Revert "Change ovStore data names to be POSIX compliant. Import canu-…

…specific object store methods from meryl-utility. Issue #1732."

This reverts commit 3f55aa6.

src/Makefile

@@ -384,8 +384,31 @@ ifeq (${OSTYPE}, SunOS)
   endif
 endif
 
-
+#  Some filesystems cannot use < or > in file names, but for reasons unknown
+#  (or, at least, reasons we're not going to admit to), files in the overlap
+#  store are named ####<###>.  Enabling POSIX_FILE_NAMES Will change the
+#  names to ####.###.
+#
+#  Be aware this will break object store compatibility.
 #
+ifeq ($(POSIX_FILE_NAMES), 1)
+  CXXFLAGS += -DPOSIX_FILE_NAMES
+
+else
+  #  Try to create non-<posix> file names.  It's tempting to use 'wildcard' instead
+  #  of the 'ls', but it doesn't work.
+  $(shell touch "non-<posix>-name" > /dev/null 2>&1)
+
+  ifeq (non-<posix>-name, $(shell ls "non-<posix>-name" 2> /dev/null))
+    #$(info Extended POSIX filenames allowed.)
+  else
+    #$(info POSIX filenames required.)
+    CXXFLAGS += -DPOSIX_FILE_NAMES
+  endif
+
+  $(shell rm -f "non-<posix>-name")
+endif
+
 #  Set compiler and flags based on discovered hardware
 #
 #  By default, debug symbols are included in all builds (even optimized).

src/main.mk

@@ -58,6 +58,7 @@ SOURCES      := utility/src/utility/runtime.C \
                 utility/src/utility/hexDump.C \
                 utility/src/utility/md5.C \
                 utility/src/utility/mt19937ar.C \
+                utility/src/utility/objectStore.C \
                 utility/src/utility/speedCounter.C \
                 utility/src/utility/sweatShop.C \
                 \
@@ -90,8 +91,6 @@ SOURCES      := utility/src/utility/runtime.C \
                 stores/libsnappy/snappy-stubs-internal.cc \
                 stores/libsnappy/snappy.cc \
                 \
-                stores/objectStore.C \
-                \
                 overlapInCore/overlapReadCache.C \
                 \
                 overlapInCore/liboverlap/Binomial_Bound.C \

src/pipelines/canu/OverlapStore.pm

@@ -724,63 +724,6 @@ sub deleteOverlapIntermediateFiles ($$@) {
 
 
 
-#
-#  Scan the overlap store for old-format file names.  If any are found,
-#  create new-format names as symlinks to the original files.
-#
-sub updateOverlapStoreFiles ($$$) {
-    my $asm     = shift @_;
-    my $tag     = shift @_;
-    my $base    = shift @_;
-
-    my %oldToNew;
-    my @newExists;
-
-    #  Scan the store for any old-format files.
-    #  Remember if new-format links exist too.
-    open(L, "ls $base/$asm.ovlStore/ | ");
-    while (<L>) {
-        chomp;
-
-        if (m/^(\d\d\d\d)<(\d\d\d)>$/) {
-            my $old = "$1<$2>";
-            my $new = "$1-$2";
-
-            $oldToNew{$old} = $new;
-        }
-
-        if (m/^(\d\d\d\d)-(\d\d\d)$/) {
-            my $old = "$1<$2>";
-            my $new = "$1-$2";
-
-            push @newExists, $old;
-        }
-    }
-    close(L);
-
-    #  Forget about old-format names with new-format links already present.
-    foreach my $nn (@newExists) {
-        delete $oldToNew{$nn};
-    }
-
-    #  If there are any old-format names left, make links for them, logging
-    #  whatever we do.
-    if (scalar(%oldToNew) > 0) {
-        print STDERR "--\n";
-        print STDERR "-- UPDATING $base/$asm.ovlStore data files to new name format:\n";
-
-        foreach my $oo (keys %oldToNew) {
-            print STDERR "--   '$oo' -> '$oldToNew{$oo}'\n";
-            system("ln -s '$oo' '$base/$asm.ovlStore/$oldToNew{$oo}'");
-        }
-
-        print STDERR "--\n";
-    }
-}
-
-
-
-
 sub createOverlapStore ($$) {
     my $asm     = shift @_;
     my $tag     = shift @_;
@@ -793,13 +736,6 @@ sub createOverlapStore ($$) {
     $base = "trimming"    if ($tag eq "obt");
     $base = "unitigging"  if ($tag eq "utg");
 
-    #  A compatibility fix for renaming ovlStore data files from 0000<000> to 0000-000.
-    #  This change occurred around July 7 2020.
-
-    updateOverlapStoreFiles($asm, $tag, $base);
-
-    #  Now, if the directory exists, we have a store.
-
     goto allDone   if ((-d "$base/$asm.ovlStore") || (fileExists("$base/$asm.ovlStore.tar.gz")));
     goto allDone   if ((-d "$base/$asm.ctgStore") || (fileExists("$base/$asm.ctgStore.tar.gz")));