--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq-hts_1.0/mex/get_reads.cpp	Wed May 09 20:43:47 2012 -0400
@@ -0,0 +1,293 @@
+/*
+*  This program 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.
+*
+*   Written (W) 2010-2011 Jonas Behr, Regina Bohnert, Gunnar Raetsch
+*   Copyright (C) 2010-2011 Max Planck Society
+*/
+
+
+#include <stdio.h>
+#include <string.h>
+#include <signal.h>
+#include <mex.h>
+#include <algorithm>
+#include <vector>
+	using std::vector;
+#include "get_reads_direct.h"
+#include "mex_input.h"
+#include "read.h"
+
+#define MAXLINE 10000
+
+/*
+ * input: 
+ * 1 bam file
+ * 2 chromosome
+ * 3 region start (1-based index)
+ * 4 region end (1-based index)
+ * 5 strand (either '+' or '-' or '0')
+ * [6] collapse flag: if true the reads are collapsed to a coverage track
+ * [7] subsample percentage: percentage of reads to be subsampled (in per mill)
+ * [8] intron length filter
+ * [9] exon length filter
+ * [10] mismatch filter
+ * [11] bool: use mapped reads for coverage
+ * [12] bool: use spliced reads for coverage
+ * [13] return maxminlen
+ * [14] return pair coverage
+ *
+ * output: 
+ * 1 coverage
+ * [2] intron cell array
+ * [3] pair coverage
+ * [4] pair list
+ *
+ * example call: 
+ * [cov introns] = get_reads('polyA_left_I+_el15_mm1_spliced.bam', 'I', 10000, 12000, '-', 1, 30);
+ */
+void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]) {
+  
+  if (nrhs<5 || nrhs>14 || (nlhs<1 || nlhs>4)) {
+    fprintf(stderr, "usage: [x [introns] [pair]] = get_reads(fname, chr, start, end, strand, [collapse], [subsample], [max intron length], [min exonlength], [max mismatches], [mapped], [spliced], [maxminlen], [pair]);\n");
+    return; 
+  }
+  
+  /* obligatory arguments
+   * **********************/
+  char *fname = get_string(prhs[0]);
+	//fprintf(stdout, "arg1: %s\n", fname);
+  char *chr = get_string(prhs[1]);
+	//fprintf(stdout, "arg2: %s\n", chr);
+  int from_pos = get_int(prhs[2]);
+	//fprintf(stdout, "arg3: %d\n", from_pos);
+  int to_pos = get_int(prhs[3]);
+	//fprintf(stdout, "arg4: %d\n", to_pos);
+  char *strand = get_string(prhs[4]);
+	//fprintf(stdout, "arg5: %s\n", strand);
+
+  if (from_pos>to_pos)
+     mexErrMsgTxt("Start (arg 3) must be <= end (arg 4)\n");
+
+  if (strand[0]!='+' && strand[0]!='-' && strand[0]!='0') 
+    mexErrMsgTxt("Unknown strand (arg 5): either + or - or 0");
+
+  /* optional arguments
+   * ******************/	
+  int collapse = 0;
+  if (nrhs>=6)
+    collapse = get_int(prhs[5]);
+  
+  int subsample = 1000;	
+  if (nrhs>=7)
+    subsample = get_int(prhs[6]);
+	  
+  int intron_len_filter = 1e9;
+  if (nrhs>=8)
+    intron_len_filter = get_int(prhs[7]);
+
+  int exon_len_filter = -1;
+  if (nrhs>=9)
+    exon_len_filter = get_int(prhs[8]);
+
+  int filter_mismatch = 1e9;
+  if (nrhs>=10)
+    filter_mismatch = get_int(prhs[9]);
+
+  int mapped = 1;
+  if (nrhs>=11)
+    mapped = get_int(prhs[10]);
+
+  int spliced = 1;
+  if (nrhs>=12)
+    spliced = get_int(prhs[11]);
+
+  int maxminlen = 0;
+  if (nrhs>=13)
+    maxminlen = get_int(prhs[12]);
+
+  int pair_cov = 0;
+	if (nrhs>=14)
+		pair_cov = get_int(prhs[13]);
+
+  /* call function to get reads
+   * **************************/	
+  char region[MAXLINE];
+  sprintf(region, "%s:%i-%i", chr, from_pos, to_pos);
+
+  vector<CRead*> all_reads;
+  
+  get_reads_from_bam(fname, region, &all_reads, strand[0], subsample);
+ 
+  /* filter reads
+   * **************/	
+  int left = 0;
+  int right = 0;
+  
+  vector<CRead*> reads;
+  for (int i=0; i<all_reads.size(); i++) {
+    if (all_reads[i]->left)
+      left++;
+    if (all_reads[i]->right)
+      right++;
+    if (all_reads[i]->max_intron_len()<intron_len_filter && all_reads[i]->min_exon_len()>exon_len_filter && all_reads[i]->get_mismatches()<=filter_mismatch)
+      reads.push_back(all_reads[i]);
+  }
+
+ 
+  /* prepare output
+   * **************/	
+  int num_rows = reads.size();
+  int num_pos = to_pos-from_pos+1;
+ 
+  if (pair_cov==1 && nlhs>=3) {
+    // sort reads by read_id
+    printf("\n\nleft:%i right:%i \n\n", left, right);
+    sort(reads.begin(), reads.end(), CRead::compare_by_read_id);
+  }
+  
+  // read coverages collapsed 
+  if (collapse) {
+    plhs[0] = mxCreateNumericMatrix(1, num_pos, mxUINT32_CLASS, mxREAL);
+    uint32_t *mask_ret = (uint32_t*) mxGetData(plhs[0]);
+    if (num_pos>0 && mask_ret==NULL)
+      mexErrMsgTxt("Error allocating memory\n");
+    if (mapped && spliced) {
+      for (int i=0; i<reads.size(); i++) {
+	reads[i]->get_coverage(from_pos, to_pos, mask_ret);
+      }
+    } else {
+      for (int i=0; i<reads.size(); i++) {
+	ssize_t num_exons = reads[i]->block_starts.size();
+	if ((num_exons==1 && mapped) || (num_exons>1 && spliced))
+	  reads[i]->get_coverage(from_pos, to_pos, mask_ret);
+      }
+    }
+  }
+  // reads not collapsed
+  else {
+    uint32_t nzmax = 0; // maximal number of nonzero elements 
+    int len = to_pos-from_pos+1;
+    for (uint i=0; i<reads.size(); i++) {
+      for (uint n = 0; n < reads[i]->block_starts.size(); n++) {
+	uint32_t from, to;
+	if (reads[i]->block_starts[n]+reads[i]->start_pos-from_pos >= 0)
+	  from = reads[i]->block_starts[n]+reads[i]->start_pos-from_pos;
+	else
+	  from = 0;
+	if (reads[i]->block_starts[n]+reads[i]->start_pos-from_pos+reads[i]->block_lengths[n] >= 0)
+	  to = reads[i]->block_starts[n]+reads[i]->start_pos-from_pos+reads[i]->block_lengths[n];
+	else
+	  to = 0;
+	for (int bp=from; bp<to&bp<len; bp++) {
+	  nzmax++;
+	}
+      }
+    }
+    // 1st row: row indices
+    // 2nd row: column indices
+    plhs[0] = mxCreateDoubleMatrix(2, nzmax, mxREAL);
+    double *mask_ret = (double*) mxGetData(plhs[0]);
+    if (nzmax>0 && mask_ret==NULL)
+      mexErrMsgTxt("Error allocating memory\n");
+    uint32_t mask_ret_c = 0; // counter
+    for (uint i=0; i<reads.size(); i++) {
+      reads[i]->get_reads_sparse(from_pos, to_pos, mask_ret, mask_ret_c, i);
+    }
+    if (mask_ret_c!=2*nzmax)
+      mexErrMsgTxt("Error filling index arrays for sparse matrix\n");
+  }
+  // introns
+  if (maxminlen==0 && nlhs>=2) {
+      vector<int> intron_list;
+      for (int i=0; i<reads.size(); i++) {
+        reads[i]->get_introns(&intron_list);
+      }
+      
+      plhs[1] = mxCreateNumericMatrix(2, intron_list.size()/2, mxUINT32_CLASS, mxREAL);
+      uint32_t *p_intron_list = (uint32_t*) mxGetData(plhs[1]);
+      for (int p = 0; p<intron_list.size(); p++) {
+        p_intron_list[p] = intron_list[p];
+      }
+      intron_list.clear();	
+    } else if (nlhs>=2) {
+      vector<uint32_t> intron_starts;
+      vector<uint32_t> intron_ends;
+      vector<uint32_t> block_len1;
+      vector<uint32_t> block_len2;
+      for (int i=0; i<reads.size(); i++) {
+        reads[i]->get_introns(&intron_starts, &intron_ends, &block_len1, &block_len2);
+      }
+      
+      plhs[1] = mxCreateNumericMatrix(4, intron_starts.size(), mxINT32_CLASS, mxREAL);
+      uint32_t *p_intron_list = (uint32_t*) mxGetData(plhs[1]);
+      for (int p = 0; p<intron_starts.size(); p++) {	
+        p_intron_list[4*p] = intron_starts[p];
+        p_intron_list[(4*p)+1] = intron_ends[p];
+        p_intron_list[(4*p)+2] = block_len1[p];
+        p_intron_list[(4*p)+3] = block_len2[p];
+      }   
+      intron_starts.clear() ; 
+      intron_ends.clear() ;
+      block_len1.clear() ;
+      block_len2.clear() ;
+  }
+  if (pair_cov==1 && nlhs>=3) {
+    plhs[2] = mxCreateNumericMatrix(1, num_pos, mxUINT32_CLASS, mxREAL);
+    uint32_t *p_pair_map = (uint32_t*) mxGetData(plhs[2]);
+    if (num_pos>0 && p_pair_map==NULL)
+      mexErrMsgTxt("Error allocating memory\n");
+    
+    vector<int> pair_ids;
+    
+    int take_cnt = 0;
+    int discard_cnt = 0; 
+    // find consecutive reads with the same id
+    for (int i=0; i<((int) reads.size())-1; i++) {
+      int j = i+1;
+      while(j<reads.size() && strcmp(reads[i]->read_id, reads[j]->read_id) == 0) {
+        if ((reads[i]->left && reads[j]->right) || (reads[j]->left && reads[i]->right) && (reads[i]->reverse != reads[j]->reverse)) {
+	      if (reads[i]->get_last_position()==-1 || reads[j]->get_last_position()==-1)
+	        break;
+          if (reads[i]->get_last_position()<reads[j]->start_pos && reads[j]->start_pos-reads[i]->get_last_position()<60000) {
+            int from = std::max(0, reads[i]->get_last_position()-from_pos);
+            int to = std::min(num_pos-1, reads[j]->start_pos-from_pos);
+            pair_ids.push_back(i);
+            pair_ids.push_back(j);
+            for (int k=from; k<to; k++)
+              p_pair_map[k]++;
+            take_cnt++;
+          } else if (reads[i]->start_pos>reads[j]->get_last_position() && reads[j]->get_last_position()-reads[i]->start_pos<60000) {
+            int from = std::max(0, reads[j]->get_last_position()-from_pos);
+            int to = std::min(num_pos-1, reads[i]->start_pos-from_pos);
+            pair_ids.push_back(i);
+            pair_ids.push_back(j);
+            for (int k=from; k<to; k++)
+              p_pair_map[k]++;
+            take_cnt++;
+          } else
+            discard_cnt++;
+        }
+        else
+          discard_cnt++;
+        j++;
+      }
+    }
+    printf("take:%i, discard:%i \n", take_cnt, discard_cnt);
+    
+    if (nlhs>=4) {
+      plhs[3] = mxCreateNumericMatrix(2, pair_ids.size()/2, mxUINT32_CLASS, mxREAL);
+      uint32_t *pair_ids_ret = (uint32_t*) mxGetData(plhs[3]);
+      if (pair_ids.size()>0 && pair_ids_ret==NULL)
+        mexErrMsgTxt("Error allocating memory\n");
+      for (int i=0; i<pair_ids.size(); i++) {
+        pair_ids_ret[i] = pair_ids[i];
+      }
+    }
+  }
+  for (int i=0; i<all_reads.size(); i++)
+    delete all_reads[i];
+}
+