/*
 * Lib.c
 * 
 * Copyright (c) 2011-2013 BGI-Shenzhen <soap at genomics dot org dot cn>. 
 *
 * This file is part of SOAPdenovo-Trans.
 *
 * SOAPdenovo-Trans is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * SOAPdenovo-Trans is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with SOAPdenovo-Trans.  If not, see <http://www.gnu.org/licenses/>.
 *
 */

#include "stdinc.h"
#include "newhash.h"
#include "extfunc.h"
#include "extvab.h"

static char tabs[2][1024];

int getMaxLongReadLen (int num_libs)
{
	int i;
	int maxLong = 0;
	boolean Has = 0;

	for (i = 0; i < num_libs; i++)
	{
		if (lib_array[i].asm_flag != 4)
		{
			continue;
		}

		Has = 1;
		maxLong = maxLong < lib_array[i].rd_len_cutoff ? lib_array[i].rd_len_cutoff : maxLong;
	}

	if (!Has)
	{
		return maxLong;
	}
	else
	{
		return maxLong > 0 ? maxLong : maxReadLen;
	}
}

static boolean splitColumn (char *line)
{
	int len = strlen (line);
	int i = 0, j;
	int tabs_n = 0;

	while (i < len)
	{
		if (line[i] >= 32 && line[i] <= 126 && line[i] != '=')
		{
			j = 0;

			while (i < len && line[i] >= 32 && line[i] <= 126 && line[i] != '=')
			{
				tabs[tabs_n][j++] = line[i];
				i++;
			}

			tabs[tabs_n][j] = '\0';
			tabs_n++;

			if (tabs_n == 2)
			{
				return 1;
			}
		}

		i++;
	}

	if (tabs_n == 2)
	{
		return 1;
	}
	else
	{
		return 0;
	}
}

static int cmp_lib (const void *a, const void *b)
{
	LIB_INFO *A, *B;

	A = (LIB_INFO *) a;
	B = (LIB_INFO *) b;

	if (A->avg_ins > B->avg_ins)
	{
		return 1;
	}
	else if (A->avg_ins == B->avg_ins)
	{
		return 0;
	}
	else
	{
		return -1;
	}
}

void scan_libInfo (char *libfile)
{
	FILE *fp;
	char line[1024], ch;
	int i, j, index;
	int libCounter;
	boolean flag;

	fp = ckopen (libfile, "r");
	num_libs = 0;

	while (fgets (line, 1024, fp))
	{
		ch = line[5];
		line[5] = '\0';

		if (strcmp (line, "[LIB]") == 0)
		{
			num_libs++;
		}

		if (!num_libs)
		{
			line[5] = ch;
			flag = splitColumn (line);

			if (!flag)
			{
				continue;
			}

			if (strcmp (tabs[0], "max_rd_len") == 0)
			{
				maxReadLen = atoi (tabs[1]);
			}
		}
	}

	//count file numbers of each type
	lib_array = (LIB_INFO *) ckalloc (num_libs * sizeof (LIB_INFO));

	for (i = 0; i < num_libs; i++)
	{
		lib_array[i].asm_flag = 3;
		lib_array[i].rank = 0;
		lib_array[i].pair_num_cut = 0;
		lib_array[i].rd_len_cutoff = 0;
		lib_array[i].map_len = 0;
		lib_array[i].num_s_a_file = 0;
		lib_array[i].num_s_q_file = 0;
		lib_array[i].num_p_file = 0;
		lib_array[i].num_a1_file = 0;
		lib_array[i].num_a2_file = 0;
		lib_array[i].num_q1_file = 0;
		lib_array[i].num_q2_file = 0;
		lib_array[i].num_b_file = 0;	//init
	}

	libCounter = -1;
	rewind (fp);
	i = -1;

	while (fgets (line, 1024, fp))
	{
		ch = line[5];
		line[5] = '\0';

		if (strcmp (line, "[LIB]") == 0)
		{
			i++;
			continue;
		}

		line[5] = ch;
		flag = splitColumn (line);

		if (!flag)
		{
			continue;
		}

		if (strcmp (tabs[0], "f1") == 0)
		{
			lib_array[i].num_a1_file++;
		}
		else if (strcmp (tabs[0], "q1") == 0)
		{
			lib_array[i].num_q1_file++;
		}
		else if (strcmp (tabs[0], "f2") == 0)
		{
			lib_array[i].num_a2_file++;
		}
		else if (strcmp (tabs[0], "q2") == 0)
		{
			lib_array[i].num_q2_file++;
		}
		else if (strcmp (tabs[0], "f") == 0)
		{
			lib_array[i].num_s_a_file++;
		}
		else if (strcmp (tabs[0], "q") == 0)
		{
			lib_array[i].num_s_q_file++;
		}
		else if (strcmp (tabs[0], "p") == 0)
		{
			lib_array[i].num_p_file++;
		}
		else if (strcmp (tabs[0], "b") == 0)	//start with "b", it's the bam file       
		{
			lib_array[i].num_b_file++;
		}
	}

	//allocate memory for filenames
	for (i = 0; i < num_libs; i++)
	{
		if (lib_array[i].num_s_a_file)
		{
			lib_array[i].s_a_fname = (char **) ckalloc (lib_array[i].num_s_a_file * sizeof (char *));

			for (j = 0; j < lib_array[i].num_s_a_file; j++)
			{
				lib_array[i].s_a_fname[j] = (char *) ckalloc (1024 * sizeof (char));
			}
		}

		if (lib_array[i].num_s_q_file)
		{
			lib_array[i].s_q_fname = (char **) ckalloc (lib_array[i].num_s_q_file * sizeof (char *));

			for (j = 0; j < lib_array[i].num_s_q_file; j++)
			{
				lib_array[i].s_q_fname[j] = (char *) ckalloc (1024 * sizeof (char));
			}
		}

		if (lib_array[i].num_p_file)
		{
			lib_array[i].p_fname = (char **) ckalloc (lib_array[i].num_p_file * sizeof (char *));

			for (j = 0; j < lib_array[i].num_p_file; j++)
			{
				lib_array[i].p_fname[j] = (char *) ckalloc (1024 * sizeof (char));
			}
		}

		if (lib_array[i].num_a1_file)
		{
			lib_array[i].a1_fname = (char **) ckalloc (lib_array[i].num_a1_file * sizeof (char *));

			for (j = 0; j < lib_array[i].num_a1_file; j++)
			{
				lib_array[i].a1_fname[j] = (char *) ckalloc (1024 * sizeof (char));
			}
		}

		if (lib_array[i].num_a2_file)
		{
			lib_array[i].a2_fname = (char **) ckalloc (lib_array[i].num_a2_file * sizeof (char *));

			for (j = 0; j < lib_array[i].num_a2_file; j++)
			{
				lib_array[i].a2_fname[j] = (char *) ckalloc (1024 * sizeof (char));
			}
		}

		if (lib_array[i].num_q1_file)
		{
			lib_array[i].q1_fname = (char **) ckalloc (lib_array[i].num_q1_file * sizeof (char *));

			for (j = 0; j < lib_array[i].num_q1_file; j++)
			{
				lib_array[i].q1_fname[j] = (char *) ckalloc (1024 * sizeof (char));
			}
		}

		if (lib_array[i].num_q2_file)
		{
			lib_array[i].q2_fname = (char **) ckalloc (lib_array[i].num_q2_file * sizeof (char *));

			for (j = 0; j < lib_array[i].num_q2_file; j++)
			{
				lib_array[i].q2_fname[j] = (char *) ckalloc (1024 * sizeof (char));
			}
		}
		if (lib_array[i].num_b_file)	//allot memory for bam file name                
		{
			lib_array[i].b_fname = (char **) ckalloc (lib_array[i].num_b_file * sizeof (char *));
			for (j = 0; j < lib_array[i].num_b_file; j++)
				lib_array[i].b_fname[j] = (char *) ckalloc (1024 * sizeof (char));
		}
	}

	// get file names
	for (i = 0; i < num_libs; i++)
	{
		lib_array[i].curr_type = 1;
		lib_array[i].curr_index = 0;
		lib_array[i].fp1 = NULL;
		lib_array[i].fp2 = NULL;
		lib_array[i].num_s_a_file = 0;
		lib_array[i].num_s_q_file = 0;
		lib_array[i].num_p_file = 0;
		lib_array[i].num_a1_file = 0;
		lib_array[i].num_a2_file = 0;
		lib_array[i].num_q1_file = 0;
		lib_array[i].num_q2_file = 0;
		lib_array[i].num_b_file = 0;	//init          
		lib_array[i].fp3 = NULL;
	}

	libCounter = -1;
	rewind (fp);
	i = -1;

	while (fgets (line, 1024, fp))
	{
		ch = line[5];
		line[5] = '\0';

		if (strcmp (line, "[LIB]") == 0)
		{
			i++;
			continue;
		}

		line[5] = ch;
		flag = splitColumn (line);

		if (!flag)
		{
			continue;
		}

		if (strcmp (tabs[0], "f1") == 0)
		{
			index = lib_array[i].num_a1_file++;
			strcpy (lib_array[i].a1_fname[index], tabs[1]);
		}
		else if (strcmp (tabs[0], "q1") == 0)
		{
			index = lib_array[i].num_q1_file++;
			strcpy (lib_array[i].q1_fname[index], tabs[1]);
		}
		else if (strcmp (tabs[0], "f2") == 0)
		{
			index = lib_array[i].num_a2_file++;
			strcpy (lib_array[i].a2_fname[index], tabs[1]);
		}
		else if (strcmp (tabs[0], "q2") == 0)
		{
			index = lib_array[i].num_q2_file++;
			strcpy (lib_array[i].q2_fname[index], tabs[1]);
		}
		else if (strcmp (tabs[0], "f") == 0)
		{
			index = lib_array[i].num_s_a_file++;
			strcpy (lib_array[i].s_a_fname[index], tabs[1]);
		}
		else if (strcmp (tabs[0], "q") == 0)
		{
			index = lib_array[i].num_s_q_file++;
			strcpy (lib_array[i].s_q_fname[index], tabs[1]);
		}
		else if (strcmp (tabs[0], "p") == 0)
		{
			index = lib_array[i].num_p_file++;
			strcpy (lib_array[i].p_fname[index], tabs[1]);
		}
		else if (strcmp (tabs[0], "b") == 0)
		{		//bam file                     
			index = lib_array[i].num_b_file++;
			strcpy (lib_array[i].b_fname[index], tabs[1]);
		}
		else if (strcmp (tabs[0], "min_ins") == 0)
		{
			lib_array[i].min_ins = atoi (tabs[1]);
		}
		else if (strcmp (tabs[0], "max_ins") == 0)
		{
			lib_array[i].max_ins = atoi (tabs[1]);
		}
		else if (strcmp (tabs[0], "avg_ins") == 0)
		{
			lib_array[i].avg_ins = atoi (tabs[1]);
		}
		else if (strcmp (tabs[0], "rd_len_cutoff") == 0)
		{
			lib_array[i].rd_len_cutoff = atoi (tabs[1]);
		}
		else if (strcmp (tabs[0], "reverse_seq") == 0)
		{
			lib_array[i].reverse = atoi (tabs[1]);
		}
		else if (strcmp (tabs[0], "asm_flags") == 0)
		{
			lib_array[i].asm_flag = atoi (tabs[1]);
		}
		else if (strcmp (tabs[0], "rank") == 0)
		{
			lib_array[i].rank = atoi (tabs[1]);
		}
		else if (strcmp (tabs[0], "pair_num_cutoff") == 0)
		{
			lib_array[i].pair_num_cut = atoi (tabs[1]);
		}
		else if (strcmp (tabs[0], "rd_len_cutoff") == 0)
		{
			lib_array[i].rd_len_cutoff = atoi (tabs[1]);
		}
		else if (strcmp (tabs[0], "map_len") == 0)
		{
			lib_array[i].map_len = atoi (tabs[1]);
		}
	}

	fclose (fp);
	qsort (&lib_array[0], num_libs, sizeof (LIB_INFO), cmp_lib);
}

void free_libs ()
{
	if (!lib_array)
	{
		return;
	}

	int i, j;

	for (i = 0; i < num_libs; i++)
	{
		printf ("[LIB] %d, avg_ins %d, reverse %d \n", i, lib_array[i].avg_ins, lib_array[i].reverse);

		if (lib_array[i].num_s_a_file)
		{
			//printf("%d single fasta files\n",lib_array[i].num_s_a_file);
			for (j = 0; j < lib_array[i].num_s_a_file; j++)
			{
				free ((void *) lib_array[i].s_a_fname[j]);
			}

			free ((void *) lib_array[i].s_a_fname);
		}

		if (lib_array[i].num_s_q_file)
		{
			//printf("%d single fastq files\n",lib_array[i].num_s_q_file);
			for (j = 0; j < lib_array[i].num_s_q_file; j++)
			{
				free ((void *) lib_array[i].s_q_fname[j]);
			}

			free ((void *) lib_array[i].s_q_fname);
		}

		if (lib_array[i].num_p_file)
		{
			//printf("%d paired fasta files\n",lib_array[i].num_p_file);
			for (j = 0; j < lib_array[i].num_p_file; j++)
			{
				free ((void *) lib_array[i].p_fname[j]);
			}

			free ((void *) lib_array[i].p_fname);
		}

		if (lib_array[i].num_a1_file)
		{
			//printf("%d read1 fasta files\n",lib_array[i].num_a1_file);
			for (j = 0; j < lib_array[i].num_a1_file; j++)
			{
				free ((void *) lib_array[i].a1_fname[j]);
			}

			free ((void *) lib_array[i].a1_fname);
		}

		if (lib_array[i].num_a2_file)
		{
			//printf("%d read2 fasta files\n",lib_array[i].num_a2_file);
			for (j = 0; j < lib_array[i].num_a2_file; j++)
			{
				free ((void *) lib_array[i].a2_fname[j]);
			}

			free ((void *) lib_array[i].a2_fname);
		}

		if (lib_array[i].num_q1_file)
		{
			//printf("%d read1 fastq files\n",lib_array[i].num_q1_file);
			for (j = 0; j < lib_array[i].num_q1_file; j++)
			{
				free ((void *) lib_array[i].q1_fname[j]);
			}

			free ((void *) lib_array[i].q1_fname);
		}

		if (lib_array[i].num_q2_file)
		{
			//printf("%d read2 fastq files\n",lib_array[i].num_q2_file);
			for (j = 0; j < lib_array[i].num_q2_file; j++)
			{
				free ((void *) lib_array[i].q2_fname[j]);
			}

			free ((void *) lib_array[i].q2_fname);
		}
		if (lib_array[i].num_b_file)
		{		//free the bam file name                    
			//printf("%d bam files\n",lib_array[i].num_b_file);                     
			for (j = 0; j < lib_array[i].num_b_file; j++)
				free ((void *) lib_array[i].b_fname[j]);
			free ((void *) lib_array[i].b_fname);
		}
	}

	num_libs = 0;
	free ((void *) lib_array);
}

void alloc_pe_mem (int gradsCounter)
{
	if (gradsCounter)
	{
		pes = (PE_INFO *) ckalloc (gradsCounter * sizeof (PE_INFO));
	}
}

void free_pe_mem ()
{
	if (pes)
	{
		free ((void *) pes);
		pes = NULL;
	}
}