.gitignore

@@ -21,3 +21,4 @@
 /.cproject
 /.project
 /.pydevproject
+tmp.kfg
\ No newline at end of file

CHANGES.md

 # NCBI External Developer Release:
 
 
+## SRA Toolkit 2.9.0
+**February 23, 2018**
+
+  **bam-load**: an issue with accessing WGS accessions was fixed  
+  **bam-load**: bam-load will generate an error and quit when too many spots have been encountered  
+  **bam-load**: renamed an internal function to avoid a name conflict  
+  **bam-load, fastq-load**: updated to use better thread termination signaling  
+  **bam-load, sra-stat**: Updated sra-stat to extract statistics of alterations made by loaders for inclusion in its report  
+  **build**: Created a script that allows to add a new volume to existing repository  
+  **build**: Fixed configure allowing to run it on Perl with version >= v5.26 that has "." removed from @INC  
+  **build**: added "smoke tests"  
+  **build**: recognize version of libhdf5 that does not allow static linking and do not try to use it  
+  **build, doc**: added wiki page: Building-from-source-:--configure-options-explained  
+  **build, ncbi-vdb, sra-tools**: the installation script now saves configuration files if they were modified by the user  
+  **build, sra-tools**: "make runtests" now invokes "make all"  
+  **build, vdb-sql**: modified build to avoid vdb-sql in absence of libxml2  
+  **fastq-dump**: minor change to help text  
+  **fastq-dump, vdb**: Fixed crashing of fastq-dump when dumping multiple runs with -split-3 option specified  
+  **fastq-load**: preserves spot names when the platform is Illumina  
+  **kfg**: added searching of configuration files in ../etc/ncbi/ relative to the binaries  
+  **kfg, prefetch**: set limit of Aspera usage to 450m  
+  **kfg, prefetch, remote-fuser, vfs**: Updated resolving of cache location of non-accession objects  
+  **klib**: Reverted KTimeMakeTime to use UTC  
+  **kns**: Accept the same http_proxy specifications as wget  
+  **kns**: Added possibility to report server's IP address after network error  
+  **kns**: Ignore HTTP headers sent multiple times  
+  **kns**: Improved reporting of network errors  
+  **kns**: fixed generation of invalid error code in response to dropped connection  
+  **latf-load**: now processing multi-line sequences and qualities  
+  **latf-load**: pacbio spot names with a range are now processed correctly  
+  **pileup-stats**: pileup-stats now exits with code 3 if called without arguments  
+  **prefetch**: fixed a bug in prefech when it printed invalid error messages after failure of reading from server  
+  **sra-search**: added option --fasta for output in FASTA format  
+  **sra-search**: added option to display version number  
+  **sra-search**: added option to search unaligned and partially aligned fragments only  
+  **sra-search**: improved performance in reference-driven mode  
+  **sra-search**: various efficiency/readability improvements in the code   
+  **sra-sort**: Created a separate version  of sra-sort for Complete Genomics  
+  **sra-sort**: Fixed race condition in sra-sort when result was not completed when using fast drives  
+  **sra-stat**: Added calculation of N50, L50, N90, L90 statistics  
+  **sra-stat**: Fixed: sra-stat prints the path of alignment reference when the path is remote (http)  
+  **sra-stat**: Improved performance when calculating bases statistics  
+  **sra-stat**: The maximum number of reads that can be processed was Increased to 4K.  
+  **sra-tools, vdb**: access to vdb/ngs via SQLite  
+  **srapath**: srapath allows to get results of name resolver CGI  
+  **vdb-config**: vdb-config does not fail when /repository/user/default-path is not set in configuration  
+  **vdb-validate**: added a check of sum(READ_LEN) against length(READ)  
+  **vfs**: Name resolving service was updated and switched to protocol version 3.0  
+
+
 ## SRA Toolkit 2.8.2
 **March 6, 2017**
 
@@ -191,5 +241,3 @@
   **var-expand**: a tool for batch variation expansion  
   **vdb-config**: now handles standard options such as --option-file  
   **vdb-validate**: Added code to continue with the next row when column has discontiguous blobs  
-
-

build/Makefile.env

@@ -366,7 +366,7 @@ LDFLAGS = $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(LDPATHS)
 # MallocScribble=1 is for catching allocation problems on Mac
 #
 ifeq ($(RUNTESTS_OVERRIDE),)
-runtests: std $(TEST_TOOLS)
+runtests: all $(TEST_TOOLS)
 	@ export VDB_CONFIG=$(VDB_CONFIG);export LD_LIBRARY_PATH=$(LIBDIR):$$LD_LIBRARY_PATH;export MallocScribble=1;\
 	for i in $(TEST_TOOLS);\
 	do\
@@ -384,7 +384,7 @@ endif
 # $(SLOWTESTSDATADIR) should be used to create temporary test files
 SLOWTESTSDATADIR ?= /panfs/pan1.be-md.ncbi.nlm.nih.gov/sra-test/slowtests/$(shell whoami)
 
-slowtests: std $(SLOW_TEST_TOOLS)
+slowtests: all $(SLOW_TEST_TOOLS)
 	@ export LD_LIBRARY_PATH=$(LIBDIR):$$LD_LIBRARY_PATH;\
 	for i in $(SLOW_TEST_TOOLS);\
 	do\

build/Makefile.install

@@ -44,6 +44,18 @@ endif
 #fake root for debugging
 #uncomment this line and change the test for root ( see under install: ) to succeed:
 #ROOT = ~/root
+ifeq (linux, $(OS))
+    ifeq (0, $(shell id -u))
+        LINUX_ROOT = true
+    endif
+endif
+
+ifeq (true, $(LINUX_ROOT))
+    KONFIG_DIR = $(ROOT)/etc/ncbi
+    PROFILE_FILE = $(ROOT)/etc/profile.d/ncbi-vdb
+else
+    KONFIG_DIR = $(INST_BINDIR)/ncbi
+endif
 
 EXE_TARGET = $(INST_BINDIR)
 PROFILE_FILE = $(ROOT)/etc/profile.d/sra-tools
@@ -62,31 +74,17 @@ $(TOOLS_TO_INSTALL):
       $(COPY) $(BINDIR)/$@$(EXEX) $(BINDIR)/$@$(VERSION_EXEX) $(BINDIR)/$@$(MAJVERS_EXEX) $(INST_BINDIR) && \
       echo "done"
 
-ifeq (linux, $(OS))
-    ifeq (0, $(shell id -u))
-        LINUX_ROOT = true
-    endif
-endif
+copykfg:
+	@ echo "Installing configuration files to $(KONFIG_DIR)"
+	@ $(TOP)/build/install-kfg.sh default.kfg   $(BINDIR)/ncbi          $(KONFIG_DIR) $(TOP)/shared/kfgsums
+	@ $(TOP)/build/install-kfg.sh certs.kfg     $(BINDIR)/ncbi          $(KONFIG_DIR) $(TOP)/shared/kfgsums
+	@ $(TOP)/build/install-kfg.sh vdb-copy.kfg  $(TOP)/tools/vdb-copy   $(KONFIG_DIR) $(TOP)/shared/kfgsums
+	@ # rename obsolete ncbi-vdb.kfg
+	@ if [ -f $(KONFIG_DIR)/ncbi-vdb.kfg ] ; \
+        then mv -v $(KONFIG_DIR)/ncbi-vdb.kfg  $(KONFIG_DIR)/ncbi-vdb.kfg.orig  ; fi
 
-install: installexes
+install: installexes copykfg
 ifeq (true, $(LINUX_ROOT))
-	@ # install configuration file(s)
-	@ printf "Installing configuration files to $(ROOT)/etc/ncbi/..."
-	( mkdir -p $(ROOT)/etc/ncbi && \
-	  cp -p $(TOP)/tools/vdb-copy/vdb-copy.kfg $(ROOT)/etc/ncbi ; \
-	  if [ -f $(BINDIR)/ncbi/default.kfg ] ; then \
-	    if [ -f $(ROOT)/etc/ncbi/default.kfg ] ; then \
-          mv -v $(ROOT)/etc/ncbi/default.kfg $(ROOT)/etc/ncbi/default.kfg.orig;\
-	    fi; \
-	    cp -p $(BINDIR)/ncbi/default.kfg $(ROOT)/etc/ncbi ; \
-	  fi; \
-	  if [ -f $(BINDIR)/ncbi/certs.kfg ] ; then \
-	    if [ -f $(ROOT)/etc/ncbi/certs.kfg ] ; then \
-          mv -v $(ROOT)/etc/ncbi/certs.kfg $(ROOT)/etc/ncbi/certs.kfg.orig; \
-	    fi; \
-	    cp -p $(BINDIR)/ncbi/certs.kfg $(ROOT)/etc/ncbi ; \
-	  fi ) && echo done
-	@ #
 	@ echo "Updating $(PROFILE_FILE).[c]sh"
 	@ printf \
 "#version $(VERSION)\n"\
@@ -100,25 +98,6 @@ ifeq (true, $(LINUX_ROOT))
 "if ( \$$status ) setenv PATH $(EXE_TARGET):\$$PATH\n"\
         >$(PROFILE_FILE).csh && chmod 644 $(PROFILE_FILE).csh || true;
 	@ #TODO: check version of the files above
-else    
-	@ # install configuration file(s)
-	@ printf "Installing configuration files to $(INST_BINDIR)/ncbi/..."
-	( mkdir -p $(INST_BINDIR)/ncbi && \
-	  cp -p $(TOP)/tools/vdb-copy/vdb-copy.kfg $(INST_BINDIR)/ncbi/ ; \
-	  if [ -f $(BINDIR)/ncbi/default.kfg ] ; then \
-	    if [ -f $(INST_BINDIR)/ncbi/default.kfg ] ; then \
-          mv -v $(INST_BINDIR)/ncbi/default.kfg \
-                $(INST_BINDIR)/ncbi/default.kfg.orig; \
-	    fi; \
-	    cp -p $(BINDIR)/ncbi/default.kfg $(INST_BINDIR)/ncbi ; \
-	  fi; \
-	  if [ -f $(BINDIR)/ncbi/certs.kfg ] ; then \
-	    if [ -f $(INST_BINDIR)/ncbi/certs.kfg ] ; then \
-          mv -v $(INST_BINDIR)/ncbi/certs.kfg \
-                $(INST_BINDIR)/ncbi/certs.kfg.orig; \
-	    fi; \
-	    cp -p $(BINDIR)/ncbi/certs.kfg $(INST_BINDIR)/ncbi ; \
-	  fi ) && echo done
 endif
 
 #-------------------------------------------------------------------------------

build/Makefile.vers

@@ -23,4 +23,4 @@
 # ===========================================================================
 
 # SRA-TOOLS and library version
-VERSION = 2.8.2
+VERSION = 2.9.0

test/general-loader/runtestcase.sh → build/install-kfg.sh

@@ -22,87 +22,33 @@
 #  Please cite the author in any work or product based on this material.
 #
 # ===========================================================================
-#echo "$0 $*"
 
-# $1 - path to sra-tools executables (general-loader, vdb-dump)
-# $2 - name of the dumper executable (vdb-dump, kdbmeta etc.)
-# $3 - work directory (expected results under expected/, actual results and temporaries created under actual/)
-# $4 - test case ID (expect a file input/$3.gl to exist)
-# $5 - expected return code
-# $6 - command line options for general-loader
-# $7 - command line options for dumper
+# install-kfg.sh
+#   copies file $1 from $2 to $3.
+#   Will create a backup copy if the file's md5 is not found in $4 (assumed to be a user's edit)
 #
-# return codes:
-# 0 - passed
-# 1 - could not create temp dir
-# 2 - unexpected return code from general-loader
-# 3 - vdb-dump failed on the output of general-loader
-# 4 - outputs differ
 
-BINDIR=$1
-DUMPER=$2
-WORKDIR=$3
-CASEID=$4
-RC=$5
-LOAD_OPTIONS=$6
-DUMP_OPTIONS=$7
+FILE_NAME=$1
+SRC_DIR=$2
+KONFIG_DIR=$3
+MD5SUMS=$4
 
-DUMP="$BINDIR/$DUMPER"
-LOAD="$BINDIR/general-loader"
-TEMPDIR=$WORKDIR/actual/$CASEID
+SRC_FILE=$2/$1
+TGT_FILE=$3/$1
 
-echo "running test case $CASEID"
+mkdir -p ${KONFIG_DIR}
 
-mkdir -p $TEMPDIR
-if [ "$?" != "0" ] ; then
-    echo "cannot create "
-    exit 1
-fi
-rm -rf $TEMPDIR/*
+#echo "installing $1 from $2 to $3, mdsums = $4"
 
-CMD="cat input/$CASEID.gl | $LOAD $LOAD_OPTIONS 1>$TEMPDIR/load.stdout 2>$TEMPDIR/load.stderr"
-#echo $CMD
-eval $CMD
-rc="$?"
-if [ "$rc" != "$RC" ] ; then
-    echo "$LOAD returned $rc, expected $RC"
-    echo "command executed:"
-    echo $CMD
-    cat $TEMPDIR/load.stderr
-    exit 2
+# create a backup if installed file has been modified by user
+if [ -f ${TGT_FILE} ] ; then
+    md5=$(md5sum ${TGT_FILE} | awk '{print $1;}')
+    #echo "$1 md5=$md5"
+    if [ "$(grep ${md5} ${MD5SUMS})" == "" ] ; then
+        # not a known version of the file; create a backup copy
+        mv -b -v ${TGT_FILE} ${TGT_FILE}.orig
     fi
-
-if [ "$rc" == "0" ] ; then
-    CMD="$DUMP $TEMPDIR/db $DUMP_OPTIONS 1>$TEMPDIR/dump.stdout 2>$TEMPDIR/dump.stderr"
-    #echo $CMD
-    eval $CMD || ( echo "$CMD" && exit 3 )
-    
-    # remove timestamps, date from metadata
-    sed -i -e 's/<timestamp>.*<\/timestamp>/<timestamp\/>/g' $TEMPDIR/dump.stdout
-    sed -i -e 's/date=".*" name/date="" name/g' $TEMPDIR/dump.stdout
-    
-    diff $WORKDIR/expected/$CASEID.stdout $TEMPDIR/dump.stdout >$TEMPDIR/diff
-    rc="$?"
-else
-    # remove timestamps
-    sed -i -e 's/^....-..-..T..:..:.. //g' $TEMPDIR/load.stderr
-    # remove pathnames
-    sed -i -e 's=/.*/==g' $TEMPDIR/load.stderr
-    # remove source locations
-    sed -i -e 's=: .*:[0-9]*:[^ ]*:=:=g' $TEMPDIR/load.stderr
-    # remove version number
-    sed -i -e 's=general-loader\(\.[0-9]*\)*=general-loader=g' $TEMPDIR/load.stderr
-    diff $WORKDIR/expected/$CASEID.stderr $TEMPDIR/load.stderr >$TEMPDIR/diff
-    rc="$?"
 fi
 
-if [ "$rc" != "0" ] ; then
-    cat $TEMPDIR/diff
-    echo "command executed:"
-    echo $CMD
-    exit 4
-fi    
-
-rm -rf $TEMPDIR
-
-exit 0
+# copy to the install location
+cp ${SRC_FILE} ${TGT_FILE}

configure

@@ -41,5 +41,5 @@ else
         echo >&2 "configure: error: perl not found."; exit 1; }
 
     cd $CURDIR/setup
-    perl -w konfigure.perl "$@"
+    perl  konfigure.perl "$@"
 fi

debian/changelog

+sra-sdk (2.9.0+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * debhelper 11
+
+ -- Andreas Tille <tille@debian.org>  Sat, 24 Mar 2018 07:41:44 +0100
+
 sra-sdk (2.8.2-5+dfsg-1) unstable; urgency=medium
 
   * New upstream version

debian/compat

-10
+11

debian/control

@@ -4,7 +4,7 @@ Uploaders: Charles Plessy <plessy@debian.org>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                libngs-sdk-dev,
                libncbi-vdb-dev,
                libfuse-dev,

debian/patches/certs.kfg.patch

@@ -22,6 +22,6 @@ Description: Point to correct location of kfg config files in libncbi-vdb2 packa
  #uncomment this line and change the test for root ( see under install: ) to succeed:
  #ROOT = ~/root
 +ROOT=$(CURDIR)/debian/sra-toolkit
- 
- EXE_TARGET = $(INST_BINDIR)
- PROFILE_FILE = $(ROOT)/etc/profile.d/sra-tools
+ ifeq (linux, $(OS))
+     ifeq (0, $(shell id -u))
+         LINUX_ROOT = true

debian/patches/dont_use_static_lib.patch

@@ -42,17 +42,6 @@ Description: Don't use static library
  NGS_PILEUP_LIBS = \
  	-sncbi-ngs-c++    \
 -	-sncbi-vdb-static \
-+	-sncbi-vdb \
- 	-sngs-c++         \
- 	-skapp \
- 	-stk-version \
---- a/tools/pileup-stats/Makefile
-+++ b/tools/pileup-stats/Makefile
-@@ -71,7 +71,7 @@ PILEUP_STATS_LIB =    \
- 	-L$(NGS_LIBDIR)   \
- 	-sgeneral-writer  \
- 	-sncbi-ngs-c++    \
--	-sncbi-vdb-static \
 +	-sncbi-vdb \
  	-sngs-c++         \
  	-skapp \
@@ -68,34 +57,3 @@ Description: Don't use static library
  
  #-------------------------------------------------------------------------------
  # fastq-dump
---- a/test/general-loader/Makefile
-+++ b/test/general-loader/Makefile
-@@ -62,7 +62,7 @@ TEST_GEN_LOAD_OBJ = \
- 	$(addsuffix .$(OBJX),$(TEST_GEN_LOAD_SRC))
- 
- TEST_GEN_LOAD_LIB =   \
--	-sncbi-wvdb-static  \
-+	-sncbi-wvdb  \
-     -sload              \
- 	-skapp              \
-     -sktst              \
-@@ -125,7 +125,7 @@ setup:
- 
- $(TEST_BINDIR)/makeinputs: makeinputs.cpp
- 	@# generate numbered input streams for tool tests
--	$(CXX) makeinputs.cpp testsource.cpp -o $(TEST_BINDIR)/makeinputs -I$(INCDIRS) -L$(VDB_LIBDIR) -lncbi-vdb-static
-+	$(CXX) makeinputs.cpp testsource.cpp -o $(TEST_BINDIR)/makeinputs -I$(INCDIRS) -L$(VDB_LIBDIR) -lncbi-vdb
- 
- tool-tests: $(TEST_BINDIR)/makeinputs
- 	@mkdir -p input && $(TEST_BINDIR)/makeinputs && rm $(TEST_BINDIR)/makeinputs
---- a/tools/general-loader/Makefile
-+++ b/tools/general-loader/Makefile
-@@ -121,7 +121,7 @@ GEN_LOAD_OBJ = \
- 	$(addsuffix .$(OBJX),$(GEN_LOAD_SRC))
- 
- GEN_LOAD_LIBS = \
--	-sncbi-wvdb-static \
-+	-sncbi-wvdb \
- 	-sload \
- 	-skapp \
- 	-stk-version \

debian/patches/e285ecd3fcd39eac2051ea7bccd5257c6dfb72ab.patch

-From: "durbrowk@ncbi.nlm.nih.gov" <kmdurbrow@me.com>
-Date: Wed, 5 Apr 2017 12:50:07 -0400
-Subject: [PATCH] renamed function to resolve name clash with gnutards
-Bugs-Debian: https://bugs.debian.org/882349
-Origin: Upstream
-        https://github.com/ncbi/sra-tools/commit/e285ecd3fcd39eac2051ea7bccd5257c6dfb72ab
-
----
- tools/bam-loader/bam.c | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
---- a/tools/bam-loader/bam.c
-+++ b/tools/bam-loader/bam.c
-@@ -3997,7 +3997,7 @@ static unsigned insert_B(unsigned const
-     return n;
- }
- 
--static unsigned canonicalize(uint32_t cigar[], unsigned n)
-+static unsigned canonicalizeCIGAR(uint32_t cigar[], unsigned n)
- {
-     unsigned i;
-     
-@@ -4042,7 +4042,7 @@ static unsigned GetCGCigar(BAM_Alignment
-     memmove(cigar, getCigarBase(self), n * 4);
- 
-     if (n > 1)
--        n = canonicalize(cigar, n); /* just in case */
-+        n = canonicalizeCIGAR(cigar, n); /* just in case */
-     
-     for (i = 0, S = 0; i < gaps; ++i) {
-         unsigned const s = seg[2 * i + 0];

debian/patches/find_configure_libs.patch

@@ -4,12 +4,12 @@ Description: Help configure finding Debian packaged libraries
 
 --- a/setup/konfigure.perl
 +++ b/setup/konfigure.perl
-@@ -1506,7 +1506,7 @@ sub check_compiler {
+@@ -1522,7 +1522,7 @@ sub check_compiler {
              $flags = $n;
              $log = '                      int main() {                     }\n'
          } elsif ($n eq 'hdf5') {
--            $library = '-lhdf5';
-+            $library = '-lhdf5_serial';
+-            $library = '-Wl,-Bstatic -lhdf5 -Wl,-Bdynamic -ldl -lm -lz';
++            $library = '-lhdf5_serial -Wl,-Bdynamic -ldl -lm -lz';
              $log = '#include <hdf5.h>  \n int main() { H5close         (); }\n'
          } elsif ($n eq 'fuse') {
              $flags = '-D_FILE_OFFSET_BITS=64';

debian/patches/find_hdf5_serial.patch

@@ -4,10 +4,10 @@ Description: Debian has several flavours of hdf5 - use serial here
 
 --- a/setup/konfigure.perl
 +++ b/setup/konfigure.perl
-@@ -1507,7 +1507,7 @@ sub check_compiler {
+@@ -1523,7 +1523,7 @@ sub check_compiler {
              $log = '                      int main() {                     }\n'
          } elsif ($n eq 'hdf5') {
-             $library = '-lhdf5_serial';
+             $library = '-lhdf5_serial -Wl,-Bdynamic -ldl -lm -lz';
 -            $log = '#include <hdf5.h>  \n int main() { H5close         (); }\n'
 +            $log = '#include <hdf5/serial/hdf5.h>  \n int main() { H5close         (); }\n'
          } elsif ($n eq 'fuse') {

debian/patches/find_ncbi-vdb.patch

@@ -29,7 +29,7 @@ Description: Make sure libncbi-vdb will be found
                locbldpath=>'$Bin/../../OUTDIR/ncbi-vdb',
 --- a/setup/konfigure.perl
 +++ b/setup/konfigure.perl
-@@ -1307,6 +1307,9 @@ sub find_in_dir {
+@@ -1323,6 +1323,9 @@ sub find_in_dir {
          } elsif (-e "$dir/interfaces/$include") {
              println $dir unless ($AUTORUN);
              $found_inc = "$dir/interfaces";
@@ -39,7 +39,7 @@ Description: Make sure libncbi-vdb will be found
          } else {
              print "$dir: " if ($OPT{'debug'});
              println 'no' unless ($AUTORUN);
-@@ -1319,7 +1322,7 @@ sub find_in_dir {
+@@ -1335,7 +1338,7 @@ sub find_in_dir {
              my $buildarch = `dpkg-architecture -qDEB_BUILD_MULTIARCH`;
              chomp $buildarch;
              my $libdir  = File::Spec->catdir($dir, 'lib', $buildarch);

debian/patches/find_ngs-sdk.patch

@@ -4,7 +4,7 @@ Description: ngs-sdk header files are in /usr/include
 
 --- a/setup/konfigure.perl
 +++ b/setup/konfigure.perl
-@@ -435,6 +435,7 @@ if ($TOOLS =~ /gcc$/) {
+@@ -448,6 +448,7 @@ if ( $PKG{REQ} ) {
  
  my @dependencies;
  
@@ -12,7 +12,7 @@ Description: ngs-sdk header files are in /usr/include
  my %DEPEND_OPTIONS;
  foreach my $href (DEPENDS()) {
      $_ = $href->{name};
-@@ -937,7 +938,7 @@ EndText
+@@ -953,7 +954,7 @@ EndText
  
      if ($PKG{LNG} eq 'JAVA') {
          L($F,
@@ -21,7 +21,7 @@ Description: ngs-sdk header files are in /usr/include
      }
  
      print $F <<EndText;
-@@ -1315,7 +1316,9 @@ sub find_in_dir {
+@@ -1331,7 +1332,9 @@ sub find_in_dir {
          print "\tlibraries... " unless ($AUTORUN);
          if ($lib) {
              my $builddir = File::Spec->catdir($dir, $OS, $TOOLS, $ARCH, $BUILD);

debian/patches/ignore_failing_tests_for_the_moment.patch

@@ -4,7 +4,7 @@ Description: Exclude failing tests
 
 --- a/test/fastq-loader/Makefile
 +++ b/test/fastq-loader/Makefile
-@@ -104,7 +104,7 @@ smalltests: $(TEST_TOOLS)
+@@ -128,7 +128,7 @@ smalltests: $(TEST_TOOLS)
  #           1.2 phred 64
  	$(SMALLRUN) 1.2 0 $(SRCDIR)/input/1.2.fastq --quality PHRED_64
  #           1.3 phred 33, decimal qualities
@@ -13,7 +13,7 @@ Description: Exclude failing tests
  #           1.4 logodds 64
  	$(SMALLRUN) 1.4 0 $(SRCDIR)/input/1.4.fastq --quality LOGODDS
  #
-@@ -131,9 +131,9 @@ smalltests: $(TEST_TOOLS)
+@@ -155,9 +155,9 @@ smalltests: $(TEST_TOOLS)
  #           2.8.1 handling of N in reads, ALTREAD is a physical column
  	$(SMALLRUN) 2.8.1 0 $(SRCDIR)/input/2.8.1.fastq --quality PHRED_33
  #           2.9 mismatching length of sequence and quality (qualities shorter)
@@ -25,7 +25,7 @@ Description: Exclude failing tests
  #
  #       Multiple files
  #           3.1 reads+qualities together
-@@ -161,19 +161,19 @@ smalltests: $(TEST_TOOLS)
+@@ -185,19 +185,19 @@ smalltests: $(TEST_TOOLS)
       -o actual/4.1.obj --quality PHRED_33 \
       | grep "Cache size: 10M" >/dev/null
  #           4.3.1 --cache-size      rejected if invalid
@@ -50,7 +50,7 @@ Description: Exclude failing tests
  #   Gzipped input
  	$(SMALLRUN) 5.0 0 $(SRCDIR)/input/5.0.fastq.gz --quality PHRED_33
  #   Misparsed quality
-@@ -185,7 +185,7 @@ smalltests: $(TEST_TOOLS)
+@@ -209,7 +209,7 @@ smalltests: $(TEST_TOOLS)
  #   secondary read numbers other than 3
  	$(SMALLRUN) 8.0 0 $(SRCDIR)/input/8.0.fastq --quality PHRED_33
  #   reject inconsistent secondary read numbers
@@ -61,12 +61,11 @@ Description: Exclude failing tests
  #   accepting ascii quality values up to 126
 --- a/test/Makefile
 +++ b/test/Makefile
-@@ -37,7 +37,7 @@ include $(TOP)/build/Makefile.config
+@@ -37,7 +37,6 @@ include $(TOP)/build/Makefile.config
  SUBDIRS =    \
+ 	dump-test       \
  	vdb-config      \
- 	fastq-loader    \
 -	vcf-loader      \
-+	# vcf-loader      \
- 	kget            \
- 	general-loader  \
- 	vschema         \
+ 	align-info      \
+ 	align-cache     \
+ 	vdb-validate    \

debian/patches/series

@@ -15,4 +15,3 @@ link_debian_packaged_libmbed.patch
 seek_dynamic_libs.patch
 certs.kfg.patch
 drop_tests.patch
-e285ecd3fcd39eac2051ea7bccd5257c6dfb72ab.patch

debian/patches/set_explicit_path_to_schemata.patch

@@ -13,62 +13,6 @@ Description: In Debian */*.vschema is installed to /usr/lib/ncbi-vdb/
  const string TempFileFixture::DbType = "NCBI:align:db:alignment_unsorted";
  
  ///////////////////////////////////////////////// FASTQ-based tests for CommonWriter 
---- a/test/general-loader/makeinputs.cpp
-+++ b/test/general-loader/makeinputs.cpp
-@@ -69,7 +69,7 @@ OneTableOneColumnWithDefaults( const str
-     TestSource source;
-     TestSource::packed = p_packed;
-     
--    source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" );
-+    source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" );
-     source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) );
-     
-     source . NewTableEvent ( 1, tableName ); 
-@@ -104,7 +104,7 @@ ErrorMessage( const string& p_caseId, bo
-     TestSource source;
-     TestSource::packed = p_packed;
-     
--    source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" );
-+    source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" );
-     source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) );
-     
-     source . NewTableEvent ( 1, tableName ); 
-@@ -123,7 +123,7 @@ EmptyDefaultValue( const string& p_caseI
-     TestSource source;
-     TestSource::packed = p_packed;
-     
--    source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" );
-+    source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" );
-     source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) );
-     
-     source . NewTableEvent ( 1, tableName ); 
-@@ -143,7 +143,7 @@ MoveAhead( const string& p_caseId, bool
-     TestSource source;
-     TestSource::packed = p_packed;
-     
--    source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" );
-+    source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" );
-     source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) );
-     
-     source . NewTableEvent ( 1, tableName ); 
-@@ -172,7 +172,7 @@ IntegerCompression( const string& p_case
-     TestSource source;
-     TestSource::packed = true;
-     
--    source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" );
-+    source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" );
-     source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) );
-     
-     source . NewTableEvent ( 1, tableName ); 
-@@ -194,7 +194,7 @@ SoftwareIdString( const string& p_caseId
-     TestSource source;
-     TestSource::packed = true;
-     
--    source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" );
-+    source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" );
-     source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) );
-     
-     source . SoftwareNameEvent ( string ( "some software" ), string ( "9.8.7654" ) );
 --- a/tools/fastq-loader/fastq-loader.c
 +++ b/tools/fastq-loader/fastq-loader.c
 @@ -253,7 +253,7 @@ rc_t CC Usage (const Args * args)
@@ -168,23 +112,3 @@ Description: In Debian */*.vschema is installed to /usr/lib/ncbi-vdb/
  #define PACBIO_SCHEMA_DB    "NCBI:SRA:PacBio:smrt:db"
  
  
---- a/test/general-loader/test-general-loader.cpp
-+++ b/test/general-loader/test-general-loader.cpp
-@@ -488,7 +488,7 @@ FIXTURE_TEST_CASE ( BadSchemaFileName_Lo
- 
- FIXTURE_TEST_CASE ( BadSchemaName, GeneralLoaderFixture )
- {
--    SetUpStream ( GetName(), "align/align.vschema", "bad schema name" );
-+    SetUpStream ( GetName(), "/usr/lib/ncbi-vdb/align/align.vschema", "bad schema name" );
-     m_source . OpenStreamEvent();
- 
-     REQUIRE ( Run ( m_source . MakeSource (), SILENT_RC ( rcVDB, rcMgr, rcCreating, rcSchema, rcNotFound ) ) );
-@@ -496,7 +496,7 @@ FIXTURE_TEST_CASE ( BadSchemaName, Gener
- 
- FIXTURE_TEST_CASE ( BadSchemaName_Long, GeneralLoaderFixture )
- {
--    SetUpStream ( GetName(), "align/align.vschema", string ( GeneralLoader :: MaxPackedString + 1, 'x' ) );
-+    SetUpStream ( GetName(), "/usr/lib/ncbi-vdb/align/align.vschema", string ( GeneralLoader :: MaxPackedString + 1, 'x' ) );
-     m_source . OpenStreamEvent();
- 
-     REQUIRE ( Run ( m_source . MakeSource (), SILENT_RC ( rcVDB, rcMgr, rcCreating, rcSchema, rcNotFound ) ) );