--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq-hts_1.0/mex/get_bam_properties.cpp	Wed May 09 20:43:47 2012 -0400
@@ -0,0 +1,216 @@
+/*
+*  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) 2009-2011 Regina Bohnert
+*   Copyright (C) 2009-2011 Max Planck Society
+*/
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <signal.h>
+#include <ctype.h>
+#include <assert.h>
+
+#include <vector>
+  using std::vector;
+#include <string>
+  using std::string;
+#include <algorithm>
+  using std::find; 
+  using std::min;
+
+#include <mex.h>
+
+
+char *get_string(const mxArray *prhs);
+
+typedef unsigned int uint32_t;
+typedef unsigned char uint8_t;
+
+/*
+ * [read_len num_reads] = get_bam_properties(fname, path_samtools, contig_name)
+ *
+ * -- input --
+ * prhs[0] file name of paired reads in BAM format (sorted by read id)
+ * prhs[1] path to samtools
+ * prhs[2] contig name
+ *
+ * -- output --
+ * plhs[0] length of read
+ * plhs[1] number of unique reads
+*/
+void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]) {
+  // checks for the right number of arguments
+  if (nrhs !=3 || nlhs > 2) {
+    mexErrMsgTxt("number of input and output args should be 3 and 2\nUSAGE:\n     [read_len, num_reads] = get_bam_properties(fname, path_samtools, contig_name)\n");
+    return;
+  }
+
+  signal(SIGCHLD, SIG_IGN); // avoid zombies
+
+  // read input arguments
+  char *fname = get_string(prhs[0]);
+  char *path_samtools = get_string(prhs[1]);
+  char *contig_name = get_string(prhs[2]);
+  char command[10000];
+  
+  sprintf(command, "%s./samtools view %s %s 2>/dev/null", path_samtools, fname, contig_name);
+  //printf("%s\n", command);
+
+  // get number of unique reads
+  int status;
+  uint32_t num_unique_reads = 0;
+  char command2[10000];
+  sprintf(command2, "%s | cut -f 1 | sort -u | wc -l", command);
+  FILE* fp = popen(command2, "r");
+  if (fp == NULL) {
+    mexErrMsgTxt("Error using popen\n");
+  }
+  int num_scans = 1;
+  num_scans = fscanf(fp, "%d", &num_unique_reads);
+  if (num_scans != 1) {
+    rewind(fp);
+    char ret[1000];
+    fgets(ret, 1000, fp);
+    fprintf(stdout, "%s", ret);
+    mexErrMsgTxt("Could not determine number of reads\n");
+  }
+  status = pclose(fp);
+  //printf("%i", num_unique_reads);
+  
+  // select reads for given positions and strand
+  int num_rows_selected = min((int) num_unique_reads, 100);
+  sprintf(command, "%s | head -n %i | cut -f 1-11", command, num_rows_selected);
+  fp = popen(command, "r");
+  if (fp == NULL) {
+    mexErrMsgTxt("Error using popen\n");
+  }
+  /* SAM format
+     1: read id, 2: flag, 3: reference name, 4: start (1-based, incl.), 5: mapping quality,
+     6: CIGAR, 7: mate reference name, 8: mate start (1-based, incl.), 9: insert size, 10: read, 11: quality
+     12+: additional tags  
+  */
+  uint32_t read_idx = 0, row_idx = 0, num_col = 0;
+  uint32_t flag = 0, start_pos = 0, map_score = 0, mate_end_pos = 0, num_matches = 0, num_del = 0, num_ins = 0, ins_size = 0;
+  char ri [1000], read_contig_name [1000], cg [1000], mate_read_id [1000], read [1000], read_qual [1000];
+  string last_read_id;
+  vector<uint32_t> block_lengths, block_starts;
+  vector<string> read_ids;
+  vector<string>::iterator it;
+  
+  uint32_t read_len = 0;
+  bool empty_line = true;
+  int num_rows = 0;
+  while(empty_line && num_rows < num_rows_selected) {
+    num_col = fscanf(fp, "%s\t%i\t%s\t%i\t%i\t%s\t%s\t%i\t%i\t%s\t%s", &ri, &flag, &read_contig_name, &start_pos, &map_score, &cg, &mate_read_id, &mate_end_pos, &ins_size, &read, &read_qual);
+    if (num_col != 11) {
+      mexErrMsgTxt("error reading SAM line\n");
+    }
+    
+    string cigar = (string) cg;
+    // ignore lines with reads w/o mapping information 
+    if (start_pos == 0 || cigar.compare("*")==0) {
+      continue;
+    }
+    // parse CIGAR
+    uint last_c = 0;
+    string last_str;
+    num_matches = 0;
+    char *end = NULL;
+    uint32_t tmp_nm = 0, tmp_nd = 0, tmp_ni = 0;
+    uint32_t last_block_start = 0, last_block_length = 0, last_intron_len = 0;
+    block_lengths.clear(); block_starts.clear();
+    
+    for (uint c = 0; c < cigar.size(); c++) {
+      switch (cigar[c]) {
+      case 'M':
+	last_str = cigar.substr(last_c, c-last_c);
+	tmp_nm = strtoul(last_str.c_str(), &end, 10);
+	if (*end != '\0')
+	  mexErrMsgTxt("error: number of mismatches\n");
+	end = NULL;
+	last_block_length += tmp_nm;
+	num_matches += tmp_nm;
+	last_c = c + 1;
+	break;
+      case 'I':
+	last_str = cigar.substr(last_c, c-last_c);
+	tmp_ni = strtoul(last_str.c_str(), &end, 10);
+	if (*end != '\0')
+	  mexErrMsgTxt("error: number of insertions\n");
+	end = NULL;
+	num_ins += tmp_ni;
+	last_c = c + 1;
+	break;
+      case 'D':
+	last_str = cigar.substr(last_c, c-last_c);
+	tmp_nd = strtoul(last_str.c_str(), &end, 10);
+	if (*end != '\0')
+	  mexErrMsgTxt("error: number of deletions\n");
+	end = NULL;
+	num_del += tmp_nd;
+	last_block_length += tmp_nd;
+	last_c = c + 1;
+	break;
+      case 'N':
+	last_str = cigar.substr(last_c, c-last_c);
+	last_intron_len = strtoul(last_str.c_str(), &end, 10);
+	end = NULL;
+	last_c = c + 1;
+	break;
+      case 'S':
+	break;
+      case 'H':
+	break;
+      case 'P':
+	break;
+      default:
+	break;
+      }
+      if (cigar[c] == 'N' || c==cigar.size()-1) {
+	block_starts.push_back(last_block_start);
+	last_block_start = last_block_start + last_block_length + last_intron_len;
+	last_intron_len = 0;
+	block_lengths.push_back(last_block_length);
+	last_block_length = 0;
+      }
+    }
+    read_len = 0;
+    for (uint n = 0; n < block_lengths.size(); n++) {
+      read_len += block_lengths[n];
+    }
+    empty_line = false;
+  } // end of stream parsing
+	
+  status = pclose(fp);
+  
+  if (empty_line) 
+    mexErrMsgTxt("Could not determine read length\n");
+  
+  plhs[0] = mxCreateDoubleScalar((double) read_len);
+  plhs[1] = mxCreateDoubleScalar((double) num_unique_reads);
+  
+  return;
+}
+
+
+char *get_string(const mxArray *prhs) {
+  char *buf;
+  int buflen;
+  if (!prhs)
+    mexErrMsgTxt("get_string called with NULL pointer arg");
+  if (!mxIsChar(prhs))
+    mexErrMsgTxt("input is not a string");
+  if (mxGetM(prhs) != 1)
+    mexErrMsgTxt("input is not a row vector");
+  buflen = mxGetN(prhs) + 1;
+  buf = (char*) malloc(buflen);
+  /* copy the string from prhs into buf and add terminating NULL char */
+  if (mxGetString(prhs, buf, buflen))
+    mexErrMsgTxt("not enough space");
+  return buf;
+}