Have the basic bam prep and seed collection parts of the tools comple…

…te. Just need to implement the actual algorithm now! Also may want to add some unit tests for the seed collector just to make sure there are no problems.

configure.ac

@@ -78,26 +78,10 @@ AC_CHECK_HEADERS([getopt.h])
 AC_CHECK_LIB(pthread, pthread_exit)
 AC_CHECK_LIB(z, gzread)
 
-## Check for boost
-BOOST_REQUIRE([1.52])
 
-# Header only
-BOOST_STRING_ALGO
-BOOST_FOREACH
-BOOST_UNORDERED
 
-# Header + lib
-BOOST_FILESYSTEM
-BOOST_PROGRAM_OPTIONS
-BOOST_SYSTEM
-BOOST_THREADS
-BOOST_TEST
-
-# Combine BOOST variables (apart for BOOST_TEST)
-BOOST_LDFLAGS="${BOOST_FILESYSTEM_LDFLAGS} ${BOOST_PROGRAM_OPTIONS_LDFLAGS} ${BOOST_SYSTEM_LDFLAGS} ${BOOST_THREAD_LDFLAGS}"
-BOOST_LIBS="${BOOST_FILESYSTEM_LIBS} ${BOOST_PROGRAM_OPTIONS_LIBS} ${BOOST_SYSTEM_LIBS} ${BOOST_THREAD_LIBS}"
-
-# Allow users to specify custom directories for seqan library and doxygen.  This might save some users from having to set the environment variables manually.
+# Allow users to specify custom directories for samtools and bamtools.  
+# This might save some users from having to set the environment variables manually.
 
 AC_ARG_WITH([samtools],
         [AS_HELP_STRING([--with-samtools=PREFIX],
@@ -133,15 +117,40 @@ LDFLAGS="${BAMTOOLS_LDFLAGS} ${SAMTOOLS_LDFLAGS} ${AM_LDFLAGS} ${LDFLAGS}"
 
 #### Put any header or lib checks here ####
 
+AC_CHECK_HEADER([api/BamMultiReader.h], [], [
+    AC_MSG_ERROR([Bamtools not found. Please ensure that the bamtools include directory can be found on the CPPFLAGS env var. Also check that the Bamtools lib directory can be found on the LDFLAGS env var.])
+])
 
-AC_CHECK_LIB([bam], [fai_build], [], [echo "Samtools not found" exit -1], [])
-AC_CHECK_HEADER([api/BamMultiReader.h], [], [echo "Bamtools not found" exit -1], [])
+AC_CHECK_LIB(bam, fai_build, [], [
+    AC_MSG_ERROR([Samtools not found. Please ensure that the Samtools include directory can be found on the CPPFLAGS env var. Also check that the Samtools lib directory can be found on the LDFLAGS env var.])
+])
 
 # Restore the previous CPPFLAGS
 CPPFLAGS=${OLD_CPPFLAGS}
 LDFLAGS=${OLD_LDFLAGS}
 
 
+## Check for boost
+BOOST_REQUIRE([1.52])
+
+# Header only
+BOOST_STRING_ALGO
+BOOST_FOREACH
+BOOST_UNORDERED
+
+# Header + lib
+BOOST_FILESYSTEM
+BOOST_PROGRAM_OPTIONS
+BOOST_SYSTEM
+BOOST_THREADS
+BOOST_TEST
+
+# Combine BOOST variables (apart for BOOST_TEST)
+BOOST_LDFLAGS="${BOOST_FILESYSTEM_LDFLAGS} ${BOOST_PROGRAM_OPTIONS_LDFLAGS} ${BOOST_SYSTEM_LDFLAGS} ${BOOST_THREAD_LDFLAGS}"
+BOOST_LIBS="${BOOST_FILESYSTEM_LIBS} ${BOOST_PROGRAM_OPTIONS_LIBS} ${BOOST_SYSTEM_LIBS} ${BOOST_THREAD_LIBS}"
+
+
+
 #########
 
 AC_SUBST([AM_CPPFLAGS])

include/seed_collector.hpp

@@ -22,7 +22,7 @@
 #include <boost/foreach.hpp>
 
 #include <api/BamReader.h>
-#include <api/BamMultiReader.h>
+#include <api/BamWriter.h>
 
 using std::vector;
 
@@ -33,46 +33,77 @@ namespace portculis {
 class SeedCollector {
 private:
 
-    vector<string> bamFiles;    
-    bool collectiveMode;
-
-    vector<BamReader> singleReaders;
-    BamMultiReader multiReader;
+    string sortedBam;    
+    string seedFile;
+    bool verbose;
 
+    BamReader reader;
+    BamWriter writer;
+
     SamHeader header;
     RefVector refs;
 
 protected:
 
+    bool isPotentialSeed(BamAlignment& al) {
+        BOOST_FOREACH(CigarOp op, al.CigarData) {
+            if (op.Type == 'N') {
+                return true;
+            }
+        }
+
+        return false;        
+    }
 
 public:
 
-    SeedCollector(vector<string> _bamFiles, bool _collectiveMode) : 
-            bamFiles(_bamFiles), collectiveMode(_collectiveMode) {
+    SeedCollector(string _sortedBam, string _seedFile, bool _verbose) : 
+            sortedBam(_sortedBam), seedFile(_seedFile), verbose(_verbose) {
 
-        if (collectiveMode) {
-            if (!multiReader.Open(bamFiles)) {
-                throw "Could not open bam files";
-            }
-
-            header = reader.GetHeader();
-            refs = reader.GetReferenceData();
+        if (!reader.Open(sortedBam)) {
+            throw "Could not open bam reader";
         }
-        else {
-            BOOST_FOREACH(string bamFile, bamFiles) {
-                BamReader reader;                
-                if (!reader.Open(bamFile)) {
-                    throw "Could not open bam files";
-                }
-                singleReaders.push_back(reader);
-            }
-        }                
 
+        if (!writer.Open(seedFile, header, refs)) {
+            throw "Could not open bam writer";
+        }
+
+        header = reader.GetHeader();
+        refs = reader.GetReferenceData();
+
+        if (verbose) {
+
+            cout << endl << "Collecting seeds from: " << sortedBam << endl;
+            cout << "Header:" << endl << header.ToString() << endl;
+            cout << "Refs:" << endl;
+
+            BOOST_FOREACH(RefData ref, refs) {
+               cout << ref.RefLength << " - " << ref.RefName << endl;
+            }
+        }
+    }
+
+    virtual ~SeedCollector() {
+        reader.Close();
+        writer.Close();
     }
 
-    void sort() {
+    uint64_t collect() {
 
+        BamAlignment al;
+        uint64_t count = 0;
+        while(reader.GetNextAlignment(al))
+        {
+            if (isPotentialSeed(al)) {
+                writer.SaveAlignment(al);
+                count++;
+            }
+        }
+
+        return count;
     }
+
+
 };
 }
 

src/Makefile.am

@@ -9,7 +9,9 @@ portculis_CPPFLAGS = -DCPLUSPLUS @BAMTOOLS_CPPFLAGS@ @SAMTOOLS_CPPFLAGS@ @BOOST_
 portculis_LDFLAGS = @BAMTOOLS_LDFLAGS@ @SAMTOOLS_LDFLAGS@ @BOOST_LDFLAGS@ @AM_LDFLAGS@
 portculis_LDADD = -lbam -lbamtools @BOOST_LIBS@ -lpthread -lz
 portculis_SOURCES = \
+	genome_mapper.hpp \
+	seed_collector.hpp \
 	bamtools_sort.h \
-	bamtools_sort.cpp \    
+	bamtools_sort.cpp \
 	portculis.cc