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free.c
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free.c
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#include <stdio.h>
#include "free.h"
#include "split_read.h"
void free_splits(bam_info* in_bam)
{
int i;
splitRead *sfcPtr, *sfcPtrNext;
SplitsInfo *aPtr;
SplitRow *tmp, *tmp_next;
posMapSplitRead *ptrSplitMapPtr, *ptrSplitMapNext;
sfcPtr = in_bam->listSplitRead;
while( sfcPtr != NULL)
{
sfcPtrNext = sfcPtr->next;
if( sfcPtr->readName != NULL)
free( sfcPtr->readName);
if( sfcPtr->chromosome_name != NULL)
free( sfcPtr->chromosome_name);
ptrSplitMapPtr = sfcPtr->ptrSplitMap;
while(ptrSplitMapPtr != NULL)
{
ptrSplitMapNext = ptrSplitMapPtr->next;
if(ptrSplitMapPtr != NULL)
free( ptrSplitMapPtr);
ptrSplitMapPtr = ptrSplitMapNext;
}
free( sfcPtr);
sfcPtr = sfcPtrNext;
}
in_bam->listSplitRead = NULL;
aPtr = all_split_reads;
if( aPtr != NULL)
{
tmp = aPtr->head;
while( tmp != NULL)
{
tmp_next = tmp->next;
free( tmp);
tmp = tmp_next;
}
aPtr->head = NULL;
aPtr->tail = NULL;
free( aPtr);
}
all_split_reads = NULL;
}
void free_SVs(svs* sv_all, int sv_count)
{
int count;
for(count = 0; count < sv_count; count++)
{
if(sv_all[count].chr_name != NULL)
free(sv_all[count].chr_name);
}
free(sv_all);
}
void free_DS(bam_info* in_bam, parameters *params)
{
/* Free bams and related libraries */
free( in_bam->sample_name);
free( in_bam);
/* Free params struct */
free( params->bam_file);
free( params->del_file);
free( params->dup_file);
free( params->ref_genome);
free( params->outprefix);
free( params->outdir);
free( params->sonic_file);
free( params->sonic_info);
free( params->mappability_file);
free( params);
if(hash_table_count != NULL)
free(hash_table_count);
if(hash_table_iter != NULL)
free(hash_table_iter);
}