Merge pull request #23 from mourisl/centrifuger_quant

Update to centrifuger-quant

CentrifugerInspect.cpp

@@ -28,7 +28,7 @@ static struct option long_options[] = {
   {"conversion-table", no_argument, 0, ARGV_CONVERSION_TABLE},
   {"taxonomy-tree", no_argument, 0, ARGV_TAXONOMY_TREE},
   {"name-table", no_argument, 0, ARGV_NAME_TABLE},
-  {"size-table", no_argument, 0, ARGV_INSPECT_SIZE_TABLE},
+  {"size-table", no_argument, 0, ARGV_SIZE_TABLE},
   {"index-size", no_argument, 0, ARGV_INSPECT_INDEXSIZE},
   { (char *)0, 0, 0, 0} 
 } ;
@@ -108,7 +108,7 @@ int main(int argc, char *argv[])
   {
     taxonomy.PrintNameTable(stdout) ;
   }
-  else if (inspectItem == ARGV_INSPECT_SIZE_TABLE)
+  else if (inspectItem == ARGV_SIZE_TABLE)
   {
     size_t i ;
     size_t n = taxonomy.GetNodeCount() ;

CentrifugerQuant.cpp

@@ -8,17 +8,25 @@
 
 char usage[] = "./centrifuger-quant [OPTIONS]:\n"
 	"Required:\n"
-  "\t-x FILE: index prefix\n"
   "\t-c FILE: classification result file\n"
-  //"When not giving "-x"\n"
-  //"\t--taxonomy-tree FILE: taxonomy tree, i.e., nodes.dmp file\n"
-  //"\t--name-table FILE: name table, i.e., names.dmp file\n"
-  //"\t--size-table FILE: size table, table of contig (or genome) sizes\n"
-  //"\t--conversion-table FILE: a table that converts any id to a taxonomy id\n"
+  "\t-x FILE: index prefix\n"
+  "\tWhen not giving -x\n"
+  "\t\t--taxonomy-tree FILE: taxonomy tree, i.e., nodes.dmp file\n"
+  "\t\t--name-table FILE: name table, i.e., names.dmp file\n"
+  "\t\t--size-table FILE: size table (optional), table of contig (or genome) sizes.\n"
+  "Optional:\n"
+  "\t--min-score INT: only consider reads with score at least <int> \n"
+  "\t--min-length INT: only consider reads with classified length at least <int>\n"
+  ""
 	;
 
 static const char *short_options = "x:c:" ;
 static struct option long_options[] = {
+  { "taxonomy-tree", required_argument, 0, ARGV_TAXONOMY_TREE},
+  { "name-table", required_argument, 0, ARGV_NAME_TABLE},
+  { "size-table", required_argument, 0, ARGV_SIZE_TABLE},
+  { "min-score", required_argument, 0, ARGV_QUANT_MINSCORE},
+  { "min-length", required_argument, 0, ARGV_QUANT_MINLENGTH},
   { (char *)0, 0, 0, 0} 
 } ;
 
@@ -35,7 +43,13 @@ int main(int argc, char *argv[])
 
   char *idxPrefix = NULL ; 
   char *classificationFile = NULL ;
-
+	size_t classificationMinScore = 0 ;
+  int classificationMinLength = 0 ;
+
+  char *taxonomyFile = NULL ; // taxonomy tree file
+  char *nameTable = NULL ;
+  char *sizeTable = NULL ;
+
   while (1)
   {
     c = getopt_long( argc, argv, short_options, long_options, &option_index ) ;
@@ -51,6 +65,26 @@ int main(int argc, char *argv[])
     {
       classificationFile = strdup(optarg) ;
     }
+    else if (c == ARGV_QUANT_MINSCORE)
+    {
+      classificationMinScore = atoi(optarg) ;
+    }
+    else if (c == ARGV_QUANT_MINLENGTH)
+    {
+      classificationMinLength = atoi(optarg) ;
+    }
+    else if (c == ARGV_TAXONOMY_TREE)
+    {
+      taxonomyFile = strdup(optarg) ;  
+    }
+    else if (c == ARGV_NAME_TABLE)
+    {
+      nameTable = strdup(optarg) ;
+    }
+    else if (c == ARGV_SIZE_TABLE)
+    {
+      sizeTable = strdup(optarg) ;
+    }
     else
     {
       fprintf(stderr, "Unknown parameter found.\n%s", usage) ;
@@ -59,23 +93,36 @@ int main(int argc, char *argv[])
   }
 
 	Utils::PrintLog("Centrifuger-quant v" CENTRIFUGER_VERSION " starts." ) ;
-  if (idxPrefix == NULL)
+  if (idxPrefix == NULL && 
+      (taxonomyFile == NULL || nameTable == NULL))
   {
-    Utils::PrintLog("Need to use -x to specify index prefix.") ;
+    Utils::PrintLog("Need to use -x to specify index prefix, or --taxonomy-tree/--name-table/(--size-table) to specify the taxonomy structure.") ;
     return EXIT_FAILURE ;
   }
 
   Quantifier quantifier ;
-  quantifier.Init(idxPrefix) ;
-  quantifier.LoadReadAssignments(classificationFile, 0) ;
+  if (idxPrefix)
+    quantifier.Init(idxPrefix) ;
+  else
+    quantifier.Init(taxonomyFile, nameTable, sizeTable) ;
+  quantifier.LoadReadAssignments(classificationFile, classificationMinScore, classificationMinLength, 0) ;
+  Utils::PrintLog("Finish loading the read classification result.") ;
 
   quantifier.Quantification() ;
 
   quantifier.Output(stdout, 0) ;
 
-  free(idxPrefix) ;
   free(classificationFile) ;
-
+
+  if (idxPrefix != NULL)
+    free(idxPrefix) ;
+  else
+  {
+    free(taxonomyFile) ;
+    free(nameTable) ;
+    free(sizeTable) ;
+  }
+
 	Utils::PrintLog("Centrifuger-quant finishes." ) ;
   return 0 ;
 }