updated

Author: kjenike1

cpp/Makefile

@@ -7,8 +7,6 @@ INCLUDE=./htslib
 SRC=.
 BUILD=build
 
-#ANCHOR_BIN=anchor
-#SW_BIN = $(BIN)/sw
 
 KMC_API_DIR = ../KMC/kmc_api
 KMC_DUMP_DIR = ../KMC/kmc_dump
@@ -28,9 +26,9 @@ OBJS = $(patsubst %, $(BUILD)/%, $(_OBJS))
 
 DEPENDS := $(patsubst %.o, %.d, $(OBJS))
 
-all: dirs anchor
+all: dirs run_anchor
 
-anchor: build/anchor.o
+run_anchor: build/anchor.o
 	$(CC) $(KMC_API_OBJS) $(CFLAGS) $< -o $@ -lz $(HTS_LIB) $(LIBS)
 
 -include $(DEPENDS)

cpp/anchor.cpp

@@ -80,6 +80,7 @@ struct KMCdb {
 
                         size_t s = name.find(' ');
                         chrs_out << name.substr(0,s) << "\t" << chr_num << "\t" << ksize << "\t0\n";
+		        chrs_out.flush();
                         chr_num += 1;
                     }
                     name = line.substr(1);
@@ -92,6 +93,7 @@ struct KMCdb {
             auto ksize = write_bits(chr_num, seq, bitmap1, bitmap100, bitsum_out);
             size_t s = name.find(' ');
             chrs_out << name.substr(0,s) << "\t" << chr_num << "\t" << ksize << "\t0\n";
+	    chrs_out.flush();
         }
 
         bgzf_index_dump(bitmap1, basename.c_str(), ".gzi");
@@ -169,6 +171,7 @@ struct KMCdb {
                 bitsum_out << "\t" << c;
             }
             bitsum_out << "\n";
+	    bitsum_out.flush();
         }
         return popcnts.size();