265 lines
7.4 KiB
C
265 lines
7.4 KiB
C
#include <string.h>
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#include "list.h"
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#include "process.h"
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#include "dapDB.h"
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#include "bapDB.h"
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#include "flat_sd.h"
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#include "misc.h"
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void open_for_read(List *from)
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{
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char *a;
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if ( (a = assoc(from,db_type)) == NULL)
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crash("Type not specified for source database\n");
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else if (strcmp(a,db_type_RS_flat_file) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_SD_flat_file) == 0)
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flat_sd_open_for_read(from);
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else if (strcmp(a,db_type_sap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_early_xdap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_middle_xdap) == 0)
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xdap_middle_open_for_read(from);
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else if (strcmp(a,db_type_late_xdap) == 0)
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xdap_late_open_for_read(from);
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else
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crash("Source database type not supported\n");
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}
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void open_for_write(List *to)
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{
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char *a;
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if ( (a = assoc(to,db_type)) == NULL)
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crash("Type not specified for source database\n");
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else if (strcmp(a,db_type_RS_flat_file) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_SD_flat_file) == 0)
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flat_sd_open_for_write(to);
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else if (strcmp(a,db_type_sap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_early_xdap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_middle_xdap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_late_xdap) == 0)
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xdap_late_open_for_write(to);
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else
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crash("Source database type not supported\n");
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}
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void close_files(List *to)
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{
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char *a;
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if ( (a = assoc(to,db_type)) == NULL)
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crash("Type not specified for source database\n");
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else if (strcmp(a,db_type_RS_flat_file) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_SD_flat_file) == 0)
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flat_sd_close(to);
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else if (strcmp(a,db_type_sap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_early_xdap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_middle_xdap) == 0)
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xdap_middle_close(to);
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else if (strcmp(a,db_type_late_xdap) == 0)
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xdap_late_close(to);
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else
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crash("Source database type not supported\n");
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}
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List *read_header(List *from)
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{
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char *a;
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if ( (a = assoc(from,db_type)) == NULL)
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crash("Type not specified for source database\n");
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else if (strcmp(a,db_type_RS_flat_file) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_SD_flat_file) == 0)
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return (List *)flat_sd_read_header();
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else if (strcmp(a,db_type_sap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_early_xdap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_middle_xdap) == 0)
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return (List *)xdap_middle_read_header();
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else if (strcmp(a,db_type_late_xdap) == 0)
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return (List *)xdap_late_read_header();
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else
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crash("Source database type not supported\n");
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return (List *)0; /* stops warnings */
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}
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void write_header(List *to, List *l)
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{
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char *a;
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if ( (a = assoc(to,db_type)) == NULL)
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crash("Type not specified for source database\n");
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else if (strcmp(a,db_type_RS_flat_file) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_SD_flat_file) == 0)
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flat_sd_write_header(l);
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else if (strcmp(a,db_type_sap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_early_xdap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_middle_xdap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_late_xdap) == 0)
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xdap_late_write_header(l);
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else
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crash("Source database type not supported\n");
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}
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List *read_gel_data(List *from)
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{
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char *a;
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if ( (a = assoc(from,db_type)) == NULL)
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crash("Type not specified for source database\n");
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else if (strcmp(a,db_type_RS_flat_file) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_SD_flat_file) == 0)
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return (List *)flat_sd_read_gel_data();
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else if (strcmp(a,db_type_sap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_early_xdap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_middle_xdap) == 0)
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return (List *)xdap_middle_read_gel_data();
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else if (strcmp(a,db_type_late_xdap) == 0)
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return (List *)xdap_late_read_gel_data();
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else
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crash("Source database type not supported\n");
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return (List *)0; /* stops warnings */
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}
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void write_gel_data(List *to, List *l)
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{
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char *a;
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if ( (a = assoc(to,db_type)) == NULL)
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crash("Type not specified for source database\n");
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else if (strcmp(a,db_type_RS_flat_file) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_SD_flat_file) == 0)
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flat_sd_write_gel_data(l);
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else if (strcmp(a,db_type_sap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_early_xdap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_middle_xdap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_late_xdap) == 0)
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xdap_late_write_gel_data(l);
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else
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crash("Source database type not supported\n");
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}
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List *read_contig_data(List *from)
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{
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char *a;
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if ( (a = assoc(from,db_type)) == NULL)
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crash("Type not specified for source database\n");
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else if (strcmp(a,db_type_RS_flat_file) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_SD_flat_file) == 0)
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return (List *)flat_sd_read_contig_data();
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else if (strcmp(a,db_type_sap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_early_xdap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_middle_xdap) == 0)
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return (List *)xdap_middle_read_contig_data();
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else if (strcmp(a,db_type_late_xdap) == 0)
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return (List *)xdap_late_read_contig_data();
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else
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crash("Source database type not supported\n");
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return (List *)0; /* stops warnings */
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}
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void write_contig_data(List *to, List *l)
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{
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char *a;
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if ( (a = assoc(to,db_type)) == NULL)
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crash("Type not specified for source database\n");
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else if (strcmp(a,db_type_RS_flat_file) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_SD_flat_file) == 0)
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flat_sd_write_contig_data(l);
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else if (strcmp(a,db_type_sap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_early_xdap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_middle_xdap) == 0)
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crash("Source database type not supported\n");
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else if (strcmp(a,db_type_late_xdap) == 0)
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xdap_late_write_contig_data(l);
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else
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crash("Source database type not supported\n");
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}
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void process(List *from, List *to)
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{
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List *l;
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/*
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** Initialise read
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*/
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open_for_read(from);
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open_for_write(to);
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l = read_header(from);
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write_header(to,l);
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destroy_list(l);
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/*
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** Process Gels
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*/
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for (l = read_gel_data(from);
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!isNil(l);
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l = read_gel_data(from)) {
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write_gel_data(to,l);
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destroy_list(l);
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}
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/*
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** Process Contigs
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*/
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for (l = read_contig_data(from);
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!isNil(l);
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l = read_contig_data(from)) {
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write_contig_data(to,l);
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destroy_list(l);
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}
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/*
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** Tidy up read
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*/
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close_files(from);
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close_files(to);
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}
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