Adds support for handling FastQ files (hpg-fastq binary) and updates submodule hpg-libs. Resolves #7

Author: Joaquín Tárraga Giménez

SConstruct

@@ -86,7 +86,7 @@ aligner = envprogram.Program('#bin/hpg-aligner',
                       ]
            )
 
-bams = envprogram.Program('#bin/hpg-bam',
+bam  = envprogram.Program('#bin/hpg-bam',
              source = [Glob('src/tools/bam/*.c'), 
 	     	       Glob('src/tools/bam/aux/*.c'),
 	     	       Glob('src/tools/bam/bfwork/*.c'),
@@ -100,7 +100,13 @@ bams = envprogram.Program('#bin/hpg-bam',
                       ]
            )
 
-Depends(aligner, bams)
+fastq = envprogram.Program('#bin/hpg-fastq',
+             source = [Glob('src/tools/fastq/*.c'), 
+                       "%s/build/libhpg.a" % hpglib_path
+                      ]
+           )
+
+#Depends(aligner, bam, fastq)
 
 '''
 if 'debian' in COMMAND_LINE_TARGETS:

lib/hpg-libs

@@ -0,0 +1,106 @@
+/*
+ * commons_fastq.c
+ *
+ *  Created on: May 22, 2013
+ *      Author: jtarraga
+ *              
+ */
+
+#include "commons_fastq.h"
+
+//--------------------------------------------------------------------
+
+void free_argtable(int num_options, void **argtable) {
+  if (argtable != NULL) {
+    arg_freetable(argtable, num_options);
+    free(argtable);
+  }
+}
+
+//--------------------------------------------------------------------
+
+void usage_argtable(char *exec_name, char *command_name, void **argtable) {
+  printf("Usage: %s %s\n", exec_name, command_name);
+  arg_print_syntaxv(stdout, argtable, "\n");
+  arg_print_glossary(stdout, argtable, "%-50s\t%s\n");
+  exit(-1);
+}
+
+//--------------------------------------------------------------------
+
+int parse_range(int *min, int *max, char *range, char *msg) {
+
+  *min = NO_VALUE;
+  *max = NO_VALUE;
+
+  if (!range) {
+    return 1;
+  }
+
+  int lmin, lmax;
+  char *p, *lrange = strdup(range);
+
+  p = strstr(lrange, ",");
+  if (p) {
+    //lmax = atoi(p + 1);
+    if (strlen(p+1) == 0) {
+      lmax = NO_VALUE;
+    } else {
+      if (sscanf((p+1), "%d", &lmax) != 1) {
+	printf("\nError: Invalid maximum value in the %s (%s)\n", msg, range);
+	free(lrange);
+	return 0;
+      }
+    }
+    if (lrange == p) {
+      lmin = NO_VALUE;
+    } else {
+      *p = '\0';
+      //lmin = atoi(lrange);
+      if (sscanf(lrange, "%d", &lmin) != 1) {
+	printf("\nError: Invalid minimum value in the %s (%s)\n", msg, range);
+	free(lrange);
+	return 0;
+      }
+    }
+  } else {
+    //lmin = atoi(lrange);
+    if (sscanf(lrange, "%d", &lmin) != 1) {
+      printf("\nError: Invalid minimum value in the %s (%s)\n", msg, range);
+      free(lrange);
+      return 0;
+    }
+    lmax = NO_VALUE;
+  }
+  
+  if (lmin != NO_VALUE && lmin < 0) {
+    printf("\nError: Invalid %s (%s). Minimum value (%i) must be greater than 0\n",
+	   msg, range, lmin);
+    free(lrange);
+    return 0;
+  }
+
+  if (lmax != NO_VALUE && lmax < 0) {
+    printf("\nError: Invalid %s (%s). Maximum value (%i) must be greater than 0\n",
+	   msg, range, lmax);
+    free(lrange);
+    return 0;
+  }
+
+  if (lmin != NO_VALUE && lmax != NO_VALUE && lmin > lmax) {
+    printf("\nError: Invalid %s (%s). Maximum value (%i) must be greater than minimum value (%i)\n",
+	   msg, range, lmax, lmin);
+    free(lrange);
+    return 0;
+  }
+
+  *min = lmin;
+  *max = lmax;
+
+  // free local range
+  free(lrange);
+  return 1;
+}
+
+//--------------------------------------------------------------------
+//--------------------------------------------------------------------

src/tools/fastq/commons_fastq.c

@@ -0,0 +1,35 @@
+#ifndef COMMONS_FASTQ_H
+#define COMMONS_FASTQ_H
+
+/*
+ * fastq_commons.h
+ *
+ *  Created on: May 22, 2013
+ *      Author: jtarraga
+ *              
+ */
+
+#include <stdlib.h>
+#include <string.h>
+
+#include "argtable/argtable2.h"
+
+#include "bioformats/fastq/fastq_filter.h"
+
+//------------------------------------------------------------------------
+
+#define NO_VALUE       -1
+#define MIN_VALUE       0
+#define MAX_VALUE  100000
+
+//------------------------------------------------------------------------
+
+int parse_range(int *min, int *max, char *range, char *msg);
+
+void free_argtable(int num_filter_options, void **argtable);
+void usage_argtable(char *exec_name, char *command_name, void **argtable);
+
+#endif	/*  COMMONS_FASTQ_H  */
+
+//------------------------------------------------------------------------
+//------------------------------------------------------------------------