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| Original file line number | Diff line number | Diff line change |
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@@ -23,6 +23,7 @@ config.log | |
| config.status | ||
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| miRA | ||
| miRAtest | ||
| check_cluster | ||
| check_parse_sam | ||
| src/.deps/ | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,5 @@ | ||
| #include "cluster.h" | ||
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| #ifndef BED_FILE_IO_H | ||
| #define BED_FILE_IO_H | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,123 @@ | ||
| #include "fasta.h" | ||
| #include "errors.h" | ||
| #include "fasta.h" | ||
| #include <stdlib.h> | ||
| #include <stdio.h> | ||
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| int read_fasta_file(struct genome_sequence **sequence_table, char *filename) { | ||
| static const char name_marker = '>'; | ||
| static const int MAXLINELENGHT = 2048; | ||
| struct genome_sequence *current_seq = NULL; | ||
| int err, l; | ||
| char *sep; | ||
| char line[MAXLINELENGHT]; | ||
| FILE *fp = fopen(filename, "r"); | ||
| if (fp == NULL) { | ||
| return E_FILE_NOT_FOUND; | ||
| } | ||
| while (fgets(line, sizeof(line), fp) != NULL) { | ||
| if (line[0] == name_marker) { | ||
| if (current_seq != NULL) { | ||
| HASH_ADD_STR(*sequence_table, chrom, current_seq); | ||
| } | ||
| create_genome_sequence(¤t_seq); | ||
| sep = strchr(line, ' '); | ||
| if (sep == NULL) { | ||
| sep = strchr(line, '\n'); | ||
| } | ||
| if (sep == NULL) { | ||
| sep = strchr(line, '\0'); | ||
| } | ||
| if (sep == NULL) { | ||
| err = E_UNKNOWN_FILE_IO_ERROR; | ||
| goto parse_error; | ||
| } | ||
| l = sep - line - 1; | ||
| memcpy(current_seq->chrom, line + 1, l); | ||
| current_seq->chrom[l] = 0; | ||
| continue; | ||
| } | ||
| sep = strchr(line, '\n'); | ||
| if (sep == NULL) { | ||
| sep = strchr(line, '\0'); | ||
| } | ||
| if (sep == NULL) { | ||
| err = E_UNKNOWN_FILE_IO_ERROR; | ||
| goto parse_error; | ||
| } | ||
| err = append_to_genome_sequence(current_seq, line, sep - line); | ||
| if (err) { | ||
| goto parse_error; | ||
| } | ||
| } | ||
| HASH_ADD_STR(*sequence_table, chrom, current_seq); | ||
| fclose(fp); | ||
| return E_SUCCESS; | ||
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| parse_error: | ||
| free_sequence_table(*sequence_table); | ||
| fclose(fp); | ||
| return err; | ||
| } | ||
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| int create_genome_sequence(struct genome_sequence **seq) { | ||
| static const int STARTINGSIZE = 4096; | ||
| struct genome_sequence *s = | ||
| (struct genome_sequence *)malloc(sizeof(struct genome_sequence)); | ||
| if (s == NULL) { | ||
| return E_MALLOC_FAIL; | ||
| } | ||
| s->data = (char *)malloc(STARTINGSIZE * sizeof(char)); | ||
| if (s->data == NULL) { | ||
| free(s); | ||
| return E_MALLOC_FAIL; | ||
| } | ||
| s->capacity = STARTINGSIZE; | ||
| s->n = 0; | ||
| *seq = s; | ||
| return E_SUCCESS; | ||
| } | ||
| int strip_newlines(char **dest, size_t *nsize, char *buffer, size_t size) { | ||
| char *new_buffer = (char *)malloc(size * sizeof(char)); | ||
| size_t new_size = 0; | ||
| for (size_t i = 0; i < size; i++) { | ||
| if (buffer[i] != '\n') { | ||
| new_buffer[new_size++] = buffer[i]; | ||
| } | ||
| } | ||
| char *tmp = (char *)realloc(new_buffer, new_size * sizeof(char)); | ||
| if (tmp == NULL) { | ||
| free(new_buffer); | ||
| return E_REALLOC_FAIL; | ||
| } | ||
| *dest = tmp; | ||
| *nsize = new_size; | ||
| return E_SUCCESS; | ||
| } | ||
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| int append_to_genome_sequence(struct genome_sequence *seq, char *data, | ||
| size_t size) { | ||
| if (seq == NULL) | ||
| return E_SUCCESS; | ||
| while (seq->capacity - seq->n < size) { | ||
| seq->capacity *= 2; | ||
| char *tmp = (char *)realloc(seq->data, seq->capacity * sizeof(char)); | ||
| if (tmp == NULL) { | ||
| return E_REALLOC_FAIL; | ||
| } | ||
| seq->data = tmp; | ||
| } | ||
| memcpy(seq->data + seq->n, data, size); | ||
| seq->n += size; | ||
| return E_SUCCESS; | ||
| } | ||
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| int free_sequence_table(struct genome_sequence *table) { | ||
| struct genome_sequence *s = NULL; | ||
| struct genome_sequence *tmp = NULL; | ||
| HASH_ITER(hh, table, s, tmp) { | ||
| HASH_DEL(table, s); | ||
| free(s); | ||
| } | ||
| return E_SUCCESS; | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| #include <stddef.h> | ||
| #include "uthash.h" | ||
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| #ifndef FASTA_H | ||
| #define FASTA_H | ||
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| struct genome_sequence { | ||
| char chrom[1024]; | ||
| char *data; | ||
| size_t n; | ||
| size_t capacity; | ||
| UT_hash_handle hh; | ||
| }; | ||
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| int read_fasta_file(struct genome_sequence **sequence_table, char *filename); | ||
| int create_genome_sequence(struct genome_sequence **seq); | ||
| int strip_newlines(char **dest, size_t *nsize, char *buffer, size_t size); | ||
| int append_to_genome_sequence(struct genome_sequence *seq, char *data, | ||
| size_t size); | ||
| int free_sequence_table(struct genome_sequence *table); | ||
| #endif |
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