454 lines
8.4 KiB
C
454 lines
8.4 KiB
C
#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include <sys/types.h>
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#include "process.h"
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#include "list.h"
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#include "dapIO.h"
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#include "dapDB.h"
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#include "misc.h"
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/*
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** For dap io
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*/
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static DapIO io;
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int maxgel;
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static int cur_gel_index;
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static int cur_contig_index;
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static List *file_details()
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{
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return
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build_list(
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atom_str(db_files),
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build_list(
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atom_str(db_files_arch),
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atom_str(io.ar_file),
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nil),
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build_list(
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atom_str(db_files_rel),
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atom_str(io.rl_file),
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nil),
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build_list(
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atom_str(db_files_seq),
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atom_str(io.sq_file),
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nil),
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build_list(
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atom_str(db_files_tag),
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atom_str(io.tg_file),
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nil),
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build_list(
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atom_str(db_files_com),
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atom_str(io.cc_file),
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nil),
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nil
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);
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}
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static List *db_details()
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{
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return
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build_list(
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build_list(
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atom_str(db_max_gels),
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atom_int(io.max_gels),
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nil),
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build_list(
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atom_str(db_max_gel_length),
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atom_int(io.max_gel_length),
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nil),
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build_list(
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atom_str(db_data_class),
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atom_int(io.data_class),
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nil),
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build_list(
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atom_str(db_num_gels),
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atom_int(io.num_gels),
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nil),
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build_list(
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atom_str(db_num_contigs),
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atom_int(io.num_contigs),
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nil),
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nil);
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}
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void xdap_middle_open_for_read(List *l)
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/*
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**
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*/
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{
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char *name;
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char *version;
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name = assoc(l,db_name);
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if (! name) crash("No database name specified\n");
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version = assoc(l,db_version);
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if (! version) crash("No version specified\n");
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dap_open_for_read(&io, name, version);
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cur_gel_index = 1;
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cur_contig_index = 1;
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}
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List *xdap_middle_read_header()
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/*
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**
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*/
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{
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List *files;
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List *details;
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files = file_details();
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details = db_details();
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return
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join_list(
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build_list(
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atom_str(db_from),
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nil),
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details,
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build_list(
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files,
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nil),
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nil);
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}
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List *xdap_middle_read_gel_data()
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{
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List *gel_details;
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if (cur_gel_index > io.num_gels)
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gel_details = nil;
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else {
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dap_ar_file_rec ar_line;
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dap_rl_file_rec rl_line;
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dap_sq_file_rec sq_line;
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dap_tg_file_rec tg_line;
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int index;
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char name[13];
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char *seq;
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int length;
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int comp;
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int pos;
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int l_nbr;
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int r_nbr;
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sq_line = (char *) malloc(io.max_gel_length+1);
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dap_read_ar(&io,cur_gel_index,&ar_line);
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dap_read_rl(&io,cur_gel_index,&rl_line);
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dap_read_tg(&io,cur_gel_index,&tg_line);
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dap_read_sq(&io,cur_gel_index,sq_line);
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index = cur_gel_index;
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f2cstr(ar_line.lines.name,10,name,12);
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length = abs(rl_line.lines.length);
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comp = (rl_line.lines.length < 0);
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seq = sq_line; seq[length] = '\0';
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pos = rl_line.lines.rel_pos;
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l_nbr = rl_line.lines.left_nbr;
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r_nbr = rl_line.lines.right_nbr;
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gel_details =
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build_list(
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atom_str(gel_rec),
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build_list(
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atom_str(gel_index),
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atom_int(index),
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nil),
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build_list(
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atom_str(gel_name),
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atom_str(name),
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nil),
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build_list(
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atom_str(gel_length),
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atom_int(length),
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nil),
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build_list(
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atom_str(gel_comp),
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atom_int(comp),
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nil),
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build_list(
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atom_str(gel_seq),
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atom_str(seq),
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nil),
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build_list(
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atom_str(gel_pos),
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atom_int(pos),
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nil),
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build_list(
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atom_str(gel_l_nbr),
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atom_int(l_nbr),
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nil),
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build_list(
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atom_str(gel_r_nbr),
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atom_int(r_nbr),
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nil),
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nil);
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/* Get raw data details */
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if (tg_line.lines.comment) {
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List *raw_data_details;
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char *rd;
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int rd_length;
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int rd_cut;
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int rd_ulen;
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char rd_type[5];
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char rd_file[19];
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rd = dap_read_comment(&io, tg_line.lines.comment);
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sscanf(rd,"%6d%6d%6d%*s",&rd_length, &rd_cut, &rd_ulen);
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f2cstr(&rd[18],4,rd_type,4);
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f2cstr(&rd[22],18,rd_file,18);
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raw_data_details =
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build_list(
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build_list(
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atom_str(gel_rd_length),
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atom_int(rd_length),
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nil),
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build_list(
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atom_str(gel_rd_cut),
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atom_int(rd_cut),
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nil),
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build_list(
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atom_str(gel_rd_ulen),
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atom_int(rd_ulen),
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nil),
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build_list(
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atom_str(gel_rd_type),
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atom_str(rd_type),
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nil),
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build_list(
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atom_str(gel_rd_file),
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atom_str(rd_file),
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nil),
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nil);
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join_list (gel_details, raw_data_details, nil);
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}
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/*
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** Process tags, maintaining separate lists for
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** (a) special tags
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** (b) annotation
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** (c) edits
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*/
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{
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List *specials;
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List *notes;
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List *edits;
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int_4 next;
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specials = nil;
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notes =
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build_list(
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atom_str(gel_annotation),
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nil);
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edits =
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build_list(
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atom_str(gel_edits),
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nil);
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while (tg_line.lines.next) {
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next = tg_line.lines.next;
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dap_read_tg(&io,next,&tg_line);
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if (strncmp(tg_line.lines.type.c,"*LC*",4)==0) {
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if (tg_line.lines.comment) {
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List *lc;
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lc = build_list(
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atom_str(gel_l_cut_seq),
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atom_str(dap_read_comment(&io,tg_line.lines.comment)),
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nil);
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if (isNil(specials))
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specials = build_list(lc,nil);
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else
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specials = join_list(specials,build_list(lc,nil),nil);
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}
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} else if (strncmp(tg_line.lines.type.c,"*RC*",4)==0) {
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if (tg_line.lines.comment) {
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List *rc;
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rc = build_list(
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atom_str(gel_r_cut_seq),
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atom_str(dap_read_comment(&io,tg_line.lines.comment)),
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nil);
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if (isNil(specials))
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specials = build_list(rc,nil);
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else
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specials = join_list(specials,build_list(rc,nil),nil);
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}
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} else if (strncmp(tg_line.lines.type.c,"*",1)==0) {
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List *ed;
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char base[2];
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base[0] = tg_line.lines.type.c[3];
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base[1] = '\0';
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ed = build_list(
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build_list(
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atom_str(gel_ed_op),
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atom_str( (strncmp(tg_line.lines.type.c,"*IN",3))==0
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? gel_ed_insert : gel_ed_delete),
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nil),
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build_list(
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atom_str(gel_ed_base),
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atom_str(base),
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nil),
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build_list(
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atom_str(gel_ed_base_pos),
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atom_int( tg_line.lines.position ),
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nil),
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nil);
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edits = join_list(edits, build_list(ed,nil),nil);
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} else {
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List *an;
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char type[5];
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char *com;
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strncpy(type,tg_line.lines.type.c,4);
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type[4]='\0';
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com = dap_read_comment(&io,tg_line.lines.comment);
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an = build_list(
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build_list(
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atom_str(gel_an_pos),
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atom_int(tg_line.lines.position),
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nil),
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build_list(
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atom_str(gel_an_len),
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atom_int(tg_line.lines.length),
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nil),
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build_list(
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atom_str(gel_an_type),
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atom_str(type),
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nil),
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(com == NULL) ? nil :
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build_list(
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atom_str(gel_an_comment),
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atom_str(com),
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nil),
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nil);
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notes = join_list(notes,build_list(an,nil),nil);
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}
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}
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if (isNil(specials))
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gel_details = join_list(gel_details,build_list(edits,nil),build_list(notes,nil),nil);
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else
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gel_details = join_list(gel_details,specials,build_list(edits,nil),build_list(notes,nil),nil);
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}
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cur_gel_index++;
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free(sq_line);
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}
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return gel_details;
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}
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List *xdap_middle_read_contig_data()
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{
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List *contig_details;
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if (cur_contig_index > io.num_contigs)
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contig_details = nil;
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else {
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dap_rl_file_rec rl_line;
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int length;
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int index;
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int left_end;
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int right_end;
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index = io.max_gels-cur_contig_index;
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dap_read_rl(&io,index,&rl_line);
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length = rl_line.clines.length;
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left_end = rl_line.clines.left_end;
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right_end = rl_line.clines.right_end;
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contig_details =
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build_list(
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atom_str(contig_rec),
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build_list(
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atom_str(contig_index),
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atom_int(index),
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nil),
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build_list(
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atom_str(contig_length),
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atom_int(length),
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nil),
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build_list(
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atom_str(contig_left_end),
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atom_int(left_end),
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nil),
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build_list(
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atom_str(contig_right_end),
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atom_int(right_end),
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nil),
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nil);
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cur_contig_index++;
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}
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return contig_details;
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}
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void xdap_middle_close(List *l)
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/*
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** Close all relevant files
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*/
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{
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dap_close_files(&io);
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}
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