Changeset: 3e5624ed314b for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=3e5624ed314b
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
Branch: default
Log Message:
Approvals.
diffs (truncated from 1141 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
@@ -2535,6 +2535,10 @@ 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.
@@ -2555,11 +2559,11 @@ 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
@@ -2575,6 +2579,10 @@ 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.
@@ -35789,8 +35797,8 @@ 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
@@ -3046,6 +3046,10 @@ 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.
@@ -3066,11 +3070,11 @@ 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
@@ -3086,6 +3090,10 @@ 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
@@ -1745,50 +1745,50 @@ 6641 "nils" "bigint" 64 0 6645
NULL true
6642 "minval" "clob" 0 0 6645 NULL true 8
NULL
6643 "maxval" "clob" 0 0 6645 NULL true 9
NULL
6644 "sorted" "boolean" 1 0 6645 NULL true
10 NULL
-6730 "file_id" "bigint" 64 0 6738 NULL false
0 NULL
-6731 "file_location" "clob" 0 0 6738 NULL false 1
NULL
-6732 "dbschema" "smallint" 16 0 6738 NULL false
2 NULL
-6733 "format_version" "varchar" 7 0 6738 NULL
true 3 NULL
-6734 "sorting_order" "varchar" 10 0 6738 NULL true
4 NULL
-6735 "comments" "clob" 0 0 6738 NULL true 5
NULL
-6740 "sn" "clob" 0 0 6751 NULL false 0 NULL
-6741 "file_id" "bigint" 64 0 6751 NULL false
1 NULL
-6742 "ln" "int" 32 0 6751 NULL true 2 NULL
-6743 "as" "int" 32 0 6751 NULL true 3 NULL
-6744 "m5" "clob" 0 0 6751 NULL true 4 NULL
-6745 "sp" "clob" 0 0 6751 NULL true 5 NULL
-6746 "ur" "clob" 0 0 6751 NULL true 6 NULL
-6753 "id" "clob" 0 0 6770 NULL false 0 NULL
-6754 "file_id" "bigint" 64 0 6770 NULL false
1 NULL
-6755 "cn" "clob" 0 0 6770 NULL true 2 NULL
-6756 "ds" "clob" 0 0 6770 NULL true 3 NULL
-6757 "dt" "timestamp" 7 0 6770 NULL true 4
NULL
-6758 "fo" "clob" 0 0 6770 NULL true 5 NULL
-6759 "ks" "clob" 0 0 6770 NULL true 6 NULL
-6760 "lb" "clob" 0 0 6770 NULL true 7 NULL
-6761 "pg" "clob" 0 0 6770 NULL true 8 NULL
-6762 "pi" "int" 32 0 6770 NULL true 9 NULL
-6763 "pl" "clob" 0 0 6770 NULL true 10 NULL
-6764 "pu" "clob" 0 0 6770 NULL true 11 NULL
-6765 "sm" "clob" 0 0 6770 NULL true 12 NULL
-6772 "id" "clob" 0 0 6782 NULL false 0 NULL
-6773 "file_id" "bigint" 64 0 6782 NULL false
1 NULL
-6774 "pn" "clob" 0 0 6782 NULL true 2 NULL
-6775 "cl" "clob" 0 0 6782 NULL true 3 NULL
-6776 "pp" "clob" 0 0 6782 NULL true 4 NULL
-6777 "vn" "clob" 0 0 6782 NULL true 5 NULL
-6784 "qname" "clob" 0 0 6795 NULL false 0 NULL
-6785 "flag" "smallint" 16 0 6795 NULL false 1
NULL
-6786 "rname" "clob" 0 0 6795 NULL false 2 NULL
-6787 "pos" "int" 32 0 6795 NULL false 3 NULL
-6788 "mapq" "smallint" 16 0 6795 NULL false 4
NULL
-6789 "cigar" "clob" 0 0 6795 NULL false 5 NULL
-6790 "rnext" "clob" 0 0 6795 NULL false 6 NULL
-6791 "pnext" "int" 32 0 6795 NULL false 7 NULL
-6792 "tlen" "int" 32 0 6795 NULL false 8 NULL
-6793 "seq" "clob" 0 0 6795 NULL false 9 NULL
-6794 "qual" "clob" 0 0 6795 NULL false 10 NULL
-6865 "function_id" "int" 32 0 6866 NULL true 0
NULL
+6735 "file_id" "bigint" 64 0 6743 NULL false
0 NULL
+6736 "file_location" "clob" 0 0 6743 NULL false 1
NULL
+6737 "dbschema" "smallint" 16 0 6743 NULL false
2 NULL
+6738 "format_version" "varchar" 7 0 6743 NULL
true 3 NULL
+6739 "sorting_order" "varchar" 10 0 6743 NULL true
4 NULL
+6740 "comments" "clob" 0 0 6743 NULL true 5
NULL
+6745 "sn" "clob" 0 0 6756 NULL false 0 NULL
+6746 "file_id" "bigint" 64 0 6756 NULL false
1 NULL
+6747 "ln" "int" 32 0 6756 NULL true 2 NULL
+6748 "as" "int" 32 0 6756 NULL true 3 NULL
+6749 "m5" "clob" 0 0 6756 NULL true 4 NULL
+6750 "sp" "clob" 0 0 6756 NULL true 5 NULL
+6751 "ur" "clob" 0 0 6756 NULL true 6 NULL
+6758 "id" "clob" 0 0 6775 NULL false 0 NULL
+6759 "file_id" "bigint" 64 0 6775 NULL false
1 NULL
+6760 "cn" "clob" 0 0 6775 NULL true 2 NULL
+6761 "ds" "clob" 0 0 6775 NULL true 3 NULL
+6762 "dt" "timestamp" 7 0 6775 NULL true 4
NULL
+6763 "fo" "clob" 0 0 6775 NULL true 5 NULL
+6764 "ks" "clob" 0 0 6775 NULL true 6 NULL
+6765 "lb" "clob" 0 0 6775 NULL true 7 NULL
+6766 "pg" "clob" 0 0 6775 NULL true 8 NULL
+6767 "pi" "int" 32 0 6775 NULL true 9 NULL
+6768 "pl" "clob" 0 0 6775 NULL true 10 NULL
+6769 "pu" "clob" 0 0 6775 NULL true 11 NULL
+6770 "sm" "clob" 0 0 6775 NULL true 12 NULL
+6777 "id" "clob" 0 0 6787 NULL false 0 NULL
+6778 "file_id" "bigint" 64 0 6787 NULL false
1 NULL
+6779 "pn" "clob" 0 0 6787 NULL true 2 NULL
+6780 "cl" "clob" 0 0 6787 NULL true 3 NULL
+6781 "pp" "clob" 0 0 6787 NULL true 4 NULL
+6782 "vn" "clob" 0 0 6787 NULL true 5 NULL
+6789 "qname" "clob" 0 0 6800 NULL false 0 NULL
+6790 "flag" "smallint" 16 0 6800 NULL false 1
NULL
+6791 "rname" "clob" 0 0 6800 NULL false 2 NULL
+6792 "pos" "int" 32 0 6800 NULL false 3 NULL
+6793 "mapq" "smallint" 16 0 6800 NULL false 4
NULL
+6794 "cigar" "clob" 0 0 6800 NULL false 5 NULL
+6795 "rnext" "clob" 0 0 6800 NULL false 6 NULL
+6796 "pnext" "int" 32 0 6800 NULL false 7 NULL
+6797 "tlen" "int" 32 0 6800 NULL false 8 NULL
+6798 "seq" "clob" 0 0 6800 NULL false 9 NULL
+6799 "qual" "clob" 0 0 6800 NULL false 10 NULL
+6870 "function_id" "int" 32 0 6871 NULL true 0
NULL
COMMIT;
START TRANSACTION;
CREATE TABLE "sys"."_tables" (
@@ -1850,12 +1850,12 @@ 6574 "storagemodelinput" 2000 NULL 0
tru
6622 "storagemodel" 2000 "create view sys.storagemodel as select * from
sys.storagemodel();" 1 true 0 0
6632 "tablestoragemodel" 2000 "-- A summary of the table storage
requirement is is available as a table view.\n-- The auxiliary column denotes
the maximum space if all non-sorted columns\n-- would be augmented with a hash
(rare situation)\ncreate view sys.tablestoragemodel\nas select
""schema"",""table"",max(count) as ""count"",\n\tsum(columnsize) as
columnsize,\n\tsum(heapsize) as heapsize,\n\tsum(hashes) as
hashes,\n\tsum(imprints) as imprints,\n\tsum(case when sorted = false then 8 *
count else 0 end) as auxiliary\nfrom sys.storagemodel() group by
""schema"",""table"";" 1 true 0 0
6645 "statistics" 2000 NULL 0 true 0 0
-6738 "files" 6687 NULL 0 true 0 0
-6751 "sq" 6687 NULL 0 true 0 0
-6770 "rg" 6687 NULL 0 true 0 0
-6782 "pg" 6687 NULL 0 true 0 0
-6795 "export" 6687 NULL 0 true 0 0
-6866 "systemfunctions" 2000 NULL 0 true 0 0
+6743 "files" 6687 NULL 0 true 0 0
+6756 "sq" 6687 NULL 0 true 0 0
+6775 "rg" 6687 NULL 0 true 0 0
+6787 "pg" 6687 NULL 0 true 0 0
+6800 "export" 6687 NULL 0 true 0 0
+6871 "systemfunctions" 2000 NULL 0 true 0 0
COMMIT;
START TRANSACTION;
CREATE TABLE "sys"."args" (
@@ -1868,7 +1868,7 @@ CREATE TABLE "sys"."args" (
"inout" TINYINT,
"number" INTEGER
);
-COPY 3799 RECORDS INTO "sys"."args" FROM stdin USING DELIMITERS '\t','\n','"';
+COPY 3802 RECORDS INTO "sys"."args" FROM stdin USING DELIMITERS '\t','\n','"';
2155 28 "res_0" "oid" 63 0 0 0
2156 28 "arg_1" "wrd" 64 0 1 1
2157 29 "res_0" "oid" 63 0 0 0
@@ -5605,69 +5605,72 @@ 6685 6683 "one" "int" 32 0 1
1
6686 6683 "two" "int" 32 0 1 2
6690 6689 "bam_repos" "clob" 0 0 1 0
6691 6689 "dbschema" "smallint" 16 0 1 1
-6692 6689 "nr_threads" "smallint" 16 0 1 2
-6695 6694 "bam_files" "clob" 0 0 1 0
-6696 6694 "dbschema" "smallint" 16 0 1 1
-6697 6694 "nr_threads" "smallint" 16 0 1 2
-6700 6699 "bam_file" "clob" 0 0 1 0
-6701 6699 "dbschema" "smallint" 16 0 1 1
-6704 6703 "file_id" "bigint" 64 0 1 0
-6705 6703 "dbschema" "smallint" 16 0 1 1
-6708 6707 "result" "boolean" 1 0 0 0
-6709 6707 "flag" "smallint" 16 0 1 1
-6710 6707 "name" "clob" 0 0 1 2
-6713 6712 "result" "clob" 0 0 0 0
-6714 6712 "seq" "clob" 0 0 1 1
-6717 6716 "result" "clob" 0 0 0 0
-6718 6716 "qual" "clob" 0 0 1 1
-6721 6720 "result" "int" 32 0 0 0
-6722 6720 "cigar" "clob" 0 0 1 1
-6725 6724 "output_path" "clob" 0 0 1 0
-6728 6727 "output_path" "clob" 0 0 1 0
-6798 6797 "value" "tinyint" 8 0 0 0
-6799 6797 "first" "tinyint" 8 0 1 1
-6800 6797 "last" "tinyint" 8 0 1 2
+6694 6693 "bam_files" "clob" 0 0 1 0
+6695 6693 "dbschema" "smallint" 16 0 1 1
+6698 6697 "bam_file" "clob" 0 0 1 0
+6699 6697 "dbschema" "smallint" 16 0 1 1
+6702 6701 "file_id" "bigint" 64 0 1 0
+6703 6701 "dbschema" "smallint" 16 0 1 1
+6706 6705 "result" "boolean" 1 0 0 0
+6707 6705 "flag" "smallint" 16 0 1 1
+6708 6705 "name" "clob" 0 0 1 2
+6711 6710 "result" "clob" 0 0 0 0
+6712 6710 "seq" "clob" 0 0 1 1
+6715 6714 "result" "clob" 0 0 0 0
+6716 6714 "qual" "clob" 0 0 1 1
+6719 6718 "result" "int" 32 0 0 0
+6720 6718 "cigar" "clob" 0 0 1 1
+6723 6722 "result" "char" 1 0 0 0
+6724 6722 "ref_pos" "int" 32 0 1 1
+6725 6722 "alg_seq" "clob" 0 0 1 2
+6726 6722 "alg_pos" "int" 32 0 1 3
+6727 6722 "alg_cigar" "clob" 0 0 1 4
+6730 6729 "output_path" "clob" 0 0 1 0
+6733 6732 "output_path" "clob" 0 0 1 0
6803 6802 "value" "tinyint" 8 0 0 0
6804 6802 "first" "tinyint" 8 0 1 1
6805 6802 "last" "tinyint" 8 0 1 2
-6806 6802 "stepsize" "tinyint" 8 0 1 3
-6809 6808 "value" "smallint" 16 0 0 0
-6810 6808 "first" "smallint" 16 0 1 1
-6811 6808 "last" "smallint" 16 0 1 2
+6808 6807 "value" "tinyint" 8 0 0 0
+6809 6807 "first" "tinyint" 8 0 1 1
+6810 6807 "last" "tinyint" 8 0 1 2
+6811 6807 "stepsize" "tinyint" 8 0 1 3
6814 6813 "value" "smallint" 16 0 0 0
6815 6813 "first" "smallint" 16 0 1 1
6816 6813 "last" "smallint" 16 0 1 2
-6817 6813 "stepsize" "smallint" 16 0 1 3
-6820 6819 "value" "int" 32 0 0 0
-6821 6819 "first" "int" 32 0 1 1
-6822 6819 "last" "int" 32 0 1 2
+6819 6818 "value" "smallint" 16 0 0 0
+6820 6818 "first" "smallint" 16 0 1 1
+6821 6818 "last" "smallint" 16 0 1 2
+6822 6818 "stepsize" "smallint" 16 0 1 3
6825 6824 "value" "int" 32 0 0 0
6826 6824 "first" "int" 32 0 1 1
6827 6824 "last" "int" 32 0 1 2
-6828 6824 "stepsize" "int" 32 0 1 3
-6831 6830 "value" "bigint" 64 0 0 0
-6832 6830 "first" "bigint" 64 0 1 1
-6833 6830 "last" "bigint" 64 0 1 2
+6830 6829 "value" "int" 32 0 0 0
+6831 6829 "first" "int" 32 0 1 1
+6832 6829 "last" "int" 32 0 1 2
+6833 6829 "stepsize" "int" 32 0 1 3
6836 6835 "value" "bigint" 64 0 0 0
6837 6835 "first" "bigint" 64 0 1 1
6838 6835 "last" "bigint" 64 0 1 2
-6839 6835 "stepsize" "bigint" 64 0 1 3
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