hpg-bam/chrom_alignments.c at master · opencb-hpg/hpg-bam · GitHub

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#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#include "chrom_alignments.h"

/* ******************************************************
 *       	Function implementations      		*
 * ******************************************************/

chrom_alignments_t* chrom_alignments_new(int num_alignments) {
    chrom_alignments_t* chrom_alignments_p = (chrom_alignments_t*) calloc(1, sizeof(chrom_alignments_t));
    chrom_alignments_p->bam_alignments_p = (bam1_t**) calloc(num_alignments, sizeof(bam1_t*));

#ifdef THRUST-GPU
    chrom_alignments_p->bam_alignment_coordinates_p.resize(num_alignments);
    chrom_alignments_p->indices_p.resize(num_alignments);
#else
    chrom_alignments_p->bam_alignment_coordinates_p = (int*) calloc(num_alignments, sizeof(int));
    chrom_alignments_p->indices_p = (int*) calloc(num_alignments, sizeof(int));
#endif

    pthread_mutex_init(&(chrom_alignments_p->alignment_count_lock), NULL);
    pthread_mutex_init(&(chrom_alignments_p->complete_lock), NULL);
    chrom_alignments_p->alignment_count = 0;
    chrom_alignments_p->complete = 0;
    chrom_alignments_p->allocated_alignment = num_alignments;

    chrom_alignments_p->initial_allocation = num_alignments;

    return chrom_alignments_p;
}

chrom_alignments_t* chrom_alignments_realloc(chrom_alignments_t* chrom_alignments_p, int num_alignments) {
    bam1_t** aux_alignments_p = chrom_alignments_p->bam_alignments_p;

    int* aux_coordinates_p = chrom_alignments_p->bam_alignment_coordinates_p;
    int* aux_indices_p = chrom_alignments_p->indices_p;

    chrom_alignments_p->bam_alignments_p = (bam1_t**) calloc(num_alignments, sizeof(bam1_t*));

#ifdef THRUST-GPU
    chrom_alignments_p->bam_alignment_coordinates_p.resize(num_alignments);
    chrom_alignments_p->indices_p.resize(num_alignments);
#else
    chrom_alignments_p->bam_alignment_coordinates_p = (int*) calloc(num_alignments, sizeof(int));
    chrom_alignments_p->indices_p = (int*) calloc(num_alignments, sizeof(int));
#endif

    memcpy(chrom_alignments_p->bam_alignments_p, aux_alignments_p, chrom_alignments_p->allocated_alignment * sizeof(bam1_t*));
    memcpy(chrom_alignments_p->bam_alignment_coordinates_p, aux_coordinates_p, chrom_alignments_p->allocated_alignment * sizeof(int));
    memcpy(chrom_alignments_p->indices_p, aux_indices_p, chrom_alignments_p->allocated_alignment * sizeof(int));

    chrom_alignments_p->allocated_alignment = num_alignments;

    //free the previous mallocs pointed by the aux pointers
    for (int i = 0; i < chrom_alignments_p->alignment_count; i++) {
        if (aux_alignments_p[i] == NULL) {
            bam_destroy1(aux_alignments_p[i]);
	}
    }
    free(aux_alignments_p);
    free(aux_coordinates_p);
    free(aux_indices_p);

    return chrom_alignments_p;
}

void chrom_alignments_free(chrom_alignments_t* chrom_alignments_p) {
    if (chrom_alignments_p != NULL) {
        if (chrom_alignments_p->bam_alignments_p != NULL) {
            for (int i = 0; i < chrom_alignments_p->alignment_count; i++) {
                  bam_destroy1(chrom_alignments_p->bam_alignments_p[i]);
            }

            free(chrom_alignments_p->bam_alignments_p);
        }

#ifdef THRUST-GPU
        chrom_alignments_p->bam_alignment_coordinates_p.resize(1);
        chrom_alignments_p->indices_p.resize(1);
#else
        if (chrom_alignments_p->bam_alignment_coordinates_p != NULL) {
            free(chrom_alignments_p->bam_alignment_coordinates_p);
        }
        if (chrom_alignments_p->indices_p != NULL) {
            free(chrom_alignments_p->indices_p);
        }
#endif

        free(chrom_alignments_p);
    }
}

bam1_t* chrom_alignments_get_alignment(chrom_alignments_t* chrom_alignments_p, int index) {
    bam1_t* alignment_p = NULL;

    pthread_mutex_lock(&chrom_alignments_p->alignment_count_lock);

    if (chrom_alignments_p->alignment_count > index) {
        alignment_p = chrom_alignments_p->bam_alignments_p[index];
    }

    pthread_mutex_unlock(&chrom_alignments_p->alignment_count_lock);

    return alignment_p;
}

int chrom_alignments_is_complete(chrom_alignments_t* chrom_alignments_p) {
    int complete;

    pthread_mutex_lock(&chrom_alignments_p->complete_lock);
    complete = chrom_alignments_p->complete;
    pthread_mutex_unlock(&chrom_alignments_p->complete_lock);

    return complete;
}

void chrom_alignments_set_complete(chrom_alignments_t* chrom_alignments_p, int complete) {
    pthread_mutex_lock(&chrom_alignments_p->complete_lock);
    chrom_alignments_p->complete = complete;
    pthread_mutex_unlock(&chrom_alignments_p->complete_lock);
}

alignments_list_t* alignments_list_new(int num_chromosomes) {
    alignments_list_t* list_p = (alignments_list_t*) calloc(1, sizeof(alignments_list_t));
    list_p->num_chromosomes = num_chromosomes;
    list_p->chromosomes_p = (chrom_alignments_t**) calloc(num_chromosomes, sizeof(chrom_alignments_t*));

    return list_p;
}

void alignments_list_free(alignments_list_t* list_p) {
    if (list_p != NULL) {
        if (list_p->chromosomes_p != NULL) {
            for (int i = 0; i < list_p->num_chromosomes; i++) {
                chrom_alignments_free(list_p->chromosomes_p[i]);
            }
            free(list_p->chromosomes_p);
        }
        free(list_p);
        list_p = NULL;
    }
}

void alignments_list_new_chrom_alignment(int chromosome, int num_alignments, alignments_list_t* list_p) {
    if (list_p == NULL) {
        LOG_FATAL("ERROR: list is null !!\n");
    }

    if (list_p->chromosomes_p[chromosome] != NULL) {
        char log_message[50];
        sprintf(log_message, "ERROR: chromosome %i (alignment list) is already allocated !!\n", chromosome);
        LOG_FATAL(log_message);
    }

    list_p->chromosomes_p[chromosome] = chrom_alignments_new(num_alignments);
}

chrom_alignments_t* alignments_list_get_chrom_alignment(int chromosome, alignments_list_t* list_p) {
    return list_p->chromosomes_p[chromosome];
}

void alignments_list_insert_batch(bam_batch_t* batch_p, alignments_list_t* list_p) {
    bam1_t* alignment_p;
    chrom_alignments_t* chrom_alignment_p;

    if (batch_p->type == SINGLE_CHROM_BATCH) {
        chrom_alignment_p = list_p->chromosomes_p[batch_p->alignments_p[0]->core.tid];

        pthread_mutex_lock(&(chrom_alignment_p->alignment_count_lock));
        for (int i = 0; i < batch_p->num_alignments; i++) {
            alignment_p = batch_p->alignments_p[i];
            chrom_alignment_p = list_p->chromosomes_p[alignment_p->core.tid];

            if (chrom_alignment_p->alignment_count >= chrom_alignment_p->allocated_alignment) {
                chrom_alignments_realloc(chrom_alignment_p, chrom_alignment_p->allocated_alignment + chrom_alignment_p->initial_allocation);
            }

            chrom_alignment_p->bam_alignments_p[chrom_alignment_p->alignment_count] = alignment_p;
            chrom_alignment_p->bam_alignment_coordinates_p[chrom_alignment_p->alignment_count] = (int) alignment_p->core.pos;
            chrom_alignment_p->indices_p[chrom_alignment_p->alignment_count] = chrom_alignment_p->alignment_count;
            chrom_alignment_p->alignment_count++;
        }
        pthread_mutex_unlock(&(chrom_alignment_p->alignment_count_lock));
    } else {
        for (int i = 0; i < batch_p->num_alignments; i++) {
            alignment_p = batch_p->alignments_p[i];
            chrom_alignment_p = list_p->chromosomes_p[alignment_p->core.tid];

            pthread_mutex_lock(&chrom_alignment_p->alignment_count_lock);

            if (chrom_alignment_p->alignment_count >= chrom_alignment_p->allocated_alignment) {
                chrom_alignments_realloc(chrom_alignment_p, chrom_alignment_p->allocated_alignment + chrom_alignment_p->initial_allocation);
            }

            chrom_alignment_p->bam_alignments_p[chrom_alignment_p->alignment_count] = alignment_p;
            chrom_alignment_p->bam_alignment_coordinates_p[chrom_alignment_p->alignment_count] = (int) alignment_p->core.pos;
            chrom_alignment_p->indices_p[chrom_alignment_p->alignment_count] = chrom_alignment_p->alignment_count;
            chrom_alignment_p->alignment_count++;

            pthread_mutex_unlock(&chrom_alignment_p->alignment_count_lock);
        }
    }
}