Import the freshly re-implemented 'meryl' (and 'sequence').

src/main.mk

@@ -34,6 +34,16 @@ SOURCES      := AS_global.C \
                 utility/strings.C \
                 utility/system.C \
                 \
+                utility/sequence.C \
+                \
+                utility/kmers.C \
+                utility/kmers-reader.C \
+                utility/kmers-writer.C \
+                utility/kmers-statistics.C \
+                utility/kmers-exact.C \
+                \
+                utility/bits.C \
+                \
                 utility/AS_UTL_reverseComplement.C \
                 utility/AS_UTL_stackTrace.C \
                 \
@@ -108,9 +118,7 @@ SOURCES      := AS_global.C \
                 utgcns/libpbutgcns/AlnGraphBoost.C  \
                 \
                 gfa/gfa.C \
-                gfa/bed.C \
-                \
-
+                gfa/bed.C
 
 
 ifeq (${BUILDSTACKTRACE}, 1)
@@ -177,6 +185,9 @@ SUBMAKEFILES := stores/dumpBlob.mk \
                 meryl-san/positionDB.mk \
                 meryl-san/simple-dump.mk \
                 \
+                meryl/meryl.mk \
+                \
+                sequence/sequence.mk \
                 \
                 overlapInCore/overlapInCore.mk \
                 overlapInCore/overlapInCorePartition.mk \

src/meryl/lookup.C

@@ -0,0 +1,52 @@
+
+/******************************************************************************
+ *
+ *  This file is part of 'sequence' and/or 'meryl', software programs for
+ *  working with DNA sequence files and k-mers contained in them.
+ *
+ *  Modifications by:
+ *
+ *    Brian P. Walenz beginning on 2018-FEB-26
+ *      are a 'United States Government Work', and
+ *      are released in the public domain
+ *
+ *  File 'README.license' in the root directory of this distribution contains
+ *  full conditions and disclaimers.
+ */
+
+#include "kmers.H"
+#include "bits.H"
+
+int
+main(int argc, char **argv) {
+
+  kmerCountFileReader   *rr = new kmerCountFileReader(argv[1], false, true);
+  kmerCountExactLookup  *ll = new kmerCountExactLookup(rr);
+
+  delete rr;
+
+  rr = new kmerCountFileReader(argv[2], false, true);
+
+  uint64  tested = 0;
+  uint64  found  = 0;
+
+  while (rr->nextMer()) {
+    kmer    k = rr->theFMer();
+    uint32  c = rr->theCount();
+
+    tested++;
+
+    if (ll->exists(k))
+      found++;
+
+    if ((tested % 100000) == 0)
+      fprintf(stderr, "Tested %lu kmers, found %lu.\n", tested, found);
+  }
+
+  delete ll;
+  delete rr;
+
+  fprintf(stderr, "Tested %lu kmers, found %lu.\n", tested, found);
+
+  exit(0);
+}

src/meryl/lookup.mk

@@ -0,0 +1,20 @@
+
+#  If 'make' isn't run from the root directory, we need to set these to
+#  point to the upper level build directory.
+ifeq "$(strip ${BUILD_DIR})" ""
+  BUILD_DIR    := ../$(OSTYPE)-$(MACHINETYPE)/obj
+endif
+ifeq "$(strip ${TARGET_DIR})" ""
+  TARGET_DIR   := ../$(OSTYPE)-$(MACHINETYPE)
+endif
+
+TARGET   := lookup
+SOURCES  := lookup.C \
+
+SRC_INCDIRS  := . utility
+
+TGT_LDFLAGS := -L${TARGET_DIR}/lib
+TGT_LDLIBS  := -lsequence -lbits -lkmer -lmeryl
+TGT_PREREQS := libmeryl.a
+
+SUBMAKEFILES :=