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-rw-r--r--configure.ac20
-rw-r--r--src/Makefile.am6
-rw-r--r--src/aggregator.c14
-rw-r--r--src/assign_protein_type.c72
-rw-r--r--src/assign_protein_type.h6
-rw-r--r--src/check_error.c14
-rw-r--r--src/check_error.h11
-rw-r--r--src/check_h5_error.c12
-rw-r--r--src/check_h5_error.h12
-rw-r--r--src/check_ncbi_error.c13
-rw-r--r--src/check_ncbi_error.h13
-rw-r--r--src/load_influenza_aa_dat.c31
12 files changed, 211 insertions, 13 deletions
diff --git a/src/load_influenza_aa_dat.c b/src/load_influenza_aa_dat.c
index 493c7db..91ef415 100644
--- a/src/load_influenza_aa_dat.c
+++ b/src/load_influenza_aa_dat.c
@@ -6,6 +6,8 @@
6 */6 */
77
8#include "load_influenza_aa_dat.h"8#include "load_influenza_aa_dat.h"
9#include "check_error.h"
10#include "check_h5_error.h"
9#include "hdf5_hl.h"11#include "hdf5_hl.h"
10#include <string.h>12#include <string.h>
11#include <stdlib.h>13#include <stdlib.h>
@@ -140,7 +142,10 @@ load_influenza_aa_dat (hid_t file_id)
140 * Insert the records.142 * Insert the records.
141 */143 */
142 supplementary_data p_data;144 supplementary_data p_data;
143 FILE* dat = fopen ("/home/don/exp004/genomes/INFLUENZA/influenza_aa.dat", "r");145 FILE* dat = fopen ("/home/don/exp004/genomes/INFLUENZA/influenza_aa.dat",
146 "r");
147 if (dat == NULL)
148 check_error (__FILE__, __LINE__);
144 char *line = NULL;149 char *line = NULL;
145 size_t len = 0;150 size_t len = 0;
146 int current_line = 0;151 int current_line = 0;
@@ -205,13 +210,23 @@ load_influenza_aa_dat (hid_t file_id)
205 strncpy(p_data.full_length_indicator, strsep (&running, "\t"),210 strncpy(p_data.full_length_indicator, strsep (&running, "\t"),
206 sizeof(p_data.full_length_indicator));211 sizeof(p_data.full_length_indicator));
207212
208 if (current_line == 1) 213 if (current_line == 1)
209 H5TBmake_table ("influenza_aa.dat", file_id, TABLE_NAME,NFIELDS,1,214 {
210 dst_size,field_names, dst_offset, field_type,215 herr_t status = H5TBmake_table ("influenza_aa.dat", file_id,
211 chunk_size, fill_data, compress, &p_data);216 TABLE_NAME, NFIELDS, 1,dst_size,
212 else 217 field_names, dst_offset, field_type,
213 H5TBappend_records (file_id, TABLE_NAME, 1, dst_size, dst_offset,218 chunk_size, fill_data, compress,
214 dst_sizes, &p_data);219 &p_data);
220 if (status < 0)
221 check_h5_error (status, __FILE__, __LINE__);
222 }
223 else
224 {
225 herr_t status = H5TBappend_records (file_id, TABLE_NAME, 1, dst_size,
226 dst_offset, dst_sizes, &p_data);
227 if (status < 0)
228 check_h5_error (status, __FILE__, __LINE__);
229 }
215230
216 if (running)231 if (running)
217 free (running);232 free (running);

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