jIdx*BYTES_IN_MER]);
+        vector[jIdx] += (unsigned char) quick_pow4byLetter(1, (char) word[jIdx*BYTES_IN_MER+1]);
+        vector[jIdx] += (unsigned char) quick_pow4byLetter(2, (char) word[jIdx*BYTES_IN_MER+2]);
+        vector[jIdx] += (unsigned char) quick_pow4byLetter(3, (char) word[jIdx*BYTES_IN_MER+3]);
+    }
+}
+
+uint64_t xor_decomposed_hash(unsigned char * vector1, unsigned char * vector2, uint32_t k){
+    uint64_t jIdx;
+    uint64_t diffs = 0;
+    for(jIdx=0;jIdx<k/BYTES_IN_MER;jIdx++){
+        diffs += (uint64_t) ((vector1[jIdx] ^ vector2[jIdx]) & 0x1);
+    }
+    return diffs;
+}
+
+uint64_t asciiToUint64(const char *text){
+	uint64_t number=0;
+
+	for(;*text;text++){
+		char digit=*text-'0';           
+		number=(number*10)+digit;
+	}
+	return number;
+}
+
+unsigned char complement(unsigned char c){
+    
+    switch(c){
+    case ((unsigned)'A'): return (unsigned)'T';
+    break;
+    case ((unsigned)'C'): return (unsigned)'G';
+    break;
+    case ((unsigned)'G'): return (unsigned)'C';
+    break;
+    case ((unsigned)'T'): return (unsigned)'A';
+    break;
+    case ((unsigned)'N'): return (unsigned)'N';
+    break;
+    case ((unsigned)'-'): return (unsigned)'-'; // Gaps
+    break;
+    case ((unsigned)'\0'): return (unsigned)'\0';
+    
+    }
+    
+    printf("T B: (%c) ____\n", c);
+    terror("Unrecognized nucleotide in hit");
+    return 0; 
+}
+
+void inplace_reverse_and_complement(unsigned char *d, uint64_t l){
+    uint64_t i;
+    char c;
+    for(i=0;i<l/2;i++){
+        c = d[i];
+        d[i] = d[l-i-1];
+        d[l-i-1] = c;
+        //printf("%c%c", d[i], d[l-i-1]);
+    }
+    
+    //printf("\n");
+    for(i=0;i<l;i++){
+        //printf("eeee: %d", (int)d[i]);
+        d[i] = complement(d[i]);
+    }
+}
+