Rename gatekeeper/gkpStore to sequence store/seqStore. Existing assem…

…blies should be upgradable by just renaming *.gkpStore to *.seqStore.
Jolvii85 · Apr 18, 2018 · 01d1823 · 01d1823
1 parent b83d5e1
commit 01d1823
Show file tree

Hide file tree

Showing 175 changed files with 2,929 additions and 2,390 deletions.
diff --git a/addCopyrights.dat b/addCopyrights.dat
diff --git a/addCopyrights.pl b/addCopyrights.pl
@@ -225,7 +225,9 @@ ($@)
             $authcopy{$1} .= "$2\n";
 
         } elsif (m/^D\s+(\S+)\s+(\S+)$/) {
-            $derived{$1} .= "$2\n";
+            $authcopy{$1} .= $authcopy{$2};   #  Include all authors of old file in new file.
+            #$derived{$1}  .= $derived{$2};
+            $derived{$1}  .= "$2\n";
 
         } else {
             die "invalid addCopyrights.dat line '$_'\n";

diff --git a/src/AS_UTL/AS_UTL_decodeRange.H b/src/AS_UTL/AS_UTL_decodeRange.H
@@ -23,6 +23,10 @@
  *      are Copyright 2015 Battelle National Biodefense Institute, and
  *      are subject to the BSD 3-Clause License
  *
+ *    Brian P. Walenz beginning on 2018-APR-03
+ *      are a 'United States Government Work', and
+ *      are released in the public domain
+ *
  *  File 'README.licenses' in the root directory of this distribution contains
  *  full conditions and disclaimers for each license.
  */

diff --git a/src/AS_UTL/AS_UTL_fileIO.C b/src/AS_UTL/AS_UTL_fileIO.C
@@ -491,7 +491,7 @@ AS_UTL_fseek(FILE *stream, off_t offset, int whence) {
   //  If the stream is already at the correct position, just return.
   //
   //  Unless we're on FreeBSD.  For unknown reasons, FreeBSD fails
-  //  updating the gkpStore with mate links.  It seems to misplace the
+  //  updating the seqStore with mate links.  It seems to misplace the
   //  file pointer, and ends up writing the record to the wrong
   //  location.  ftell() is returning the correct current location,
   //  and so AS_PER_genericStore doesn't seek() and just writes to the

diff --git a/src/AS_UTL/bitPacking.H b/src/AS_UTL/bitPacking.H
@@ -35,6 +35,10 @@
  *      are Copyright 2014 Battelle National Biodefense Institute, and
  *      are subject to the BSD 3-Clause License
  *
+ *    Brian P. Walenz beginning on 2018-JAN-30
+ *      are a 'United States Government Work', and
+ *      are released in the public domain
+ *
  *  File 'README.licenses' in the root directory of this distribution contains
  *  full conditions and disclaimers for each license.
  */

diff --git a/src/AS_UTL/dnaAlphabets.H b/src/AS_UTL/dnaAlphabets.H
@@ -36,6 +36,10 @@
  *      are Copyright 2014 Battelle National Biodefense Institute, and
  *      are subject to the BSD 3-Clause License
  *
+ *    Brian P. Walenz beginning on 2018-JAN-30
+ *      are a 'United States Government Work', and
+ *      are released in the public domain
+ *
  *  File 'README.licenses' in the root directory of this distribution contains
  *  full conditions and disclaimers for each license.
  */

diff --git a/src/AS_UTL/memoryMappedFile.C b/src/AS_UTL/memoryMappedFile.C
@@ -19,7 +19,19 @@
  *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2017-OCT-02
+ *    Brian P. Walenz from 2012-FEB-16 to 2013-AUG-01
+ *      are Copyright 2012-2013 J. Craig Venter Institute, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz from 2014-NOV-26 to 2015-APR-21
+ *      are Copyright 2014-2015 Battelle National Biodefense Institute, and
+ *      are subject to the BSD 3-Clause License
+ *
+ *    Sergey Koren beginning on 2015-DEC-15
+ *      are a 'United States Government Work', and
+ *      are released in the public domain
+ *
+ *    Brian P. Walenz beginning on 2016-JAN-11
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *

diff --git a/src/Makefile b/src/Makefile
@@ -623,7 +623,7 @@ all: UPDATE_VERSION MAKE_DIRS \
      ${TARGET_DIR}/lib/site_perl/canu/Defaults.pm \
      ${TARGET_DIR}/lib/site_perl/canu/ErrorEstimate.pm \
      ${TARGET_DIR}/lib/site_perl/canu/Execution.pm \
-     ${TARGET_DIR}/lib/site_perl/canu/Gatekeeper.pm \
+     ${TARGET_DIR}/lib/site_perl/canu/SequenceStore.pm \
      ${TARGET_DIR}/lib/site_perl/canu/Grid.pm \
      ${TARGET_DIR}/lib/site_perl/canu/Grid_Cloud.pm \
      ${TARGET_DIR}/lib/site_perl/canu/Grid_DNANexus.pm \
@@ -720,8 +720,8 @@ ${TARGET_DIR}/lib/site_perl/canu/ErrorEstimate.pm: pipelines/canu/ErrorEstimate.
 ${TARGET_DIR}/lib/site_perl/canu/Execution.pm: pipelines/canu/Execution.pm
 	cp -pf pipelines/canu/Execution.pm ${TARGET_DIR}/lib/site_perl/canu/
 
-${TARGET_DIR}/lib/site_perl/canu/Gatekeeper.pm: pipelines/canu/Gatekeeper.pm
-	cp -pf pipelines/canu/Gatekeeper.pm ${TARGET_DIR}/lib/site_perl/canu/
+${TARGET_DIR}/lib/site_perl/canu/SequenceStore.pm: pipelines/canu/SequenceStore.pm
+	cp -pf pipelines/canu/SequenceStore.pm ${TARGET_DIR}/lib/site_perl/canu/
 
 ${TARGET_DIR}/lib/site_perl/canu/Grid.pm: pipelines/canu/Grid.pm
 	cp -pf pipelines/canu/Grid.pm ${TARGET_DIR}/lib/site_perl/canu/

diff --git a/src/bogart/AS_BAT_MergeOrphans.C b/src/bogart/AS_BAT_MergeOrphans.C
@@ -19,7 +19,7 @@
  *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2016-DEC-07
+ *    Brian P. Walenz beginning on 2016-MAR-11
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *

diff --git a/src/bogart/AS_BAT_MergeOrphans.H b/src/bogart/AS_BAT_MergeOrphans.H
@@ -19,7 +19,7 @@
  *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2016-DEC-07
+ *    Brian P. Walenz beginning on 2016-MAR-11
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *

diff --git a/src/bogart/AS_BAT_OptimizePositions.C b/src/bogart/AS_BAT_OptimizePositions.C
@@ -19,7 +19,15 @@
  *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2017-JUL-17
+ *    Brian P. Walenz from 2010-NOV-23 to 2013-AUG-01
+ *      are Copyright 2010-2013 J. Craig Venter Institute, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz on 2014-DEC-19
+ *      are Copyright 2014 Battelle National Biodefense Institute, and
+ *      are subject to the BSD 3-Clause License
+ *
+ *    Brian P. Walenz beginning on 2016-JAN-11
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *

diff --git a/src/bogart/AS_BAT_OverlapCache.C b/src/bogart/AS_BAT_OverlapCache.C
@@ -158,7 +158,7 @@ OverlapCache::OverlapCache(const char *ovlStorePath,
   _maxEvalue     = AS_OVS_encodeEvalue(maxErate);
   _minOverlap    = minOverlap;
 
-  //  Allocate space to load overlaps.  With a NULL gkpStore we can't call the bgn or end methods.
+  //  Allocate space to load overlaps.  With a NULL seqStore we can't call the bgn or end methods.
 
   _ovsMax  = 0;
   _ovs     = NULL;
@@ -536,7 +536,7 @@ OverlapCache::loadOverlaps(ovStore *ovlStore, bool doSave) {
   for (uint32 rr=0; rr<RI->numReads()+1; rr++)
     _ovsMax = max(_ovsMax, ovlStore->numOverlaps(rr));
 
-  _ovs     = ovOverlap::allocateOverlaps(NULL /* gkpStore */, _ovsMax);
+  _ovs     = ovOverlap::allocateOverlaps(NULL /* seqStore */, _ovsMax);
   _ovsSco  = new uint64 [_ovsMax];
   _ovsTmp  = new uint64 [_ovsMax];
 

diff --git a/src/bogart/AS_BAT_OverlapCache.H b/src/bogart/AS_BAT_OverlapCache.H
@@ -44,7 +44,7 @@
 
 #include "AS_global.H"
 #include "ovStore.H"
-#include "gkStore.H"
+#include "sqStore.H"
 #include "memoryMappedFile.H"
 
 //  CA8 used to re-encode the error rate into a smaller-precision number.  This was

diff --git a/src/bogart/AS_BAT_PlaceReadUsingOverlaps.C b/src/bogart/AS_BAT_PlaceReadUsingOverlaps.C
@@ -19,7 +19,15 @@
  *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2016-AUG-12
+ *    Brian P. Walenz from 2010-NOV-23 to 2013-SEP-08
+ *      are Copyright 2010-2013 J. Craig Venter Institute, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz from 2014-OCT-09 to 2015-AUG-05
+ *      are Copyright 2014-2015 Battelle National Biodefense Institute, and
+ *      are subject to the BSD 3-Clause License
+ *
+ *    Brian P. Walenz beginning on 2016-JAN-11
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *

diff --git a/src/bogart/AS_BAT_PlaceReadUsingOverlaps.H b/src/bogart/AS_BAT_PlaceReadUsingOverlaps.H
@@ -19,7 +19,15 @@
  *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2016-AUG-12
+ *    Brian P. Walenz from 2010-DEC-06 to 2013-AUG-01
+ *      are Copyright 2010-2013 J. Craig Venter Institute, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz from 2014-DEC-19 to 2015-JUN-03
+ *      are Copyright 2014-2015 Battelle National Biodefense Institute, and
+ *      are subject to the BSD 3-Clause License
+ *
+ *    Brian P. Walenz beginning on 2016-JAN-11
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *

diff --git a/src/bogart/AS_BAT_ReadInfo.C b/src/bogart/AS_BAT_ReadInfo.C
@@ -28,15 +28,15 @@
 
 
 
-ReadInfo::ReadInfo(const char *gkpStorePath,
+ReadInfo::ReadInfo(const char *seqStorePath,
                    const char *prefix,
                    uint32      minReadLen) {
 
-  gkStore  *gkpStore = gkStore::gkStore_open(gkpStorePath);
+  sqStore  *seqStore = sqStore::sqStore_open(seqStorePath);
 
   _numBases     = 0;
-  _numReads     = gkpStore->gkStore_getNumReads();
-  _numLibraries = gkpStore->gkStore_getNumLibraries();
+  _numReads     = seqStore->sqStore_getNumReads();
+  _numLibraries = seqStore->sqStore_getNumLibraries();
 
   _readStatus    = new ReadStatus [_numReads + 1];
 
@@ -53,9 +53,9 @@ ReadInfo::ReadInfo(const char *gkpStorePath,
   uint32 numLoaded  = 0;
 
   for (uint32 fi=1; fi<=_numReads; fi++) {
-    gkRead  *read = gkpStore->gkStore_getRead(fi);
-    uint32   iid  = read->gkRead_readID();
-    uint32   len  = read->gkRead_sequenceLength();
+    sqRead  *read = seqStore->sqStore_getRead(fi);
+    uint32   iid  = read->sqRead_readID();
+    uint32   len  = read->sqRead_sequenceLength();
 
     if (len < minReadLen) {
       numSkipped++;
@@ -65,12 +65,12 @@ ReadInfo::ReadInfo(const char *gkpStorePath,
     _numBases += len;
 
     _readStatus[iid].readLength = len;
-    _readStatus[iid].libraryID  = read->gkRead_libraryID();
+    _readStatus[iid].libraryID  = read->sqRead_libraryID();
 
     numLoaded++;
   }
 
-  gkpStore->gkStore_close();
+  seqStore->sqStore_close();
 
   if (minReadLen > 0)
     writeStatus("ReadInfo()-- Using %d reads, ignoring %u reads less than " F_U32 " bp long.\n",

diff --git a/src/bogart/AS_BAT_ReadInfo.H b/src/bogart/AS_BAT_ReadInfo.H
@@ -28,7 +28,7 @@
 
 #include "AS_global.H"
 #include "ovStore.H"
-#include "gkStore.H"
+#include "sqStore.H"
 
 
 
@@ -47,7 +47,7 @@ struct ReadStatus {
 
 class ReadInfo {
 public:
-  ReadInfo(const char *gkpStorePath, const char *prefix, uint32 minReadLen);
+  ReadInfo(const char *seqStorePath, const char *prefix, uint32 minReadLen);
   ~ReadInfo();
 
   uint64  memoryUsage(void) {

diff --git a/src/bogart/AS_BAT_Unitig_AddRead.C b/src/bogart/AS_BAT_Unitig_AddRead.C
@@ -19,7 +19,15 @@
  *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2016-AUG-12
+ *    Brian P. Walenz from 2010-NOV-23 to 2013-AUG-01
+ *      are Copyright 2010,2012-2013 J. Craig Venter Institute, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz on 2014-DEC-19
+ *      are Copyright 2014 Battelle National Biodefense Institute, and
+ *      are subject to the BSD 3-Clause License
+ *
+ *    Brian P. Walenz beginning on 2016-JAN-11
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *

diff --git a/src/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C b/src/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C
@@ -19,7 +19,15 @@
  *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2016-AUG-12
+ *    Brian P. Walenz from 2010-NOV-23 to 2013-AUG-01
+ *      are Copyright 2010-2013 J. Craig Venter Institute, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz from 2014-DEC-19 to 2015-MAR-06
+ *      are Copyright 2014-2015 Battelle National Biodefense Institute, and
+ *      are subject to the BSD 3-Clause License
+ *
+ *    Brian P. Walenz beginning on 2016-JAN-11
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *