Changeset: 071a759385fb for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=071a759385fb
Added Files:
sql/test/BugTracker-2015/Tests/import-non-ascii.Bug-3864.sql
sql/test/BugTracker-2015/Tests/import-non-ascii.Bug-3864.stable.err
sql/test/BugTracker-2015/Tests/import-non-ascii.Bug-3864.stable.out
sql/test/BugTracker-2015/Tests/window_function_crash.Bug-3861.sql
sql/test/BugTracker-2015/Tests/window_function_crash.Bug-3861.stable.err
sql/test/BugTracker-2015/Tests/window_function_crash.Bug-3861.stable.out
sql/test/SQLite_regress/sqllogictest/Tests/select1.test.stable.out.int128
sql/test/SQLite_regress/sqllogictest/Tests/select2.test.stable.out.int128
sql/test/SQLite_regress/sqllogictest/Tests/select3.test.stable.out.int128
sql/test/SQLite_regress/sqllogictest/Tests/select4.test.stable.out.int128
Modified Files:
clients/Tests/MAL-signatures.stable.out
clients/Tests/MAL-signatures.stable.out.int128
clients/Tests/SQL-dump.stable.out
clients/Tests/SQL-dump.stable.out.int128
sql/test/BugTracker-2015/Tests/All
sql/test/BugTracker-2015/Tests/msqldump-merge-and-remote-tables.Bug-3774.sql
sql/test/BugTracker-2015/Tests/msqldump_generates_incorrect_syntax_ON_UPDATE_null.Bug-3839.sql
sql/test/SQLite_regress/sqllogictest/Tests/select1.test.stable.out
sql/test/SQLite_regress/sqllogictest/Tests/select2.test.stable.out
sql/test/SQLite_regress/sqllogictest/Tests/select3.test.stable.out
sql/test/SQLite_regress/sqllogictest/Tests/select4.test.stable.err
sql/test/SQLite_regress/sqllogictest/Tests/select4.test.stable.out
sql/test/Tests/systemfunctions.stable.out
sql/test/Tests/systemfunctions.stable.out.int128
sql/test/leaks/Tests/check1.stable.out
sql/test/leaks/Tests/check1.stable.out.int128
sql/test/leaks/Tests/check2.stable.out
sql/test/leaks/Tests/check2.stable.out.int128
sql/test/leaks/Tests/check3.stable.out
sql/test/leaks/Tests/check3.stable.out.int128
sql/test/leaks/Tests/check4.stable.out
sql/test/leaks/Tests/check4.stable.out.int128
sql/test/leaks/Tests/check5.stable.out
sql/test/leaks/Tests/check5.stable.out.int128
Branch: leftmart
Log Message:
Merge with default branch.
diffs (truncated from 41277 to 300 lines):
diff --git a/clients/Tests/MAL-signatures.stable.out
b/clients/Tests/MAL-signatures.stable.out
--- a/clients/Tests/MAL-signatures.stable.out
+++ b/clients/Tests/MAL-signatures.stable.out
@@ -2536,6 +2536,10 @@ command batbam.reverse_seq(seqs:bat[:oid
address reverse_seq_bat;
comment Reverse a bat of DNA sequences.
+command
batbam.seq_char(ref_pos:int,alg_seq:bat[:oid,:str],alg_pos:bat[:oid,:int],alg_cigar:bat[:oid,:str]):bat[:oid,:str]
+address seq_char_bat;
+comment Calculate the character in the alignment string (alg_str) that is
aligned to position 'ref_pos', conforming to the given cigar string (bat based
version)
+
command batbam.seq_length(cigars:bat[:oid,:str]):bat[:oid,:int]
address seq_length_bat;
comment Calculate the real length of a bat of DNA sequences, given their CIGAR
string.
@@ -2556,11 +2560,11 @@ pattern bam.bam_loader_file(bam_file:str
address bam_loader_file;
comment Read bam_file and store it in the given dbschema
-pattern bam.bam_loader_files(bam_files:str,dbschema:sht,nr_threads:sht):void
+pattern bam.bam_loader_files(bam_files:str,dbschema:sht):void
address bam_loader_files;
comment Read all bam files in the file list stored in the file bam_files
(separated by a newline) and store them in the given dbschema
-pattern bam.bam_loader_repos(bam_repos:str,dbschema:sht,nr_threads:sht):void
+pattern bam.bam_loader_repos(bam_repos:str,dbschema:sht):void
address bam_loader_repos;
comment Read all bam files in the given bam_repos directory (non-recursive)
and store them in the given dbschema
@@ -2576,6 +2580,10 @@ pattern bam.sam_export(output_path:str):
address sam_exportf;
comment Export results in the bam.export table to a SAM file
+command bam.seq_char(ref_pos:int,alg_seq:str,alg_pos:int,alg_cigar:str):str
+address seq_char;
+comment Calculate the character in the alignment string (alg_str) that is
aligned to position 'ref_pos', conforming to the given cigar string
+
command bam.seq_length(cigar:str):int
address seq_length;
comment Calculate the real length of a DNA sequence, given its CIGAR string.
@@ -31245,6 +31253,10 @@ command bat.getSize(b:bat[:oid,:any_1]):
address BKCgetSize;
comment Calculate the actual size of the BAT descriptor, heaps, hashes and
imprint indices in bytes rounded to the memory page size (see
bbp.getPageSize()).
+pattern bat.hasorderidx(bv:bat[:oid,:any_1]):bit
+address OIDXhasorderidx;
+comment Return true if order index exists
+
command bat.imprintsize(b:bat[:oid,:dbl]):lng
address CMDBATimprintsize;
comment Return the storage size of the imprints index structure.
@@ -35806,8 +35818,8 @@ pattern calc.flt(v:void):flt
address CMDvarCONVERT;
comment Cast VALUE to flt
-function calc.geomcollection{unsafe}(wkt:str):wkb;
-function calc.geometry{unsafe}(wkt:str):wkb;
+unsafe function calc.geomcollection(wkt:str):wkb;
+unsafe function calc.geometry(wkt:str):wkb;
pattern calc.hash(v:any):wrd
address MKEYhash;
pattern calc.hash(v:dbl):wrd
diff --git a/clients/Tests/MAL-signatures.stable.out.int128
b/clients/Tests/MAL-signatures.stable.out.int128
--- a/clients/Tests/MAL-signatures.stable.out.int128
+++ b/clients/Tests/MAL-signatures.stable.out.int128
@@ -3047,6 +3047,10 @@ command batbam.reverse_seq(seqs:bat[:oid
address reverse_seq_bat;
comment Reverse a bat of DNA sequences.
+command
batbam.seq_char(ref_pos:int,alg_seq:bat[:oid,:str],alg_pos:bat[:oid,:int],alg_cigar:bat[:oid,:str]):bat[:oid,:str]
+address seq_char_bat;
+comment Calculate the character in the alignment string (alg_str) that is
aligned to position 'ref_pos', conforming to the given cigar string (bat based
version)
+
command batbam.seq_length(cigars:bat[:oid,:str]):bat[:oid,:int]
address seq_length_bat;
comment Calculate the real length of a bat of DNA sequences, given their CIGAR
string.
@@ -3067,11 +3071,11 @@ pattern bam.bam_loader_file(bam_file:str
address bam_loader_file;
comment Read bam_file and store it in the given dbschema
-pattern bam.bam_loader_files(bam_files:str,dbschema:sht,nr_threads:sht):void
+pattern bam.bam_loader_files(bam_files:str,dbschema:sht):void
address bam_loader_files;
comment Read all bam files in the file list stored in the file bam_files
(separated by a newline) and store them in the given dbschema
-pattern bam.bam_loader_repos(bam_repos:str,dbschema:sht,nr_threads:sht):void
+pattern bam.bam_loader_repos(bam_repos:str,dbschema:sht):void
address bam_loader_repos;
comment Read all bam files in the given bam_repos directory (non-recursive)
and store them in the given dbschema
@@ -3087,6 +3091,10 @@ pattern bam.sam_export(output_path:str):
address sam_exportf;
comment Export results in the bam.export table to a SAM file
+command bam.seq_char(ref_pos:int,alg_seq:str,alg_pos:int,alg_cigar:str):str
+address seq_char;
+comment Calculate the character in the alignment string (alg_str) that is
aligned to position 'ref_pos', conforming to the given cigar string
+
command bam.seq_length(cigar:str):int
address seq_length;
comment Calculate the real length of a DNA sequence, given its CIGAR string.
diff --git a/clients/Tests/SQL-dump.stable.out
b/clients/Tests/SQL-dump.stable.out
--- a/clients/Tests/SQL-dump.stable.out
+++ b/clients/Tests/SQL-dump.stable.out
@@ -1647,156 +1647,156 @@ 5533 "minflt" "bigint" 64 0
5537 NULL tr
5534 "majflt" "bigint" 64 0 5537 NULL true
10 NULL
5535 "nvcsw" "bigint" 64 0 5537 NULL true 11
NULL
5536 "stmt" "clob" 0 0 5537 NULL true 12 NULL
-5676 "user" "clob" 0 0 5682 NULL true 0 NULL
-5677 "login" "timestamp" 7 0 5682 NULL true 1
NULL
-5678 "sessiontimeout" "bigint" 64 0 5682 NULL
true 2 NULL
-5679 "lastcommand" "timestamp" 7 0 5682 NULL true
3 NULL
-5680 "querytimeout" "bigint" 64 0 5682 NULL true
4 NULL
-5681 "active" "boolean" 1 0 5682 NULL true
5 NULL
-5759 "name" "clob" 0 0 5762 NULL true 0 NULL
-5760 "def" "clob" 0 0 5762 NULL true 1 NULL
-5761 "status" "clob" 0 0 5762 NULL true 2
NULL
-5768 "name" "clob" 0 0 5770 NULL true 0 NULL
-5769 "value" "clob" 0 0 5770 NULL true 1 NULL
-5806 "qtag" "bigint" 64 0 5814 NULL true 0
NULL
-5807 "user" "clob" 0 0 5814 NULL true 1 NULL
-5808 "started" "timestamp" 7 0 5814 NULL true
2 NULL
-5809 "estimate" "timestamp" 7 0 5814 NULL true
3 NULL
-5810 "progress" "int" 32 0 5814 NULL true 4
NULL
-5811 "status" "clob" 0 0 5814 NULL true 5
NULL
-5812 "tag" "oid" 63 0 5814 NULL true 6 NULL
-5813 "query" "clob" 0 0 5814 NULL true 7 NULL
-5840 "rowid" "bigint" 64 0 5844 NULL true 0
NULL
-5841 "fldid" "int" 32 0 5844 NULL true 1 NULL
-5842 "message" "clob" 0 0 5844 NULL true 2
NULL
-5843 "input" "clob" 0 0 5844 NULL true 3 NULL
-6464 "keyword" "varchar" 40 0 6467 NULL false
0 NULL
-6469 "table_type_id" "smallint" 16 0 6475 NULL false
0 NULL
-6472 "table_type_name" "varchar" 25 0 6475 NULL
false 1 NULL
-6477 "dependency_type_id" "smallint" 16 0 6483 NULL
false 0 NULL
-6480 "dependency_type_name" "varchar" 15 0 6483 NULL
false 1 NULL
-6498 "file_id" "int" 32 0 6500 NULL true 0
NULL
-6499 "location" "char" 256 0 6500 NULL true 1
NULL
-6502 "dim_id" "int" 32 0 6506 NULL true 0
NULL
-6503 "file_id" "int" 32 0 6506 NULL true 1
NULL
-6504 "name" "varchar" 64 0 6506 NULL true 2
NULL
-6505 "length" "int" 32 0 6506 NULL true 3
NULL
-6508 "var_id" "int" 32 0 6514 NULL true 0
NULL
-6509 "file_id" "int" 32 0 6514 NULL true 1
NULL
-6510 "name" "varchar" 64 0 6514 NULL true 2
NULL
-6511 "vartype" "varchar" 64 0 6514 NULL true
3 NULL
-6512 "ndim" "int" 32 0 6514 NULL true 4 NULL
-6513 "coord_dim_id" "int" 32 0 6514 NULL true 5
NULL
-6516 "var_id" "int" 32 0 6520 NULL true 0
NULL
-6517 "dim_id" "int" 32 0 6520 NULL true 1
NULL
-6518 "file_id" "int" 32 0 6520 NULL true 2
NULL
-6519 "dimpos" "int" 32 0 6520 NULL true 3
NULL
-6522 "obj_name" "varchar" 256 0 6528 NULL true
0 NULL
-6523 "att_name" "varchar" 256 0 6528 NULL true
1 NULL
-6524 "att_type" "varchar" 64 0 6528 NULL true
2 NULL
-6525 "value" "clob" 0 0 6528 NULL true 3 NULL
-6526 "file_id" "int" 32 0 6528 NULL true 4
NULL
-6527 "gr_name" "varchar" 256 0 6528 NULL true
5 NULL
-6554 "schema" "clob" 0 0 6569 NULL true 0
NULL
-6555 "table" "clob" 0 0 6569 NULL true 1 NULL
-6556 "column" "clob" 0 0 6569 NULL true 2
NULL
-6557 "type" "clob" 0 0 6569 NULL true 3 NULL
-6558 "mode" "clob" 0 0 6569 NULL true 4 NULL
-6559 "location" "clob" 0 0 6569 NULL true 5
NULL
-6560 "count" "bigint" 64 0 6569 NULL true 6
NULL
-6561 "typewidth" "int" 32 0 6569 NULL true 7
NULL
-6562 "columnsize" "bigint" 64 0 6569 NULL true
8 NULL
-6563 "heapsize" "bigint" 64 0 6569 NULL true
9 NULL
-6564 "hashes" "bigint" 64 0 6569 NULL true
10 NULL
-6565 "phash" "boolean" 1 0 6569 NULL true 11
NULL
-6566 "imprints" "bigint" 64 0 6569 NULL true
12 NULL
-6567 "sorted" "boolean" 1 0 6569 NULL true
13 NULL
-6568 "orderidx" "bigint" 64 0 6569 NULL true
14 NULL
-6571 "schema" "clob" 0 0 6582 NULL true 0
NULL
-6572 "table" "clob" 0 0 6582 NULL true 1 NULL
-6573 "column" "clob" 0 0 6582 NULL true 2
NULL
-6574 "type" "clob" 0 0 6582 NULL true 3 NULL
-6575 "typewidth" "int" 32 0 6582 NULL true 4
NULL
-6576 "count" "bigint" 64 0 6582 NULL true 5
NULL
-6577 "distinct" "bigint" 64 0 6582 NULL true
6 NULL
-6578 "atomwidth" "int" 32 0 6582 NULL true 7
NULL
-6579 "reference" "boolean" 1 0 6582 NULL true
8 NULL
-6580 "sorted" "boolean" 1 0 6582 NULL true
9 NULL
-6581 "orderidx" "bigint" 64 0 6582 NULL true
10 NULL
-6621 "schema" "clob" 0 0 6632 NULL true 0
NULL
-6622 "table" "clob" 0 0 6632 NULL true 1 NULL
-6623 "column" "clob" 0 0 6632 NULL true 2
NULL
-6624 "type" "clob" 0 0 6632 NULL true 3 NULL
-6625 "count" "bigint" 64 0 6632 NULL true 4
NULL
-6626 "columnsize" "bigint" 64 0 6632 NULL true
5 NULL
-6627 "heapsize" "bigint" 64 0 6632 NULL true
6 NULL
-6628 "hashes" "bigint" 64 0 6632 NULL true
7 NULL
-6629 "imprints" "bigint" 64 0 6632 NULL true
8 NULL
-6630 "sorted" "boolean" 1 0 6632 NULL true
9 NULL
-6631 "orderidx" "bigint" 64 0 6632 NULL true
10 NULL
-6634 "schema" "clob" 0 0 6642 NULL true 0
NULL
-6635 "table" "clob" 0 0 6642 NULL true 1 NULL
-6636 "count" "bigint" 64 0 6642 NULL true 2
NULL
-6637 "columnsize" "bigint" 64 0 6642 NULL true
3 NULL
-6638 "heapsize" "bigint" 64 0 6642 NULL true
4 NULL
-6639 "hashes" "bigint" 64 0 6642 NULL true
5 NULL
-6640 "imprints" "bigint" 64 0 6642 NULL true
6 NULL
-6641 "auxiliary" "bigint" 64 0 6642 NULL true
7 NULL
-6644 "column_id" "int" 32 0 6655 NULL true 0
NULL
-6645 "type" "clob" 0 0 6655 NULL true 1 NULL
-6646 "width" "int" 32 0 6655 NULL true 2 NULL
-6647 "stamp" "timestamp" 7 0 6655 NULL true 3
NULL
-6648 "sample" "bigint" 64 0 6655 NULL true
4 NULL
-6649 "count" "bigint" 64 0 6655 NULL true 5
NULL
-6650 "unique" "bigint" 64 0 6655 NULL true
6 NULL
-6651 "nils" "bigint" 64 0 6655 NULL true 7
NULL
-6652 "minval" "clob" 0 0 6655 NULL true 8
NULL
-6653 "maxval" "clob" 0 0 6655 NULL true 9
NULL
-6654 "sorted" "boolean" 1 0 6655 NULL true
10 NULL
-6740 "file_id" "bigint" 64 0 6748 NULL false
0 NULL
-6741 "file_location" "clob" 0 0 6748 NULL false 1
NULL
-6742 "dbschema" "smallint" 16 0 6748 NULL false
2 NULL
-6743 "format_version" "varchar" 7 0 6748 NULL
true 3 NULL
-6744 "sorting_order" "varchar" 10 0 6748 NULL true
4 NULL
-6745 "comments" "clob" 0 0 6748 NULL true 5
NULL
-6750 "sn" "clob" 0 0 6761 NULL false 0 NULL
-6751 "file_id" "bigint" 64 0 6761 NULL false
1 NULL
-6752 "ln" "int" 32 0 6761 NULL true 2 NULL
-6753 "as" "int" 32 0 6761 NULL true 3 NULL
-6754 "m5" "clob" 0 0 6761 NULL true 4 NULL
-6755 "sp" "clob" 0 0 6761 NULL true 5 NULL
-6756 "ur" "clob" 0 0 6761 NULL true 6 NULL
-6763 "id" "clob" 0 0 6780 NULL false 0 NULL
-6764 "file_id" "bigint" 64 0 6780 NULL false
1 NULL
-6765 "cn" "clob" 0 0 6780 NULL true 2 NULL
-6766 "ds" "clob" 0 0 6780 NULL true 3 NULL
-6767 "dt" "timestamp" 7 0 6780 NULL true 4
NULL
-6768 "fo" "clob" 0 0 6780 NULL true 5 NULL
-6769 "ks" "clob" 0 0 6780 NULL true 6 NULL
-6770 "lb" "clob" 0 0 6780 NULL true 7 NULL
-6771 "pg" "clob" 0 0 6780 NULL true 8 NULL
-6772 "pi" "int" 32 0 6780 NULL true 9 NULL
-6773 "pl" "clob" 0 0 6780 NULL true 10 NULL
-6774 "pu" "clob" 0 0 6780 NULL true 11 NULL
-6775 "sm" "clob" 0 0 6780 NULL true 12 NULL
-6782 "id" "clob" 0 0 6792 NULL false 0 NULL
-6783 "file_id" "bigint" 64 0 6792 NULL false
1 NULL
-6784 "pn" "clob" 0 0 6792 NULL true 2 NULL
-6785 "cl" "clob" 0 0 6792 NULL true 3 NULL
-6786 "pp" "clob" 0 0 6792 NULL true 4 NULL
-6787 "vn" "clob" 0 0 6792 NULL true 5 NULL
-6794 "qname" "clob" 0 0 6805 NULL false 0 NULL
-6795 "flag" "smallint" 16 0 6805 NULL false 1
NULL
-6796 "rname" "clob" 0 0 6805 NULL false 2 NULL
-6797 "pos" "int" 32 0 6805 NULL false 3 NULL
-6798 "mapq" "smallint" 16 0 6805 NULL false 4
NULL
-6799 "cigar" "clob" 0 0 6805 NULL false 5 NULL
-6800 "rnext" "clob" 0 0 6805 NULL false 6 NULL
-6801 "pnext" "int" 32 0 6805 NULL false 7 NULL
-6802 "tlen" "int" 32 0 6805 NULL false 8 NULL
-6803 "seq" "clob" 0 0 6805 NULL false 9 NULL
-6804 "qual" "clob" 0 0 6805 NULL false 10 NULL
-6875 "function_id" "int" 32 0 6876 NULL true 0
NULL
+5681 "user" "clob" 0 0 5687 NULL true 0 NULL
+5682 "login" "timestamp" 7 0 5687 NULL true 1
NULL
+5683 "sessiontimeout" "bigint" 64 0 5687 NULL
true 2 NULL
+5684 "lastcommand" "timestamp" 7 0 5687 NULL true
3 NULL
+5685 "querytimeout" "bigint" 64 0 5687 NULL true
4 NULL
+5686 "active" "boolean" 1 0 5687 NULL true
5 NULL
+5764 "name" "clob" 0 0 5767 NULL true 0 NULL
+5765 "def" "clob" 0 0 5767 NULL true 1 NULL
+5766 "status" "clob" 0 0 5767 NULL true 2
NULL
+5773 "name" "clob" 0 0 5775 NULL true 0 NULL
+5774 "value" "clob" 0 0 5775 NULL true 1 NULL
+5811 "qtag" "bigint" 64 0 5819 NULL true 0
NULL
+5812 "user" "clob" 0 0 5819 NULL true 1 NULL
+5813 "started" "timestamp" 7 0 5819 NULL true
2 NULL
+5814 "estimate" "timestamp" 7 0 5819 NULL true
3 NULL
+5815 "progress" "int" 32 0 5819 NULL true 4
NULL
+5816 "status" "clob" 0 0 5819 NULL true 5
NULL
+5817 "tag" "oid" 63 0 5819 NULL true 6 NULL
+5818 "query" "clob" 0 0 5819 NULL true 7 NULL
+5845 "rowid" "bigint" 64 0 5849 NULL true 0
NULL
+5846 "fldid" "int" 32 0 5849 NULL true 1 NULL
+5847 "message" "clob" 0 0 5849 NULL true 2
NULL
+5848 "input" "clob" 0 0 5849 NULL true 3 NULL
+6469 "keyword" "varchar" 40 0 6472 NULL false
0 NULL
+6474 "table_type_id" "smallint" 16 0 6480 NULL false
0 NULL
+6477 "table_type_name" "varchar" 25 0 6480 NULL
false 1 NULL
+6482 "dependency_type_id" "smallint" 16 0 6488 NULL
false 0 NULL
+6485 "dependency_type_name" "varchar" 15 0 6488 NULL
false 1 NULL
+6503 "file_id" "int" 32 0 6505 NULL true 0
NULL
+6504 "location" "char" 256 0 6505 NULL true 1
NULL
+6507 "dim_id" "int" 32 0 6511 NULL true 0
NULL
+6508 "file_id" "int" 32 0 6511 NULL true 1
NULL
+6509 "name" "varchar" 64 0 6511 NULL true 2
NULL
+6510 "length" "int" 32 0 6511 NULL true 3
NULL
+6513 "var_id" "int" 32 0 6519 NULL true 0
NULL
+6514 "file_id" "int" 32 0 6519 NULL true 1
NULL
+6515 "name" "varchar" 64 0 6519 NULL true 2
NULL
+6516 "vartype" "varchar" 64 0 6519 NULL true
3 NULL
+6517 "ndim" "int" 32 0 6519 NULL true 4 NULL
+6518 "coord_dim_id" "int" 32 0 6519 NULL true 5
NULL
+6521 "var_id" "int" 32 0 6525 NULL true 0
NULL
+6522 "dim_id" "int" 32 0 6525 NULL true 1
NULL
+6523 "file_id" "int" 32 0 6525 NULL true 2
NULL
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