New upstream version 2.9.3

user.status

vgcore.*

/bin64

/build/COMP.mac

/build/Makefile.config*

/build/MSVC/2010/ipch

/build/MSVC/2010/ncbi-vdb.opensdf

/centos

/ilib64

/lib64

/mac

/Makefile.config.mac.arch

/reconfigure

/schema

/test-bin64

user.status

/win

*.opensdf

*.sdf

*.suo

*.log

/.cproject

/.project

/.pydevproject

# mac os x meta-files

.DS_Store

._*

*~

\#*

.\#*

core

*.pyc

.gdb_history

.vscode

.gdb_history

._*

*.suo

OUTDIR

*.ipch

/.cproject

/.project

/.pydevproject

.idea/

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

#

#                            PUBLIC DOMAIN NOTICE

#               National Center for Biotechnology Information

#

#  This software/database is a "United States Government Work" under the

#  terms of the United States Copyright Act.  It was written as part of

#  the author's official duties as a United States Government employee and

#  thus cannot be copyrighted.  This software/database is freely available

#  to the public for use. The National Library of Medicine and the U.S.

#  Government have not placed any restriction on its use or reproduction.

#

#  Although all reasonable efforts have been taken to ensure the accuracy

#  and reliability of the software and data, the NLM and the U.S.

#  Government do not and cannot warrant the performance or results that

#  may be obtained by using this software or data. The NLM and the U.S.

#  Government disclaim all warranties, express or implied, including

#  warranties of performance, merchantability or fitness for any particular

#  purpose.

#

#  Please cite the author in any work or product based on this material.

#

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

The NCBI NGS Software Development Kit

Contact: sra-tools@ncbi.nlm.nih.gov

NGS SDK 2.9.3

October 17, 2018

  ngs: changed version to match that of ncbi-vdb

NGS SDK 2.9.2

July 23, 2018

  ngs: changed version to match that of ncbi-vdb

NGS SDK 2.9.1

June 15, 2018

  build: 'make install' ignore ROOT environment variable

NGS SDK 2.9.0

February 23, 2018

  version: changed version to match that of ncbi-vdb

  build: Fixed configure allowing to run it on Perl with version >= v5.26 that has "." removed from @INC  

  kfg: added searching of configuration files in ../etc/ncbi/ relative to the binaries  

  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: fixed bug of directory not found on mac  

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

  ngs: Examples for python 2.6 were removed  

  ngs: Python examples work with Python 2.6.6  

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

  ngs-engine: optimized filtered access to unaligned runs  

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

NGS SDK 1.3.0

October 7, 2016

HTTPS-ENABLED RELEASE

  build, ngs-tools: Now ngs-tools look for its dependencies using their normal build paths and does not reconfigure them  

  build, ngs-tools: Now ngs-tools use CMAKE_INSTALL_PREFIX for installation path  

  kns: All tools and libraries now support https  

  ngs: Fixed all crashes when using null as string in ngs-java APIs  

  ngs: NGS_ReferenceGetChunk() will now return chunks potentially exceeding 5000 bases  

  ngs: fixed potential concurrency issues at exit, when called from Java  

  ngs: ngs-java and ngs-python auto-download (of native libraries) now works through HTTPS  

  ngs: read fragments of length 0 are now ignored  

  ngs, ngs-tools, ref-variation: added class ngs-vdb::VdbAlignment, featuring method IsFirst()  

  ngs-engine: improved diagnostic messages  

  ngs-tools: Fixed Makefiles to keep supporting "./configure; make" build of sra-search, alongside CMake-based build.  

NGS SDK 1.2.5

July 11, 2016

  blast, kfg, ncbi-vdb, sra-tools, vfs: restored possibility to disable local caching

  htsjdk: Several JVM crashes related to a number of open files were fixed. New property to disable auto-download was integrated into HTSJDK

  kfg: When loading configuration files on Windows USERPROFILE environment variable is used before HOME

  ngs, search, sra-search: sra-search was modified to support multiple threads.

  ngs-engine, ngs-tools, sra-tools, vfs: The "auxiliary" nodes in configuration are now ignored

  ngs-engine: Added support for blob-by-blob access to SEQUENCE table

  ngs-engine: removed a potential memory leak in NGS_CursorMake()

  ngs: Fixed a bug in ngs::Alignment::getMateReferenceSpec() affecting pre-March 2015 runs

  ngs: now supports parallel compilation with "make -j N"

  vfs: environment variable VDB_PWFILE is no longer used

NGS SDK 1.2.4

May 25, 2016

  build: MSVS 2013 toolset (12.0) is now supported across all repositories

  doc, ngs: updated javadoc to include throws and other missing tags

  examples, ngs: added DumpReferenceFASTA.py example

  htsjdk: added code to HTS-JDK  to avoid involving NGS unless we are sure that it is being requested

  ngs, ngs-engine: Added filtering to NGS of secondary alignments that do not have primary alignments

  ngs, test: ngs-python: fixed bug in String processing for Python 3.*

  ngs-engine: ncbi-ngs engine was updated: fixed a bug that made NGS read iterator return 0 reads on WGS accessions.

  ngs: Improved native library load in ngs-java, enhanced its error reporting and added a mode to disable auto-download of native libraries

  ngs: Python code will check for the latest version of the libraries and update if newer ones are available

  ngs: check for the latest version of the libraries and update if newer ones are available

  ngs: simplified ngs-python bindings

# NCBI External Developer Release:

## NCBI VDB 2.9.1

## NGS SDK 2.9.3

**October 17, 2018**

  **ngs**: changed version to match that of _ncbi-vdb_

## NGS SDK 2.9.2

**July 23, 2018**

  **ngs**: changed version to match that of _ncbi-vdb_

## NGS SDK 2.9.1

**June 15, 2018**

  **build**: 'make install' ignore ROOT environment variable  

  **kfg, kns**: Added API to instruct VDB to silently accept any server certificate as valid.  

  **kfg, vdb-config**: name resolver service now makes use of fcgi  

  **kfg, vfs**: Fixed a bug that prevented decryption of objects encrypted with non-UTF8 text password keys  

  **klib**: added check for NULL format argument to string_printf()  

  **kns**: Randomly select from multiple proxies in configuration  

  **test**: added Windows test projects for the new schema and the latest vdb  

## NCBI VDB 2.9.0

## NGS SDK 2.9.0

**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  

  **version**: changed version to match that of _ncbi-vdb_

  **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**: 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**: Examples for python 2.6 were removed  

  **ngs**: Python examples work with Python 2.6.6  

  **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**

  **blast**: Updated blast library to be able to process runs having empty rows  

  **build**: Added ability to specify ncbi-vdb/configure --with-magic-prefix. Look for libraries in (lib lib64) when running "configure --with-...-prefix"  

  **build**: configure detects location of ngs libraries  

  **build**: configure was fixed to skip options unrecognized by gcc 4.4.7  

  **build**: created sra-toolkit Debian package  

  **build**: fixed a bug in 'configure' when in could not find source files in repository saved with non-standard name  

  **build, kfg**: install updates certs.kfg along with other configuration files  

  **build, ncbi-vdb, sra-tools**: installation will back up old configuration files if they differ from the ones being installed  

  **kfs, vdb**: Fixes errors occuring when configuration is missing  

  **klib**: Fixed logging error reported as "log failure: RC(rcText,rcString,rcConverting,rcBuffer,rcInsufficient)"  

  **kns**: SRA tools respect standard set of environment variables for proxy specification  

  **kns**: rewrote socket code to use proper local error code switches, especially Windows   

  **kns**: updated mbedtls library to version 2.4.1  

  **ncbi-vdb**: configure in detects existence of ngs jar file  

  **ncbi-vdb, ngs, ngs-tools, sra-tools**: eliminated memcpy from sources due to potential for overlap  

  **test**: Improved testing framework  

  **vdb**: increased tenacity in flushing data to disk to accommodate behaviors of file systems such as Lustre.  

  **vdb-blast**: Implemented vdb-blast API for retrieving reference sequence  

## NCBI VDB 2.8.1

**December 22, 2016**

  **kfg**: added possibility to create an empty KConfig object that does not try to load any file  

## NCBI VDB 2.8.0

## NGS SDK 1.3.0

**October 7, 2016**

### HTTPS-ENABLED RELEASE

  **kfg, kns**: Use environment variables to determine the proxy for a http protocol  

  **kfg, vdb-config**: vdb-config-GUI has now option to pick up proxy-setting from environment  

  **build, ngs-tools**: Now ngs-tools look for its dependencies using their normal build paths and does not reconfigure them  

  **build, ngs-tools**: Now ngs-tools use CMAKE_INSTALL_PREFIX for installation path  

  **kns**: All tools and libraries now support https  

  **kns**: replaced all direct uses of sleep() within code to enforce standardization upon mS.  

  **kproc, ncbi-vdb**: Fixed KCondition to generate timeout error on Windows when timeout exhausted  

  **ngs**: Fixed all crashes when using null as string in ngs-java APIs  

  **ngs**: NGS_ReferenceGetChunk() will now return chunks potentially exceeding 5000 bases  

  **ngs**: fixed potential concurrency issues at exit, when called from Java  

  **ngs**: ngs-java and ngs-python auto-download (of native libraries) now works through HTTPS  

  **ngs**: read fragments of length 0 are now ignored  

  **ngs, ngs-tools, ref-variation**: added class ngs-vdb::VdbAlignment, featuring method IsFirst()  

  **ngs-engine**: improved diagnostic messages  

  **test**: updated tests to not fail outside of NCBI  

  **test-sra**: test-sra prints network information  

  **test-sra**: test-sra prints version of ncbi-vdb or ngs-sdk dynamic library  

  **vdb**: improved parameter checking on VDatabaseOpenTableRead()  

  **vdb**: new function: "VDBManagerDeleteCacheOlderThan()"  

  **vdb**: problem with buffer-overrun when compressing random data fixed  

  **vdb**: remote/aux nodes have been removed from configuration  

  **ngs-tools**: Fixed Makefiles to keep supporting "./configure; make" build of sra-search, alongside CMake-based build.  

## NCBI VDB 2.7.0

## NGS SDK 1.2.5

**July 12, 2016**

  **blast, kfg, ncbi-vdb, sra-tools, vfs**: restored possibility to disable local caching  

  **doc, ncbi-vdb**: created a Wiki page illustrating how to use the API to set up logging  

  **kdb, kfs, kns**: Added blob validation for data being fetched remotely  

  **htsjdk**: Several JVM crashes related to a number of open files were fixed. New property to disable auto-download was integrated into HTSJDK  

  **kfg**: When loading configuration files on Windows USERPROFILE environment variable is used before HOME  

  **kfg**: modified auxiliary remote access configuration to use load-balanced servers  

  **kns**: Fixed a bug when KHttpRequestPOST generated an incorrect Content-Length after retry  

  **ngs, search, sra-search**: sra-search was modified to support multiple threads.  

  **ngs-engine, ngs-tools, sra-tools, vfs**: The "auxiliary" nodes in configuration are now ignored  

  **ngs-engine**: Added support for blob-by-blob access to SEQUENCE table  

  **ngs-engine**: removed a potential memory leak in NGS_CursorMake()  

  **search**: now supports multi-threaded search  

  **vdb**: fixed a bug in VCursorFindNextRowIdDirect where it returned a wrong rowId  

  **vdb**: fixed a bug in the code used to iterate over blobs where rowmap expansion cache would reset iteration to initial row instead of respecting sequence  

  **ngs**: Fixed a bug in ngs::Alignment::getMateReferenceSpec() affecting pre-March 2015 runs  

  **ngs**: now supports parallel compilation with "make -j N"  

  **vfs**: environment variable VDB_PWFILE is no longer used  

## NCBI VDB 2.6.3

## NGS SDK 1.2.4

**May 25, 2016**

  **vdb**: Fixed a bound on memory cache that would never flush under certain access modes  

## NCBI VDB 2.6.2

**April 20, 2016**

  **kdb**: Fixed VTableDropColumn, so that it can drop static columns  

  **kfs, kns**: Fixed thread safety issues for both cache and http files  

  **kproc**: Fixed KQueue to wake waiters when sealed, fixed KSemaphore to wake waiters when canceled  

  **build**: MSVS 2013 toolset (12.0) is now supported across all repositories  

  **doc, ngs**: updated javadoc to include throws and other missing tags  

  **examples, ngs**: added DumpReferenceFASTA.py example  

  **htsjdk**: added code to HTS-JDK  to avoid involving NGS unless we are sure that it is being requested  

  **ngs, ngs-engine**: Added filtering to NGS of secondary alignments that do not have primary alignments  

  **ngs, test, ngs-python**: fixed bug in String processing for Python 3.x  

  **ngs-engine**: ncbi-ngs engine was updated - fixed a bug that made NGS read iterator return 0 reads on WGS accessions.  

  **ngs**: Improved native library load in ngs-java, enhanced its error reporting and added a mode to disable auto-download of native libraries  

  **ngs**: Python code will check for the latest version of the libraries and update if newer ones are available  

  **ngs**: check for the latest version of the libraries and update if newer ones are available  

  **ngs**: simplified ngs-python bindings  

==============================================================

EXCEPTIONS (in all cases excluding NCBI-written makefiles):

Location: {libs,interfaces}/ext/bzip2

Author:   Julian R Seward

License:  BSDish [libs/ext/bzip2/LICENSE]

Location: {libs,interfaces}/ext/zlib

Authors:  Jean-loup Gailly and Mark Adler

License:  BSDish [interfaces/ext/zlib.h]

Location: libs/klib

Author:   Douglas C. Schmidt

License:  GNU Lesser General Public [libs/klib/qsort.c]

See LICENSE from https://github.com/ncbi/ncbi-vdb

==============================================================

Copyright F.A.Q.

#

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

# default response to "make"

default: std

#-------------------------------------------------------------------------------

# environment

#

TOP ?= $(CURDIR)

include $(TOP)/build/Makefile.shell

std: subdirs

#-------------------------------------------------------------------------------

# default

#

# the sub-directories

SUBDIRS =    \

	libs \

# common targets for non-leaf Makefiles; must follow a definition of SUBDIRS

include $(TOP)/build/Makefile.targets

	ngs-sdk \

	ngs-java \

	ngs-python \

default: $(SUBDIRS)

SUBDIRS_CLN = \

	$(addsuffix _cln,$(SUBDIRS))

test: $(SUBDIRS)

SUBDIRS_INST = \

	$(addsuffix _inst,$(SUBDIRS))

$(SUBDIRS) test:

	@ $(MAKE) -C $@

SUBDIRS_TST = \

	$(addsuffix _test,$(SUBDIRS))

.PHONY: default $(SUBDIRS) test

subdirs: $(SUBDIRS)

#-------------------------------------------------------------------------------

# all

#

$(SUBDIRS_ALL):

clean: $(SUBDIRS_CLN)

#-------------------------------------------------------------------------------

# std

#

$(SUBDIRS_STD):

test: $(SUBDIRS_TST)

#-------------------------------------------------------------------------------

# install

#

install: $(SUBDIRS_INST)

install: 

	@ echo "Checking make status of object libraries..."

	@ $(MAKE) -s --no-print-directory TOP=$(CURDIR) $(SUBDIRS)

	@ $(MAKE) -s --no-print-directory TOP=$(CURDIR) -f build/Makefile.install install

uninstall:    

	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.install uninstall

.PHONY: install uninstall

#-------------------------------------------------------------------------------

# clean

#

clean: clean_test

clean_test:

	@ $(MAKE) -s -C test clean

#-------------------------------------------------------------------------------

# runtests

#

runtests: runtests_test

runtests_test:

	@ $(MAKE) -s -C test runtests

#-------------------------------------------------------------------------------

# slowtests

#

slowtests: slowtests_test

slowtests_test:

	@ $(MAKE) -s -C test slowtests

#-------------------------------------------------------------------------------

# valgrind

#

valgrind: valgrind_test

valgrind_test:

	@ $(MAKE) -s -C test valgrind

#-------------------------------------------------------------------------------

# pass-through targets

#

COMPILERS = GCC ICC VC++ CLANG

ARCHITECTURES = i386 x86_64 sparc32 sparc64

CONFIG = debug profile release

PUBLISH = scm pubtools

REPORTS = bindir targdir osdir config compilers architecture architectures

PASSTHRUS = \

	out \

	CC $(COMPILERS) \

	$(ARCHITECTURES) \

	$(CONFIG) $(PUBLISH) \

	purify purecov \

	local static dynamic

$(RHOSTS):

	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env local

	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env require-proxy-exec

	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env $@

	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env rebuild-dirlinks config

$(PASSTHRUS):

	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env $@

	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env rebuild-dirlinks config

$(REPORTS):

	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env $@

$(SUBDIRS):

	@ $(MAKE) -C $@

.PHONY: $(PASSTHRUS) $(RHOSTS) $(REPORTS)

$(SUBDIRS_CLN):

	@ $(MAKE) -C $(subst _cln,,$@) clean

$(SUBDIRS_INST):

	@ $(MAKE) -s --no-print-directory -C $(subst _inst,,$@) install

#-------------------------------------------------------------------------------

# configuration help

#

help configure:

	@ echo "Before initial build, run 'make OUTDIR=<dir> out' from"

	@ echo "the project root to set the output directory of your builds."

	@ echo

	@ echo "To select a compiler, run 'make <comp>' where"

	@ echo "comp = { "$(COMPILERS)" }."

	@ echo

	@ echo "For hosts that support cross-compilation ( only Macintosh today ),"

	@ echo "you can run 'make <arch>' where arch = { "$(ARCHITECTURES)" }."

	@ echo

	@ echo "To set a build configuration, run 'make <config>' where"

	@ echo "config = { "$(CONFIG)" }."

	@ echo

	@ echo "To select a remote build configuration, run 'make <rhost>' where"

	@ echo "rhost = { "$(RHOSTS)" }."

	@ echo

$(SUBDIRS_TST):

	@ $(MAKE) -C $(subst _test,,$@) test

.PHONY: help configure

.PHONY: $(SUBDIRS) $(SUBDIRS_CLN) $(SUBDIRS_INST)