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remove calls to reading beginnign of line #38

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merged 1 commit into from
Jun 19, 2012
Merged

remove calls to reading beginnign of line #38

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25 changes: 0 additions & 25 deletions src/alignment_file.c
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Original file line number Diff line number Diff line change
Expand Up @@ -218,31 +218,6 @@ int detect_snps(char reference_sequence[], char filename[], int length_of_genome



int read_first_few_characters_of_line(char sequence[], FILE * pFilePtr, int max_characters)
{

char *pcRes = NULL;
int lineLength = 0;
char current_line_buffer[MAX_READ_BUFFER_SMALL] = {0};


while((pcRes = fgets(current_line_buffer, MAX_READ_BUFFER_SMALL, pFilePtr)) != NULL){
if(lineLength < max_characters)
{
//append string to line buffer
strcat(sequence, current_line_buffer);
strcpy(current_line_buffer, "");
lineLength = strlen(sequence) - 1;
//if end of line character is found then exit from loop
if((sequence)[lineLength] == '\n' || (sequence)[lineLength] == '\0'){
break;
}
}
}
return 1;
}



char * read_line(char sequence[], FILE * pFilePtr)
{
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2 changes: 0 additions & 2 deletions src/alignment_file.h
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Original file line number Diff line number Diff line change
Expand Up @@ -33,8 +33,6 @@ int number_of_sequences_in_file(char filename[]);
void get_sample_names_for_header(char filename[], char ** sequence_names, int number_of_samples);
char filter_invalid_characters(char input_char);
void get_bases_for_each_snp(char filename[], int snp_locations[], char ** bases_for_snps, int length_of_genome, int number_of_snps);
int read_first_few_characters_of_line(char sequence[], FILE * pFilePtr, int max_characters);


#define MAX_READ_BUFFER 65536
#define MAX_READ_BUFFER_SMALL 1024
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12 changes: 7 additions & 5 deletions src/parse_vcf.c
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Original file line number Diff line number Diff line change
Expand Up @@ -32,14 +32,15 @@ int * column_data;
void get_integers_from_column_in_vcf(FILE * vcf_file_pointer, int * integer_values, int number_of_snps, int column_number)
{
rewind(vcf_file_pointer);
char szBuffer[100000] = {0};
char * szBuffer;
szBuffer = (char *) malloc(MAX_READ_BUFFER*sizeof(char));
int reference_index = 0;
char result[1000] = {0};

do{
strcpy(szBuffer,"");
// check the first character of the line to see if its in the header
read_first_few_characters_of_line(szBuffer, vcf_file_pointer, 50);
// check the first character of the line to see if its in the header
szBuffer = read_line(szBuffer, vcf_file_pointer);

if(szBuffer[0] == '\0')
{
Expand All @@ -61,14 +62,15 @@ void get_integers_from_column_in_vcf(FILE * vcf_file_pointer, int * integer_valu
void get_sequence_from_column_in_vcf(FILE * vcf_file_pointer, char * sequence_bases, int number_of_snps, int column_number)
{
rewind(vcf_file_pointer);
char szBuffer[10000] = {0};
char * szBuffer;
szBuffer = (char *) malloc(MAX_READ_BUFFER*sizeof(char));
int reference_index = 0;
char result[1000] = {0};

do{
strcpy(szBuffer,"");
// check the first character of the line to see if its in the header
read_first_few_characters_of_line(szBuffer, vcf_file_pointer, 1000);
szBuffer = read_line(szBuffer, vcf_file_pointer);

if(szBuffer[0] == '\0')
{
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