Changeset: b3b973d8c3da for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=b3b973d8c3da
Added Files:
sql/backends/monet5/bam/Tests/bam.py
sql/backends/monet5/bam/Tests/bam_export.SQL.py
sql/backends/monet5/bam/Tests/bam_loader_file.SQL.py
sql/backends/monet5/bam/Tests/bam_loader_file.stable.err
sql/backends/monet5/bam/Tests/bam_loader_file.stable.out
sql/backends/monet5/bam/Tests/bam_loader_files.SQL.py
sql/backends/monet5/bam/Tests/bam_loader_files.stable.err
sql/backends/monet5/bam/Tests/bam_loader_files.stable.out
sql/backends/monet5/bam/Tests/bam_loader_repos.SQL.py
sql/backends/monet5/bam/Tests/bam_loader_repos.stable.err
sql/backends/monet5/bam/Tests/bam_loader_repos.stable.out
sql/backends/monet5/bam/Tests/check_files.sql
sql/backends/monet5/bam/Tests/check_files.stable.err
sql/backends/monet5/bam/Tests/check_files.stable.out
sql/backends/monet5/bam/Tests/check_files_exact.sql
sql/backends/monet5/bam/Tests/check_files_exact.stable.err
sql/backends/monet5/bam/Tests/check_files_exact.stable.out
sql/backends/monet5/bam/Tests/drop_last_files.SQL.py
sql/backends/monet5/bam/Tests/drop_last_files.stable.err
sql/backends/monet5/bam/Tests/drop_last_files.stable.out
sql/backends/monet5/bam/Tests/query1.1.sql
sql/backends/monet5/bam/Tests/query1.1.stable.err
sql/backends/monet5/bam/Tests/query1.1.stable.out
sql/backends/monet5/bam/Tests/query1.2.sql
sql/backends/monet5/bam/Tests/query1.2.stable.err
sql/backends/monet5/bam/Tests/query1.2.stable.out
sql/backends/monet5/bam/Tests/query1.3.sql
sql/backends/monet5/bam/Tests/query1.3.stable.err
sql/backends/monet5/bam/Tests/query1.3.stable.out
sql/backends/monet5/bam/Tests/query1.4.sql
sql/backends/monet5/bam/Tests/query1.4.stable.err
sql/backends/monet5/bam/Tests/query1.4.stable.out
sql/backends/monet5/bam/Tests/query1.5.sql
sql/backends/monet5/bam/Tests/query1.5.stable.err
sql/backends/monet5/bam/Tests/query1.5.stable.out
sql/backends/monet5/bam/Tests/query1.6.sql
sql/backends/monet5/bam/Tests/query2.1.sql
sql/backends/monet5/bam/Tests/query2.1.stable.err
sql/backends/monet5/bam/Tests/query2.1.stable.out
sql/backends/monet5/bam/Tests/query2.10.sql
sql/backends/monet5/bam/Tests/query2.10.stable.err
sql/backends/monet5/bam/Tests/query2.10.stable.out
sql/backends/monet5/bam/Tests/query2.11.sql
sql/backends/monet5/bam/Tests/query2.11.stable.err
sql/backends/monet5/bam/Tests/query2.11.stable.out
sql/backends/monet5/bam/Tests/query2.12.sql
sql/backends/monet5/bam/Tests/query2.12.stable.err
sql/backends/monet5/bam/Tests/query2.12.stable.out
sql/backends/monet5/bam/Tests/query2.2.sql
sql/backends/monet5/bam/Tests/query2.2.stable.err
sql/backends/monet5/bam/Tests/query2.2.stable.out
sql/backends/monet5/bam/Tests/query2.3.sql
sql/backends/monet5/bam/Tests/query2.3.stable.err
sql/backends/monet5/bam/Tests/query2.3.stable.out
sql/backends/monet5/bam/Tests/query2.4.sql
sql/backends/monet5/bam/Tests/query2.4.stable.err
sql/backends/monet5/bam/Tests/query2.4.stable.out
sql/backends/monet5/bam/Tests/query2.5.sql
sql/backends/monet5/bam/Tests/query2.5.stable.err
sql/backends/monet5/bam/Tests/query2.5.stable.out
sql/backends/monet5/bam/Tests/query2.6.sql
sql/backends/monet5/bam/Tests/query2.6.stable.err
sql/backends/monet5/bam/Tests/query2.6.stable.out
sql/backends/monet5/bam/Tests/query2.7.sql
sql/backends/monet5/bam/Tests/query2.7.stable.err
sql/backends/monet5/bam/Tests/query2.7.stable.out
sql/backends/monet5/bam/Tests/query2.8.sql
sql/backends/monet5/bam/Tests/query2.8.stable.err
sql/backends/monet5/bam/Tests/query2.8.stable.out
sql/backends/monet5/bam/Tests/query2.9.sql
sql/backends/monet5/bam/Tests/query2.9.stable.err
sql/backends/monet5/bam/Tests/query2.9.stable.out
sql/backends/monet5/bam/Tests/sam_export.SQL.py
sql/backends/monet5/bam/Tests/sam_export.stable.err
sql/backends/monet5/bam/Tests/sam_export.stable.out
sql/backends/monet5/bam/Tests/sql/bam_export.sql
sql/backends/monet5/bam/Tests/sql/bam_loader_file.sql
sql/backends/monet5/bam/Tests/sql/bam_loader_files.sql
sql/backends/monet5/bam/Tests/sql/bam_loader_repos.sql
sql/backends/monet5/bam/Tests/sql/drop_last_files.sql
sql/backends/monet5/bam/Tests/sql/sam_export.sql
sql/backends/monet5/bam/Tests/verify_load.sql
sql/backends/monet5/bam/Tests/verify_load.stable.err
sql/backends/monet5/bam/Tests/verify_load.stable.out
Removed Files:
sql/backends/monet5/bam/Tests/benchmarks_0/benchmark1.sql
sql/backends/monet5/bam/Tests/benchmarks_0/benchmark2.sql
sql/backends/monet5/bam/Tests/benchmarks_0/query1.1.sql
sql/backends/monet5/bam/Tests/benchmarks_0/query1.2.sql
sql/backends/monet5/bam/Tests/benchmarks_0/query1.3.sql
sql/backends/monet5/bam/Tests/benchmarks_0/query1.4.sql
sql/backends/monet5/bam/Tests/benchmarks_0/query1.5.sql
sql/backends/monet5/bam/Tests/benchmarks_0/query2.1.sql
sql/backends/monet5/bam/Tests/benchmarks_0/query2.10.sql
sql/backends/monet5/bam/Tests/benchmarks_0/query2.11.sql
sql/backends/monet5/bam/Tests/benchmarks_0/query2.12.sql
sql/backends/monet5/bam/Tests/benchmarks_0/query2.2.sql
sql/backends/monet5/bam/Tests/benchmarks_0/query2.3.sql
sql/backends/monet5/bam/Tests/benchmarks_0/query2.4.sql
sql/backends/monet5/bam/Tests/benchmarks_0/query2.5.sql
sql/backends/monet5/bam/Tests/benchmarks_0/query2.6.sql
sql/backends/monet5/bam/Tests/benchmarks_0/query2.7.sql
sql/backends/monet5/bam/Tests/benchmarks_0/query2.8.sql
sql/backends/monet5/bam/Tests/benchmarks_0/query2.9.sql
sql/backends/monet5/bam/Tests/benchmarks_1/benchmark1.sql
sql/backends/monet5/bam/Tests/benchmarks_1/benchmark2.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query1.1.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query1.2.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query1.3.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query1.4.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query1.5.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query2.1.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query2.10.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query2.11.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query2.12.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query2.2.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query2.3.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query2.4.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query2.5.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query2.6.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query2.7.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query2.8.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query2.9.sql
sql/backends/monet5/bam/Tests/test.SQL.py
sql/backends/monet5/bam/Tests/test.stable.err
sql/backends/monet5/bam/Tests/test.stable.out
Modified Files:
sql/backends/monet5/bam/Tests/All
sql/backends/monet5/bam/Tests/test.modules
Branch: bamloader
Log Message:
Splitted test into many small tests
diffs (truncated from 9314 to 300 lines):
diff --git a/sql/backends/monet5/bam/Tests/All
b/sql/backends/monet5/bam/Tests/All
old mode 100644
new mode 100755
--- a/sql/backends/monet5/bam/Tests/All
+++ b/sql/backends/monet5/bam/Tests/All
@@ -1,1 +1,26 @@
-test
+bam_loader_file
+bam_loader_files
+bam_loader_repos
+check_files
+verify_load
+drop_last_files
+check_files_exact
+sam_export
+#bam_export
+query1.1
+query1.2
+query1.3
+query1.4
+query1.5
+query2.1
+query2.2
+query2.3
+query2.4
+query2.5
+query2.6
+query2.7
+query2.8
+query2.9
+query2.10
+query2.11
+query2.12
\ No newline at end of file
diff --git a/sql/backends/monet5/bam/Tests/bam.py
b/sql/backends/monet5/bam/Tests/bam.py
new file mode 100644
--- /dev/null
+++ b/sql/backends/monet5/bam/Tests/bam.py
@@ -0,0 +1,27 @@
+import os, sys, re
+try:
+ from MonetDBtesting import process
+except ImportError:
+ import process
+
+TSTSRCBASE = os.environ['TSTSRCBASE']
+TSTDIR = os.environ['TSTDIR']
+SRCDIR = os.path.join(TSTSRCBASE,TSTDIR,"Tests")
+
+def new_client():
+ return process.client('sql', stdin = process.PIPE, stdout = process.PIPE,
stderr = process.PIPE)
+
+
+def exec_sql_file(file, mapping={}):
+ c = new_client()
+
+ with open(os.path.join(SRCDIR, "sql", file), "r") as f:
+ for line in f:
+ towrite = line
+ for key in mapping:
+ towrite = towrite.replace(key, mapping[key])
+ c.stdin.write(towrite)
+
+ out, err = c.communicate()
+ sys.stdout.write(out)
+ sys.stderr.write(err)
\ No newline at end of file
diff --git a/sql/backends/monet5/bam/Tests/bam_export.SQL.py
b/sql/backends/monet5/bam/Tests/bam_export.SQL.py
new file mode 100644
--- /dev/null
+++ b/sql/backends/monet5/bam/Tests/bam_export.SQL.py
@@ -0,0 +1,13 @@
+import os
+import bam
+
+# Define output paths
+output_1 = os.path.join(bam.SRCDIR, "files", "out_sequential.bam")
+output_2 = os.path.join(bam.SRCDIR, "files", "out_pairwise.bam")
+
+# Run test with these paths
+bam.exec_sql_file("bam_export.sql", {'OUTPUT_1': output_1, 'OUTPUT_2':
output_2})
+
+# And remove our garbage
+os.remove(output_1)
+os.remove(output_2)
\ No newline at end of file
diff --git a/sql/backends/monet5/bam/Tests/bam_loader_file.SQL.py
b/sql/backends/monet5/bam/Tests/bam_loader_file.SQL.py
new file mode 100644
--- /dev/null
+++ b/sql/backends/monet5/bam/Tests/bam_loader_file.SQL.py
@@ -0,0 +1,3 @@
+import bam
+
+bam.exec_sql_file("bam_loader_file.sql", {'PWD': bam.SRCDIR})
diff --git a/sql/backends/monet5/bam/Tests/bam_loader_file.stable.err
b/sql/backends/monet5/bam/Tests/bam_loader_file.stable.err
new file mode 100644
--- /dev/null
+++ b/sql/backends/monet5/bam/Tests/bam_loader_file.stable.err
@@ -0,0 +1,453 @@
+stderr of test 'bam_loader_file` in directory 'sql/backends/monet5/bam` itself:
+
+
+# 13:29:48 >
+# 13:29:48 > "mserver5" "--debug=10" "--set" "gdk_nr_threads=0" "--set"
"mapi_open=true" "--set" "mapi_port=37021" "--set"
"mapi_usock=/var/tmp/mtest-21062/.s.monetdb.37021" "--set" "monet_prompt="
"--forcemito" "--set" "mal_listing=2"
"--dbpath=/home/robin/MonetDB/PREFIX/var/MonetDB/mTests_sql_backends_monet5_bam"
"--set" "mal_listing=0"
+# 13:29:48 >
+
+# builtin opt gdk_dbpath = /home/robin/MonetDB/PREFIX/var/monetdb5/dbfarm/demo
+# builtin opt gdk_debug = 0
+# builtin opt gdk_vmtrim = no
+# builtin opt monet_prompt = >
+# builtin opt monet_daemon = no
+# builtin opt mapi_port = 50000
+# builtin opt mapi_open = false
+# builtin opt mapi_autosense = false
+# builtin opt sql_optimizer = default_pipe
+# builtin opt sql_debug = 0
+# cmdline opt gdk_nr_threads = 0
+# cmdline opt mapi_open = true
+# cmdline opt mapi_port = 37021
+# cmdline opt mapi_usock = /var/tmp/mtest-21062/.s.monetdb.37021
+# cmdline opt monet_prompt =
+# cmdline opt mal_listing = 2
+# cmdline opt gdk_dbpath =
/home/robin/MonetDB/PREFIX/var/MonetDB/mTests_sql_backends_monet5_bam
+# cmdline opt mal_listing = 0
+# cmdline opt gdk_debug = 536870922
+# <bam_loader>: Loader started for 1 BAM file...
+# # <bam_loader> Creating schema 'bam'...
+# # CREATE SCHEMA bam;
+# # <bam_loader> Creating table 'files'...
+# # CREATE TABLE bam.files (
+# file_id BIGINT NOT
NULL,
+# file_location STRING NOT
NULL,
+# dbschema SMALLINT
NOT NULL,
+# format_version VARCHAR(7),
+# sorting_order VARCHAR(10),
+# comments STRING,
+# CONSTRAINT files_pkey_file_id PRIMARY KEY (file_id)
+# );
+# # <bam_loader> Creating table 'sq'...
+# # CREATE TABLE bam.sq (
+# sn STRING
NOT NULL,
+# file_id BIGINT NOT
NULL,
+# ln INT,
+# "as" INT,
+# m5
STRING,
+# sp
STRING,
+# ur
STRING,
+# CONSTRAINT sq_pkey_sn_file_id PRIMARY KEY (sn, file_id),
+# CONSTRAINT sq_fkey_file_id FOREIGN KEY (file_id) REFERENCES
bam.files (file_id)
+# );
+# # <bam_loader> Creating table 'rg'...
+# # CREATE TABLE bam.rg (
+# id STRING
NOT NULL,
+# file_id BIGINT NOT
NULL,
+# cn
STRING,
+# ds
STRING,
+# dt
TIMESTAMP,
+# fo
STRING,
+# ks
STRING,
+# lb
STRING,
+# pg
STRING,
+# pi INT,
+# pl
STRING,
+# pu
STRING,
+# sm
STRING,
+# CONSTRAINT rg_pkey_id_file_id PRIMARY KEY (id, file_id),
+# CONSTRAINT rg_fkey_file_id FOREIGN KEY (file_id) REFERENCES
bam.files (file_id)
+# );
+# # <bam_loader> Creating table 'pg'...
+# # CREATE TABLE bam.pg (
+# id STRING
NOT NULL,
+# file_id BIGINT NOT
NULL,
+# pn
STRING,
+# cl
STRING,
+# pp
STRING,
+# vn
STRING,
+# CONSTRAINT pg_pkey_id_file_id PRIMARY KEY (id, file_id),
+# CONSTRAINT pg_fkey_file_id FOREIGN KEY (file_id) REFERENCES
bam.files (file_id)
+# );
+# # <bam_loader> Creating table 'export'...
+# # CREATE TABLE bam.export (
+# qname STRING NOT
NULL,
+# flag SMALLINT
NOT NULL,
+# rname STRING NOT
NULL,
+# pos INT
NOT NULL,
+# mapq SMALLINT
NOT NULL,
+# cigar STRING NOT
NULL,
+# rnext STRING NOT
NULL,
+# pnext INT
NOT NULL,
+# tlen INT
NOT NULL,
+# seq STRING
NOT NULL,
+# qual STRING
NOT NULL
+# );
+# # <bam_loader> Retrieving next file id...
+# # <bam_loader> Initializing BAM wrapper for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file1.bam'...
+# # <bam_loader> Parsing header for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file1.bam'...
+# # <bam_loader> Creating alignment tables for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file1.bam'...
+# # CREATE TABLE bam.alignments_1 (
+# virtual_offset BIGINT NOT NULL,
+# qname STRING NOT
NULL,
+# flag SMALLINT
NOT NULL,
+# rname STRING NOT
NULL,
+# pos INT
NOT NULL,
+# mapq SMALLINT
NOT NULL,
+# cigar STRING NOT
NULL,
+# rnext STRING NOT
NULL,
+# pnext INT
NOT NULL,
+# tlen INT
NOT NULL,
+# seq STRING
NOT NULL,
+# qual STRING
NOT NULL,
+# CONSTRAINT alignments_1_pkey_virtual_offset PRIMARY KEY
(virtual_offset)
+# );
+#
+# CREATE TABLE bam.alignments_extra_1 (
+# tag CHAR(2)
NOT NULL,
+# virtual_offset BIGINT NOT NULL,
+# type CHAR(1)
NOT NULL,
+# value STRING,
+# CONSTRAINT alignments_extra_1_pkey_tag_virtual_offset PRIMARY
KEY (tag, virtual_offset),
+# CONSTRAINT alignments_extra_1_fkey_virtual_offset FOREIGN KEY
(virtual_offset)
+# REFERENCES bam.alignments_1 (virtual_offset)
+# );
+# # <bam_loader> Creating reader threads...
+# # <bam_loader> Waiting for reader threads to finish...
+# # <Thread 0> Starting on next file...
+# # <Thread 0> Processing alignments of file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file1.bam'
(file id 1)...
+# # <Thread 0> All alignments in file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file1.bam'
(file id 1) processed!
+# # <Thread 0> Starting on next file...
+# # <Thread 0> No files left to work on; thread done
+# # <bam_loader> Copying data into DB...
+# # COPY BINARY INTO bam.files FROM ('bam_binaries/1/files_0',
'bam_binaries/1/files_1', 'bam_binaries/1/files_2', 'bam_binaries/1/files_3',
'bam_binaries/1/files_4', 'bam_binaries/1/files_5');
+# COPY BINARY INTO bam.sq FROM ('bam_binaries/1/sq_0',
'bam_binaries/1/sq_1', 'bam_binaries/1/sq_2', 'bam_binaries/1/sq_3',
'bam_binaries/1/sq_4', 'bam_binaries/1/sq_5', 'bam_binaries/1/sq_6');
+# COPY BINARY INTO bam.pg FROM ('bam_binaries/1/pg_0',
'bam_binaries/1/pg_1', 'bam_binaries/1/pg_2', 'bam_binaries/1/pg_3',
'bam_binaries/1/pg_4', 'bam_binaries/1/pg_5');
+# COPY BINARY INTO bam.alignments_1 FROM ('bam_binaries/1/alignments_0',
'bam_binaries/1/alignments_1', 'bam_binaries/1/alignments_2',
'bam_binaries/1/alignments_3', 'bam_binaries/1/alignments_4',
'bam_binaries/1/alignments_5', 'bam_binaries/1/alignments_6',
'bam_binaries/1/alignments_7', 'bam_binaries/1/alignments_8',
'bam_binaries/1/alignments_9', 'bam_binaries/1/alignments_10',
'bam_binaries/1/alignments_11');
+# COPY BINARY INTO bam.alignments_extra_1 FROM
('bam_binaries/1/alignments_extra_0', 'bam_binaries/1/alignments_extra_1',
'bam_binaries/1/alignments_extra_2', 'bam_binaries/1/alignments_extra_3');
+#
+# # <bam_loader>: Loader finished processing 1 BAM file...
+# # <bam_loader>: Loader started for 1 BAM file...
+# # <bam_loader> Retrieving next file id...
+# # <bam_loader> Initializing BAM wrapper for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file2.sam'...
+# # <bam_loader> Parsing header for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file2.sam'...
+# # <bam_loader> Creating alignment tables for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file2.sam'...
+# # CREATE TABLE bam.alignments_2 (
+# virtual_offset BIGINT NOT NULL,
+# qname STRING NOT
NULL,
+# flag SMALLINT
NOT NULL,
+# rname STRING NOT
NULL,
+# pos INT
NOT NULL,
+# mapq SMALLINT
NOT NULL,
+# cigar STRING NOT
NULL,
+# rnext STRING NOT
NULL,
+# pnext INT
NOT NULL,
+# tlen INT
NOT NULL,
+# seq STRING
NOT NULL,
+# qual STRING
NOT NULL,
+# CONSTRAINT alignments_2_pkey_virtual_offset PRIMARY KEY
(virtual_offset)
+# );
+#
+# CREATE TABLE bam.alignments_extra_2 (
+# tag CHAR(2)
NOT NULL,
+# virtual_offset BIGINT NOT NULL,
+# type CHAR(1)
NOT NULL,
+# value STRING,
+# CONSTRAINT alignments_extra_2_pkey_tag_virtual_offset PRIMARY
KEY (tag, virtual_offset),
+# CONSTRAINT alignments_extra_2_fkey_virtual_offset FOREIGN KEY
(virtual_offset)
+# REFERENCES bam.alignments_2 (virtual_offset)
+# );
+# # <bam_loader> Creating reader threads...
+# # <bam_loader> Waiting for reader threads to finish...
+# # <Thread 0> Starting on next file...
+# # <Thread 0> Processing alignments of file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file2.sam'
(file id 2)...
+# # <Thread 0> All alignments in file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file2.sam'
(file id 2) processed!
+# # <Thread 0> Starting on next file...
+# # <Thread 0> No files left to work on; thread done
+# # <bam_loader> Copying data into DB...
+# # COPY BINARY INTO bam.files FROM ('bam_binaries/2/files_0',
'bam_binaries/2/files_1', 'bam_binaries/2/files_2', 'bam_binaries/2/files_3',
'bam_binaries/2/files_4', 'bam_binaries/2/files_5');
+# COPY BINARY INTO bam.sq FROM ('bam_binaries/2/sq_0',
'bam_binaries/2/sq_1', 'bam_binaries/2/sq_2', 'bam_binaries/2/sq_3',
'bam_binaries/2/sq_4', 'bam_binaries/2/sq_5', 'bam_binaries/2/sq_6');
+# COPY BINARY INTO bam.pg FROM ('bam_binaries/2/pg_0',
'bam_binaries/2/pg_1', 'bam_binaries/2/pg_2', 'bam_binaries/2/pg_3',
'bam_binaries/2/pg_4', 'bam_binaries/2/pg_5');
+# COPY BINARY INTO bam.alignments_2 FROM ('bam_binaries/2/alignments_0',
'bam_binaries/2/alignments_1', 'bam_binaries/2/alignments_2',
'bam_binaries/2/alignments_3', 'bam_binaries/2/alignments_4',
'bam_binaries/2/alignments_5', 'bam_binaries/2/alignments_6',
'bam_binaries/2/alignments_7', 'bam_binaries/2/alignments_8',
'bam_binaries/2/alignments_9', 'bam_binaries/2/alignments_10',
'bam_binaries/2/alignments_11');
+# COPY BINARY INTO bam.alignments_extra_2 FROM
('bam_binaries/2/alignments_extra_0', 'bam_binaries/2/alignments_extra_1',
'bam_binaries/2/alignments_extra_2', 'bam_binaries/2/alignments_extra_3');
+#
+# # <bam_loader>: Loader finished processing 1 BAM file...
+# # <bam_loader>: Loader started for 1 BAM file...
+# # <bam_loader> Retrieving next file id...
+# # <bam_loader> Initializing BAM wrapper for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file1.bam'...
+# # <bam_loader> Parsing header for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file1.bam'...
+# # <bam_loader> Checking sortedness for BAM file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file1.bam'...
+# # <bam_loader> Creating alignment tables for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file1.bam'...
+# # CREATE TABLE bam.paired_primary_alignments_3 (
+# l_virtual_offset BIGINT NOT
NULL,
+# r_virtual_offset BIGINT NOT
NULL,
+# qname STRING NOT
NULL,
+# l_flag SMALLINT
NOT NULL,
+# l_rname STRING NOT
NULL,
+# l_pos INT
NOT NULL,
+# l_mapq SMALLINT
NOT NULL,
+# l_cigar STRING NOT
NULL,
+# l_rnext STRING NOT
NULL,
+# l_pnext INT NOT
NULL,
+# l_tlen INT
NOT NULL,
_______________________________________________
checkin-list mailing list
checkin-list@monetdb.org
https://www.monetdb.org/mailman/listinfo/checkin-list
