New upstream version 2.9.0-1+dfsg

core

*.pyc

.gdb_history

.vscode

.gdb_history

# NCBI External Developer Release:

## NCBI VDB

**February 23, 2018**

  **align**: AlignAccessRefSeqEnumeratorNext no longer filters by the index  

  **align**: fixed an order-dependent bug affecting cross-table lookups  

  **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, vdb-sql**: modified build to avoid vdb-sql in absence of libxml2  

  **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  

  **kfs**: fix to improve on windows  

  **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  

  **ncbi-vdb**: add ability to make a cache-tee-file without promtion  

  **ncbi-vdb**: fixed bug of directory not found on mac  

  **ncbi-vdb, ngs-engine**: improved handling of blobs inside the NGS engine   

  **ngs-engine**: improved performance when iterating through partially aligned and unaligned reads  

  **ngs-engine**: optimized filtered access to unaligned runs  

  **sra-tools, vdb**: access to vdb/ngs via SQLite  

  **vdb**: An assert triggered by a rare condition was fixed  

  **vdb**: new api to estimate pileup-workload based on slice  

  **vdb**: new function to open HTTP-file with an arbitrary page-size  

  **vdb**: progressbar can now be created to output on stderr  

  **vfs**: Name resolving service was updated and switched to protocol version 3.0  

## NCBI VDB 2.8.2

**March 6, 2017**

	@cp $(TOP)/interfaces/ngs/ncbi/NGS.hpp $(INST_INCDIR)/ncbi-vdb

copykfg: checkversion

	@ #

	@ # install configuration file(s)

	@ echo "Installing configuration files to $(KONFIG_DIR)"

	@ mkdir -p $(KONFIG_DIR)

	@ if [ -f $(KONFIG_DIR)/certs.kfg   -a "$$(diff $(TOP)/libs/kfg/certs.kfg   $(KONFIG_DIR)/certs.kfg 2>/dev/null)" != "" ] ; \

        then mv -v $(KONFIG_DIR)/certs.kfg    $(KONFIG_DIR)/certs.kfg.orig    ; fi

	@ cp $(TOP)/libs/kfg/certs.kfg   $(KONFIG_DIR)

	@ if [ -f $(KONFIG_DIR)/default.kfg -a "$$(diff $(TOP)/libs/kfg/default.kfg $(KONFIG_DIR)/default.kfg 2>/dev/null)" != "" ] ; \

        then mv -v $(KONFIG_DIR)/default.kfg  $(KONFIG_DIR)/default.kfg.orig  ; fi

	@ $(TOP)/build/install-kfg.sh default.kfg $(TOP)/libs/kfg $(KONFIG_DIR) $(TOP)/libs/kfg/kfgsums

	@ $(TOP)/build/install-kfg.sh certs.kfg   $(TOP)/libs/kfg $(KONFIG_DIR) $(TOP)/libs/kfg/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

	@ cp $(TOP)/libs/kfg/default.kfg $(KONFIG_DIR)

install: copylibs copyincludes copykfg

ifeq (true, $(LINUX_ROOT))

# ===========================================================================

# NCBI-VDB and library version

VERSION = 2.8.2

VERSION = 2.9.0

#!/bin/bash

# ===========================================================================

#

#                            PUBLIC DOMAIN NOTICE

#

# ===========================================================================

vdb/schema/paths = "/panfs/traces01/trace_software/sdk/interfaces"

# 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)

#

FILE_NAME=$1

SRC_DIR=$2

KONFIG_DIR=$3

MD5SUMS=$4

SRC_FILE=$2/$1

TGT_FILE=$3/$1

mkdir -p ${KONFIG_DIR}

# 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 -v ${TGT_FILE} ${TGT_FILE}.orig

    fi

fi

# copy to the install location

cp ${SRC_FILE} ${TGT_FILE}