Changeset: 7eada97fdec5 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=7eada97fdec5
Added Files:
sql/backends/monet5/vaults/bam/85_bam.mal
sql/backends/monet5/vaults/bam/85_bam.sql
sql/backends/monet5/vaults/bam/BAMRecipe.pdf
sql/backends/monet5/vaults/bam/Makefile.ag
sql/backends/monet5/vaults/bam/Tests/All
sql/backends/monet5/vaults/bam/Tests/bam.py
sql/backends/monet5/vaults/bam/Tests/bam_export.SQL.py
sql/backends/monet5/vaults/bam/Tests/bam_lib.reqtests
sql/backends/monet5/vaults/bam/Tests/bam_lib.sql
sql/backends/monet5/vaults/bam/Tests/bam_lib.stable.err
sql/backends/monet5/vaults/bam/Tests/bam_lib.stable.out
sql/backends/monet5/vaults/bam/Tests/bam_lib_mal.mal
sql/backends/monet5/vaults/bam/Tests/bam_lib_mal.stable.err
sql/backends/monet5/vaults/bam/Tests/bam_lib_mal.stable.out
sql/backends/monet5/vaults/bam/Tests/bam_loader_file.SQL.py
sql/backends/monet5/vaults/bam/Tests/bam_loader_file.stable.err
sql/backends/monet5/vaults/bam/Tests/bam_loader_file.stable.out
sql/backends/monet5/vaults/bam/Tests/bam_loader_files.SQL.py
sql/backends/monet5/vaults/bam/Tests/bam_loader_files.stable.err
sql/backends/monet5/vaults/bam/Tests/bam_loader_files.stable.out
sql/backends/monet5/vaults/bam/Tests/bam_loader_repos.SQL.py
sql/backends/monet5/vaults/bam/Tests/bam_loader_repos.stable.err
sql/backends/monet5/vaults/bam/Tests/bam_loader_repos.stable.out
sql/backends/monet5/vaults/bam/Tests/check_files.reqtests
sql/backends/monet5/vaults/bam/Tests/check_files.sql
sql/backends/monet5/vaults/bam/Tests/check_files.stable.err
sql/backends/monet5/vaults/bam/Tests/check_files.stable.out
sql/backends/monet5/vaults/bam/Tests/check_files_exact.sql
sql/backends/monet5/vaults/bam/Tests/check_files_exact.stable.err
sql/backends/monet5/vaults/bam/Tests/check_files_exact.stable.out
sql/backends/monet5/vaults/bam/Tests/coverage_usecase.reqtests
sql/backends/monet5/vaults/bam/Tests/coverage_usecase.sql
sql/backends/monet5/vaults/bam/Tests/drop_last_files.SQL.py
sql/backends/monet5/vaults/bam/Tests/drop_last_files.stable.err
sql/backends/monet5/vaults/bam/Tests/drop_last_files.stable.out
sql/backends/monet5/vaults/bam/Tests/files/file1.bam
sql/backends/monet5/vaults/bam/Tests/files/file2.sam
sql/backends/monet5/vaults/bam/Tests/files/queryname/file1.bam
sql/backends/monet5/vaults/bam/Tests/files/queryname/file2.sam
sql/backends/monet5/vaults/bam/Tests/mergetable.reqtests
sql/backends/monet5/vaults/bam/Tests/mergetable.sql
sql/backends/monet5/vaults/bam/Tests/mergetable.stable.err
sql/backends/monet5/vaults/bam/Tests/mergetable.stable.out
sql/backends/monet5/vaults/bam/Tests/query1.1.reqtests
sql/backends/monet5/vaults/bam/Tests/query1.1.sql
sql/backends/monet5/vaults/bam/Tests/query1.1.stable.err
sql/backends/monet5/vaults/bam/Tests/query1.1.stable.out
sql/backends/monet5/vaults/bam/Tests/query1.2.reqtests
sql/backends/monet5/vaults/bam/Tests/query1.2.sql
sql/backends/monet5/vaults/bam/Tests/query1.2.stable.err
sql/backends/monet5/vaults/bam/Tests/query1.2.stable.out
sql/backends/monet5/vaults/bam/Tests/query1.3.reqtests
sql/backends/monet5/vaults/bam/Tests/query1.3.sql
sql/backends/monet5/vaults/bam/Tests/query1.3.stable.err
sql/backends/monet5/vaults/bam/Tests/query1.3.stable.out
sql/backends/monet5/vaults/bam/Tests/query1.4.reqtests
sql/backends/monet5/vaults/bam/Tests/query1.4.sql
sql/backends/monet5/vaults/bam/Tests/query1.4.stable.err
sql/backends/monet5/vaults/bam/Tests/query1.4.stable.out
sql/backends/monet5/vaults/bam/Tests/query1.5.reqtests
sql/backends/monet5/vaults/bam/Tests/query1.5.sql
sql/backends/monet5/vaults/bam/Tests/query1.5.stable.err
sql/backends/monet5/vaults/bam/Tests/query1.5.stable.out
sql/backends/monet5/vaults/bam/Tests/query1.6.reqtests
sql/backends/monet5/vaults/bam/Tests/query1.6.sql
sql/backends/monet5/vaults/bam/Tests/query2.1.reqtests
sql/backends/monet5/vaults/bam/Tests/query2.1.sql
sql/backends/monet5/vaults/bam/Tests/query2.1.stable.err
sql/backends/monet5/vaults/bam/Tests/query2.1.stable.out
sql/backends/monet5/vaults/bam/Tests/query2.10.reqtests
sql/backends/monet5/vaults/bam/Tests/query2.10.sql
sql/backends/monet5/vaults/bam/Tests/query2.10.stable.err
sql/backends/monet5/vaults/bam/Tests/query2.10.stable.out
sql/backends/monet5/vaults/bam/Tests/query2.11.reqtests
sql/backends/monet5/vaults/bam/Tests/query2.11.sql
sql/backends/monet5/vaults/bam/Tests/query2.11.stable.err
sql/backends/monet5/vaults/bam/Tests/query2.11.stable.out
sql/backends/monet5/vaults/bam/Tests/query2.12.reqtests
sql/backends/monet5/vaults/bam/Tests/query2.12.sql
sql/backends/monet5/vaults/bam/Tests/query2.12.stable.err
sql/backends/monet5/vaults/bam/Tests/query2.12.stable.out
sql/backends/monet5/vaults/bam/Tests/query2.12.stable.out.int128
sql/backends/monet5/vaults/bam/Tests/query2.2.reqtests
sql/backends/monet5/vaults/bam/Tests/query2.2.sql
sql/backends/monet5/vaults/bam/Tests/query2.2.stable.err
sql/backends/monet5/vaults/bam/Tests/query2.2.stable.out
sql/backends/monet5/vaults/bam/Tests/query2.2.stable.out.int128
sql/backends/monet5/vaults/bam/Tests/query2.3.reqtests
sql/backends/monet5/vaults/bam/Tests/query2.3.sql
sql/backends/monet5/vaults/bam/Tests/query2.3.stable.err
sql/backends/monet5/vaults/bam/Tests/query2.3.stable.out
sql/backends/monet5/vaults/bam/Tests/query2.4.reqtests
sql/backends/monet5/vaults/bam/Tests/query2.4.sql
sql/backends/monet5/vaults/bam/Tests/query2.4.stable.err
sql/backends/monet5/vaults/bam/Tests/query2.4.stable.out
sql/backends/monet5/vaults/bam/Tests/query2.5.reqtests
sql/backends/monet5/vaults/bam/Tests/query2.5.sql
sql/backends/monet5/vaults/bam/Tests/query2.5.stable.err
sql/backends/monet5/vaults/bam/Tests/query2.5.stable.out
sql/backends/monet5/vaults/bam/Tests/query2.5.stable.out.int128
sql/backends/monet5/vaults/bam/Tests/query2.6.reqtests
sql/backends/monet5/vaults/bam/Tests/query2.6.sql
sql/backends/monet5/vaults/bam/Tests/query2.6.stable.err
sql/backends/monet5/vaults/bam/Tests/query2.6.stable.out
sql/backends/monet5/vaults/bam/Tests/query2.7.reqtests
sql/backends/monet5/vaults/bam/Tests/query2.7.sql
sql/backends/monet5/vaults/bam/Tests/query2.7.stable.err
sql/backends/monet5/vaults/bam/Tests/query2.7.stable.out
sql/backends/monet5/vaults/bam/Tests/query2.8.reqtests
sql/backends/monet5/vaults/bam/Tests/query2.8.sql
sql/backends/monet5/vaults/bam/Tests/query2.8.stable.err
sql/backends/monet5/vaults/bam/Tests/query2.8.stable.out
sql/backends/monet5/vaults/bam/Tests/query2.9.reqtests
sql/backends/monet5/vaults/bam/Tests/query2.9.sql
sql/backends/monet5/vaults/bam/Tests/query2.9.stable.err
sql/backends/monet5/vaults/bam/Tests/query2.9.stable.out
sql/backends/monet5/vaults/bam/Tests/sam_export.SQL.py
sql/backends/monet5/vaults/bam/Tests/sam_export.reqtests
sql/backends/monet5/vaults/bam/Tests/sam_export.stable.err
sql/backends/monet5/vaults/bam/Tests/sam_export.stable.out
sql/backends/monet5/vaults/bam/Tests/sql/bam_export.sql
sql/backends/monet5/vaults/bam/Tests/sql/bam_loader_file.sql
sql/backends/monet5/vaults/bam/Tests/sql/bam_loader_files.sql
sql/backends/monet5/vaults/bam/Tests/sql/bam_loader_repos.sql
sql/backends/monet5/vaults/bam/Tests/sql/sam_export.sql
sql/backends/monet5/vaults/bam/Tests/verify_load.sql
sql/backends/monet5/vaults/bam/Tests/verify_load.stable.err
sql/backends/monet5/vaults/bam/Tests/verify_load.stable.out
sql/backends/monet5/vaults/bam/bam.mal
sql/backends/monet5/vaults/bam/bam_db_interface.c
sql/backends/monet5/vaults/bam/bam_db_interface.h
sql/backends/monet5/vaults/bam/bam_export.c
sql/backends/monet5/vaults/bam/bam_export.h
sql/backends/monet5/vaults/bam/bam_globals.c
sql/backends/monet5/vaults/bam/bam_globals.h
sql/backends/monet5/vaults/bam/bam_lib.c
sql/backends/monet5/vaults/bam/bam_lib.h
sql/backends/monet5/vaults/bam/bam_loader.c
sql/backends/monet5/vaults/bam/bam_loader.h
sql/backends/monet5/vaults/bam/bam_wrapper.c
sql/backends/monet5/vaults/bam/bam_wrapper.h
sql/backends/monet5/vaults/bam/default_schema.dia
sql/backends/monet5/vaults/bam/default_schema.png
sql/backends/monet5/vaults/bam/metadata.dia
sql/backends/monet5/vaults/bam/metadata.png
sql/backends/monet5/vaults/bam/mykstring.h
sql/backends/monet5/vaults/bam/paired_schema.dia
sql/backends/monet5/vaults/bam/paired_schema.png
Removed Files:
sql/backends/monet5/bam/85_bam.mal
sql/backends/monet5/bam/85_bam.sql
sql/backends/monet5/bam/BAMRecipe.pdf
sql/backends/monet5/bam/Makefile.ag
sql/backends/monet5/bam/Tests/All
sql/backends/monet5/bam/Tests/bam.py
sql/backends/monet5/bam/Tests/bam_export.SQL.py
sql/backends/monet5/bam/Tests/bam_lib.reqtests
sql/backends/monet5/bam/Tests/bam_lib.sql
sql/backends/monet5/bam/Tests/bam_lib.stable.err
sql/backends/monet5/bam/Tests/bam_lib.stable.out
sql/backends/monet5/bam/Tests/bam_lib_mal.mal
sql/backends/monet5/bam/Tests/bam_lib_mal.stable.err
sql/backends/monet5/bam/Tests/bam_lib_mal.stable.out
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.reqtests
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/coverage_usecase.reqtests
sql/backends/monet5/bam/Tests/coverage_usecase.sql
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/files/file1.bam
sql/backends/monet5/bam/Tests/files/file2.sam
sql/backends/monet5/bam/Tests/files/queryname/file1.bam
sql/backends/monet5/bam/Tests/files/queryname/file2.sam
sql/backends/monet5/bam/Tests/mergetable.reqtests
sql/backends/monet5/bam/Tests/mergetable.sql
sql/backends/monet5/bam/Tests/mergetable.stable.err
sql/backends/monet5/bam/Tests/mergetable.stable.out
sql/backends/monet5/bam/Tests/query1.1.reqtests
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.reqtests
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.reqtests
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.reqtests
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.reqtests
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.reqtests
sql/backends/monet5/bam/Tests/query1.6.sql
sql/backends/monet5/bam/Tests/query2.1.reqtests
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.reqtests
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.reqtests
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.reqtests
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/query2.12.stable.out.int128
sql/backends/monet5/bam/Tests/query2.2.reqtests
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/query2.2.stable.out.int128
sql/backends/monet5/bam/Tests/query2.3.reqtests
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.reqtests
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.reqtests
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/query2.5.stable.out.int128
sql/backends/monet5/bam/Tests/query2.6.reqtests
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.reqtests
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.reqtests
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.reqtests
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.reqtests
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/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
sql/backends/monet5/bam/bam.mal
sql/backends/monet5/bam/bam_db_interface.c
sql/backends/monet5/bam/bam_db_interface.h
sql/backends/monet5/bam/bam_export.c
sql/backends/monet5/bam/bam_export.h
sql/backends/monet5/bam/bam_globals.c
sql/backends/monet5/bam/bam_globals.h
sql/backends/monet5/bam/bam_lib.c
sql/backends/monet5/bam/bam_lib.h
sql/backends/monet5/bam/bam_loader.c
sql/backends/monet5/bam/bam_loader.h
sql/backends/monet5/bam/bam_wrapper.c
sql/backends/monet5/bam/bam_wrapper.h
sql/backends/monet5/bam/default_schema.dia
sql/backends/monet5/bam/default_schema.png
sql/backends/monet5/bam/metadata.dia
sql/backends/monet5/bam/metadata.png
sql/backends/monet5/bam/mykstring.h
sql/backends/monet5/bam/paired_schema.dia
sql/backends/monet5/bam/paired_schema.png
Modified Files:
configure.ag
sql/backends/monet5/Makefile.ag
sql/backends/monet5/vaults/Makefile.ag
Branch: default
Log Message:
Restructure BAM/SAM code
- Moved to the vaults dir
-- Fix unit tests
- Configure make
- Allow the BAM/SAM module to be built with both the samtools/*.h and bam/*.h
configurations
This allows the module to be built with the default libs installed on most
system (or OS X, at least)
diffs (truncated from 2588 to 300 lines):
diff --git a/configure.ag b/configure.ag
--- a/configure.ag
+++ b/configure.ag
@@ -2390,18 +2390,42 @@ if test "x$have_samtools" != xno; then
AC_CHECK_HEADER(samtools/bam.h,
[ why_have_samtools= ],
- [ why_have_samtools="samtools/bam.h header not found" ])
+ [ why_have_samtools="bam.h header not found" ])
+ if test -n "$why_have_samtools"; then
+ AC_CHECK_HEADER(bam/bam.h,
+ [ why_have_samtools= ],
+ [ why_have_samtools="Neither samtools/bam.h or
bam/bam.h header not found" ])
+ fi
+
+ if test -z "$why_have_samtools"; then
+ AC_CHECK_HEADER(samtools/sam.h,
+ [ why_have_samtools= ],
+ [ why_have_samtools="sam.h header not found" ])
+ fi
+ if test -n "$why_have_samtools"; then
+ AC_CHECK_HEADER(bam/sam.h,
+ [ why_have_samtools= ],
+ [ why_have_samtools="Neither samtools/sam.h or
bam/sam.h header not found" ])
+ fi
+
if test -z "$why_have_samtools"; then
AC_CHECK_HEADER(samtools/bgzf.h,
[ why_have_samtools= ],
- [ why_have_samtools="samtools/bgzf.h header not found"
])
+ [ why_have_samtools="bgzf.h header not found" ])
fi
+ if test -n "$why_have_samtools"; then
+ AC_CHECK_HEADER(bam/bgzf.h,
+ [ why_have_samtools= ],
+ [ why_have_samtools="Neither samtool/bgzf.h nor
bam/bgzf.h header not found" ])
+ fi
+
if test -z "$why_have_samtools"; then
AC_CHECK_LIB(bam, bam_header_read,
- AC_DEFINE(HAVE_SAMTOOLS, 1, [Define if you have the
samtools (providing the bam library)]),
+ AC_DEFINE(HAVE_SAMTOOLS, 1, [Define if you have the
samtools version 0.1.x (providing the bam library)]),
[ why_have_samtools="bam library not found" ],
[-lm -lpthread -lz])
fi
+
if test -n "$why_have_samtools"; then
if test "x$have_samtools" != xauto; then
AC_MSG_ERROR([$why_have_samtools])
diff --git a/sql/backends/monet5/Makefile.ag b/sql/backends/monet5/Makefile.ag
--- a/sql/backends/monet5/Makefile.ag
+++ b/sql/backends/monet5/Makefile.ag
@@ -4,7 +4,7 @@
#
# Copyright 2008-2015 MonetDB B.V.
-SUBDIRS = NOT_WIN32?vaults UDF HAVE_SAMTOOLS?bam LSST HAVE_GSL?gsl generator
+SUBDIRS = NOT_WIN32?vaults UDF LSST HAVE_GSL?gsl generator
INCLUDES = ../../include ../../common ../../storage ../../server \
../../../monetdb5/modules/atoms \
diff --git a/sql/backends/monet5/vaults/Makefile.ag
b/sql/backends/monet5/vaults/Makefile.ag
--- a/sql/backends/monet5/vaults/Makefile.ag
+++ b/sql/backends/monet5/vaults/Makefile.ag
@@ -4,6 +4,8 @@
#
# Copyright 2008-2015 MonetDB B.V.
+SUBDIRS = HAVE_SAMTOOLS?bam
+
INCLUDES = ../../../include \
../../../common \
../../../storage \
diff --git a/sql/backends/monet5/bam/85_bam.mal
b/sql/backends/monet5/vaults/bam/85_bam.mal
rename from sql/backends/monet5/bam/85_bam.mal
rename to sql/backends/monet5/vaults/bam/85_bam.mal
diff --git a/sql/backends/monet5/bam/85_bam.sql
b/sql/backends/monet5/vaults/bam/85_bam.sql
rename from sql/backends/monet5/bam/85_bam.sql
rename to sql/backends/monet5/vaults/bam/85_bam.sql
diff --git a/sql/backends/monet5/bam/BAMRecipe.pdf
b/sql/backends/monet5/vaults/bam/BAMRecipe.pdf
rename from sql/backends/monet5/bam/BAMRecipe.pdf
rename to sql/backends/monet5/vaults/bam/BAMRecipe.pdf
diff --git a/sql/backends/monet5/bam/Makefile.ag
b/sql/backends/monet5/vaults/bam/Makefile.ag
rename from sql/backends/monet5/bam/Makefile.ag
rename to sql/backends/monet5/vaults/bam/Makefile.ag
--- a/sql/backends/monet5/bam/Makefile.ag
+++ b/sql/backends/monet5/vaults/bam/Makefile.ag
@@ -4,22 +4,23 @@
#
# Copyright 2008-2015 MonetDB B.V.
-INCLUDES = .. \
- ../../../include \
- ../../../common \
- ../../../storage \
- ../../../server \
- ../../../../monetdb5/modules/atoms \
- ../../../../monetdb5/modules/kernel \
- ../../../../monetdb5/mal \
- ../../../../monetdb5/modules/mal \
- ../../../../monetdb5/optimizer \
- ../../../../clients/mapilib \
- ../../../../common/options \
- ../../../../common/stream \
- ../../../../gdk \
- ../../../../tools/merovingian \
- ../../../../tools/merovingian/daemon \
+INCLUDES = ../ \
+ ../../ \
+ ../../../../include \
+ ../../../../common \
+ ../../../../storage \
+ ../../../../server \
+ ../../../../../monetdb5/modules/atoms \
+ ../../../../../monetdb5/modules/kernel \
+ ../../../../../monetdb5/mal \
+ ../../../../../monetdb5/modules/mal \
+ ../../../../../monetdb5/optimizer \
+ ../../../../../clients/mapilib \
+ ../../../../../common/options \
+ ../../../../../common/stream \
+ ../../../../../gdk \
+ ../../../../../tools/merovingian \
+ ../../../../../tools/merovingian/daemon \
$(SAMTOOLS_CFLAGS)
lib__bam = {
@@ -32,8 +33,8 @@ lib__bam = {
bam_lib.c bam_lib.h \
bam_export.c bam_export.h \
mykstring.h
- LIBS = ../../../../monetdb5/tools/libmonetdb5 \
- ../../../../gdk/libbat \
+ LIBS = ../../../../../monetdb5/tools/libmonetdb5 \
+ ../../../../../gdk/libbat \
$(SAMTOOLS_LIBS)
}
diff --git a/sql/backends/monet5/bam/Tests/All
b/sql/backends/monet5/vaults/bam/Tests/All
rename from sql/backends/monet5/bam/Tests/All
rename to sql/backends/monet5/vaults/bam/Tests/All
diff --git a/sql/backends/monet5/bam/Tests/bam.py
b/sql/backends/monet5/vaults/bam/Tests/bam.py
rename from sql/backends/monet5/bam/Tests/bam.py
rename to sql/backends/monet5/vaults/bam/Tests/bam.py
diff --git a/sql/backends/monet5/bam/Tests/bam_export.SQL.py
b/sql/backends/monet5/vaults/bam/Tests/bam_export.SQL.py
rename from sql/backends/monet5/bam/Tests/bam_export.SQL.py
rename to sql/backends/monet5/vaults/bam/Tests/bam_export.SQL.py
diff --git a/sql/backends/monet5/bam/Tests/bam_lib.reqtests
b/sql/backends/monet5/vaults/bam/Tests/bam_lib.reqtests
rename from sql/backends/monet5/bam/Tests/bam_lib.reqtests
rename to sql/backends/monet5/vaults/bam/Tests/bam_lib.reqtests
diff --git a/sql/backends/monet5/bam/Tests/bam_lib.sql
b/sql/backends/monet5/vaults/bam/Tests/bam_lib.sql
rename from sql/backends/monet5/bam/Tests/bam_lib.sql
rename to sql/backends/monet5/vaults/bam/Tests/bam_lib.sql
diff --git a/sql/backends/monet5/bam/Tests/bam_lib.stable.err
b/sql/backends/monet5/vaults/bam/Tests/bam_lib.stable.err
rename from sql/backends/monet5/bam/Tests/bam_lib.stable.err
rename to sql/backends/monet5/vaults/bam/Tests/bam_lib.stable.err
--- a/sql/backends/monet5/bam/Tests/bam_lib.stable.err
+++ b/sql/backends/monet5/vaults/bam/Tests/bam_lib.stable.err
@@ -1,4 +1,4 @@
-stderr of test 'bam_lib` in directory 'sql/backends/monet5/bam` itself:
+stderr of test 'bam_lib` in directory 'sql/backends/monet5/vaults/bam` itself:
# 14:48:31 >
diff --git a/sql/backends/monet5/bam/Tests/bam_lib.stable.out
b/sql/backends/monet5/vaults/bam/Tests/bam_lib.stable.out
rename from sql/backends/monet5/bam/Tests/bam_lib.stable.out
rename to sql/backends/monet5/vaults/bam/Tests/bam_lib.stable.out
--- a/sql/backends/monet5/bam/Tests/bam_lib.stable.out
+++ b/sql/backends/monet5/vaults/bam/Tests/bam_lib.stable.out
@@ -1,4 +1,4 @@
-stdout of test 'bam_lib` in directory 'sql/backends/monet5/bam` itself:
+stdout of test 'bam_lib` in directory 'sql/backends/monet5/vaults/bam` itself:
# 14:48:31 >
diff --git a/sql/backends/monet5/bam/Tests/bam_lib_mal.mal
b/sql/backends/monet5/vaults/bam/Tests/bam_lib_mal.mal
rename from sql/backends/monet5/bam/Tests/bam_lib_mal.mal
rename to sql/backends/monet5/vaults/bam/Tests/bam_lib_mal.mal
diff --git a/sql/backends/monet5/bam/Tests/bam_lib_mal.stable.err
b/sql/backends/monet5/vaults/bam/Tests/bam_lib_mal.stable.err
rename from sql/backends/monet5/bam/Tests/bam_lib_mal.stable.err
rename to sql/backends/monet5/vaults/bam/Tests/bam_lib_mal.stable.err
--- a/sql/backends/monet5/bam/Tests/bam_lib_mal.stable.err
+++ b/sql/backends/monet5/vaults/bam/Tests/bam_lib_mal.stable.err
@@ -1,4 +1,4 @@
-stderr of test 'bam_lib_mal` in directory 'sql/backends/monet5/bam` itself:
+stderr of test 'bam_lib_mal` in directory 'sql/backends/monet5/vaults/bam`
itself:
# 16:51:57 >
diff --git a/sql/backends/monet5/bam/Tests/bam_lib_mal.stable.out
b/sql/backends/monet5/vaults/bam/Tests/bam_lib_mal.stable.out
rename from sql/backends/monet5/bam/Tests/bam_lib_mal.stable.out
rename to sql/backends/monet5/vaults/bam/Tests/bam_lib_mal.stable.out
--- a/sql/backends/monet5/bam/Tests/bam_lib_mal.stable.out
+++ b/sql/backends/monet5/vaults/bam/Tests/bam_lib_mal.stable.out
@@ -1,4 +1,4 @@
-stdout of test 'bam_lib_mal` in directory 'sql/backends/monet5/bam` itself:
+stdout of test 'bam_lib_mal` in directory 'sql/backends/monet5/vaults/bam`
itself:
# 16:51:57 >
diff --git a/sql/backends/monet5/bam/Tests/bam_loader_file.SQL.py
b/sql/backends/monet5/vaults/bam/Tests/bam_loader_file.SQL.py
rename from sql/backends/monet5/bam/Tests/bam_loader_file.SQL.py
rename to sql/backends/monet5/vaults/bam/Tests/bam_loader_file.SQL.py
diff --git a/sql/backends/monet5/bam/Tests/bam_loader_file.stable.err
b/sql/backends/monet5/vaults/bam/Tests/bam_loader_file.stable.err
rename from sql/backends/monet5/bam/Tests/bam_loader_file.stable.err
rename to sql/backends/monet5/vaults/bam/Tests/bam_loader_file.stable.err
--- a/sql/backends/monet5/bam/Tests/bam_loader_file.stable.err
+++ b/sql/backends/monet5/vaults/bam/Tests/bam_loader_file.stable.err
@@ -1,4 +1,4 @@
-stderr of test 'bam_loader_file` in directory 'sql/backends/monet5/bam` itself:
+stderr of test 'bam_loader_file` in directory 'sql/backends/monet5/vaults/bam`
itself:
# 10:22:37 >
@@ -91,9 +91,9 @@ stderr of test 'bam_loader_file` in dire
# 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'...
+# # <bam_loader> Initializing BAM wrapper for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/vaults/bam/Tests/files/file1.bam'...
+# # <bam_loader> Parsing header for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/vaults/bam/Tests/files/file1.bam'...
+# # <bam_loader> Creating alignment tables for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/vaults/bam/Tests/files/file1.bam'...
# # CREATE TABLE bam.alignments_1 (
# virtual_offset BIGINT NOT NULL,
# qname STRING NOT
NULL,
@@ -122,8 +122,8 @@ stderr of test 'bam_loader_file` in dire
# # <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> Processing alignments of file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/vaults/bam/Tests/files/file1.bam'
(file id 1)...
+# # <Thread 0> All alignments in file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/vaults/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...
@@ -136,9 +136,9 @@ stderr of test 'bam_loader_file` in dire
# # <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'...
+# # <bam_loader> Initializing BAM wrapper for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/vaults/bam/Tests/files/file2.sam'...
+# # <bam_loader> Parsing header for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/vaults/bam/Tests/files/file2.sam'...
+# # <bam_loader> Creating alignment tables for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/vaults/bam/Tests/files/file2.sam'...
# # CREATE TABLE bam.alignments_2 (
# virtual_offset BIGINT NOT NULL,
# qname STRING NOT
NULL,
@@ -167,8 +167,8 @@ stderr of test 'bam_loader_file` in dire
# # <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> Processing alignments of file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/vaults/bam/Tests/files/file2.sam'
(file id 2)...
+# # <Thread 0> All alignments in file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/vaults/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...
@@ -181,10 +181,10 @@ stderr of test 'bam_loader_file` in dire
# # <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'...
+# # <bam_loader> Initializing BAM wrapper for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/vaults/bam/Tests/files/queryname/file1.bam'...
+# # <bam_loader> Parsing header for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/vaults/bam/Tests/files/queryname/file1.bam'...
+# # <bam_loader> Checking sortedness for BAM file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/vaults/bam/Tests/files/queryname/file1.bam'...
+# # <bam_loader> Creating alignment tables for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/vaults/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,
@@ -295,8 +295,8 @@ stderr of test 'bam_loader_file` in dire
# # <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/queryname/file1.bam'
(file id 3)...
-# # <Thread 0> All alignments in file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file1.bam'
(file id 3) processed!
+# # <Thread 0> Processing alignments of file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/vaults/bam/Tests/files/queryname/file1.bam'
(file id 3)...
+# # <Thread 0> All alignments in file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/vaults/bam/Tests/files/queryname/file1.bam'
(file id 3) processed!
# # <Thread 0> Starting on next file...
# # <Thread 0> No files left to work on; thread done
# # <bam_loader> Copying data into DB...
@@ -311,10 +311,10 @@ stderr of test 'bam_loader_file` in dire
# # <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/file2.sam'...
-# # <bam_loader> Parsing header for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file2.sam'...
-# # <bam_loader> Checking sortedness for BAM file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file2.sam'...
-# # <bam_loader> Creating alignment tables for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file2.sam'...
+# # <bam_loader> Initializing BAM wrapper for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/vaults/bam/Tests/files/queryname/file2.sam'...
+# # <bam_loader> Parsing header for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/vaults/bam/Tests/files/queryname/file2.sam'...
+# # <bam_loader> Checking sortedness for BAM file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/vaults/bam/Tests/files/queryname/file2.sam'...
+# # <bam_loader> Creating alignment tables for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/vaults/bam/Tests/files/queryname/file2.sam'...
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