May 21, 2024
ngs-tools: changed version to match that of sra-tools
March 5, 2024
cloud, kns, ngs-tools, sra-tools: don't change global network timeouts when checking cloud location
kns, ngs-tools, sra-tools: fixed hanging on Mac and BSD when data access is unreliable
December 19, 2023
cloud, ngs-tools, sra-tools: accept AWS credentials in CSV format; warn when credentials file cannot be loaded; don't load credentials if user doesn't agree to pay
cloud, ngs-tools, sra-tools: fixed support of IMDSv2 to allow instance identity on Amazon Linux 2023
kns, ngs-tools, sra-tools, vfs: print NCBI_PHID after error in names resolving to simplify troubleshooting
ncbi-vdb, ngs-tools, sra-tools: added support for Arm64
ngs-tools, sra-tools, vdb, vfs: avoids multiple calls to resolve the same accession
September 19, 2023
ngs-tools: changed version to match that of sra-tools
August 29, 2023
cloud, kns, ngs-tools, sra-tools: added support of IMDSv2 to allow to use instance identity on new AWS machines
cloud, ngs-tools, sra-tools, vdb-config: fixed use of AWS credentials
kns, ngs, ngs-tools, sra-tools: fixed a bug that caused failure during accession resolution while reading HTTP stream
July 10, 2023
ngs-tools: changed version to match that of sra-tools
May 9, 2023
kfg, ngs-tools, sra-tools, vfs: stopped using old names resolver cgi
ngs-tools: updated aligns_to to use the latest libraries
December 12, 2022
ngs-tools: changed version to match that of sra-tools
November 15, 2022
build: added support for overriding cmake and ctest commands
build: will use a system-provided libmbedtls, otherwise the copy included in the source code will be used
ngs-tools: fixed configure script
ref-variation: added libraries and tools: ngs-vdb, general-writer, ref-variation, sra-search, general-loader, pileup-stats
February 10, 2022
ngs-tools: updated for sra-tools 3.0.0
October 7, 2021
klib, ngs-tools, sra-tools: status messages (-v) are printed to stderr rather than stdout
kns, ngs-tools, sra-tools: old verbose messages now happen at verbosity > 1
ncbi-vdb, ngs-tools, sra-tools, vdb, vfs: added support of SRA Lite files with simplified base quality scores
sra-search: fixed a data race in reference-driven mode
August 17, 2021
ncbi-vdb, ngs, ngs-tools, sra-tools: configure prints the version of compiler
sra-download: sra-download-manager tool has been removed
March 15, 2021
build, ncbi-vdb, ngs, ngs-tools: introduced an additional external library, libncbi-ngs
kfg, sra-tools, vfs, ngs-tools: dropped support of protected repositories
kns, sra-tools, ngs-tools: fixed formatting of HTTP requests for proxy
ncbi-vdb, ngs, ngs-tools, sra-tools, vdb: added support for 64-bit ARM (AArch64, Apple Silicon)
sra-search: no longer issues unneeded warnings in reference mode
December 16, 2020
build: added configure option to produce build in output directory relative to sources
build, ngs-tools: fixed a c++11 build issue for older compilers
kns, sra-tools, vdb: added a loop to retry failed connections when fetching SRA files
vfs: allow to find local files when remote repository is disabled
June 29, 2020
vfs, sra-tools, ngs-tools: report an error when file was encrypted for a different ngc file
May 21, 2020
kns, ngs-tools, sra-tools: added new header to HTTP requests to communicate VDB version
MAY 18, 2020
align, sra-tools, ngs-tools: fixed fetching of reference sequences from cloud
kns, sra-tools, ngs-tools: added new header to HTTP requests to communicate SRA version
kns, sra-tools, ngs-tools: introduced a additional configurable network retry loop
April 1, 2020
ncbi-vdb, ngs, ngs-tools, sra-tools: all Linux builds now use g++ 7.3 (C++11 ABI)
February 26, 2020
kns, ngs-tools:: fixed errors when using ngc file
February 18, 2020*
ngs-tools: updated for sra-tools 2.10.3
January 15, 2020
ngs-tools: updated tax tools to the latest version
March 18, 2019
ngs-tools: updated for sra-tools 2.10.0
March 18, 2019
ngs-tools: changed version to match that of sra-tools
January 31, 2019
ngs, ngs-tools: dump-ref-fasta: added an option to skip non-local references
October 11, 2018
kns: added possibility to skip server's certificate validation
kns: expect to receive HTTP status 200 when sending range-request that includes the whole file
vdb: fixed a bug in accessing pagemap process request for cursors which do not have pagemap thread running
July 23, 2018
kfg, vfs: Introduced enhanced handling of download-only NGC files that lack read/decrypt permissions
June 15, 2018
fasterq-dump: a tool to dump a whole run in fastq by using a simple query engine approach
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
kns: Randomly select from multiple proxies in configuration
ngs-tools: all tools now report their version correctly
February 23, 2018
build: Fixed configure allowing to run it on Perl with version >= v5.26 that has "." removed from @INC
build: added "smoke tests"
build: now supports "./configure && make" build in ngs-tools/; "make" works in all subdirectories; gmake invokes CMake
build, ngs-tools: added make targets runtests and slowtests
build, ngs-tools: binaries are given versioned names, with corresponding symlinks
build, ngs-tools: library dependencies search is now based on configuration files
build, sra-tools: "make runtests" now invokes "make all"
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
ngs-engine: improved performance when iterating through partially aligned and unaligned reads
ngs-engine: optimized filtered access to unaligned runs
ngs-tools: Added optional dependency on 'sra-tools' needed for some tests
ngs-tools: Created a tool to compute coverage for contigs
ngs-tools: added build instructions
ngs-tools, sra-tools: general-loader and pileup-stats have been moved from sra-tools to ngs-tools
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
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
March 6, 2017
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
kns: SRA tools respect standard set of environment variables for proxy specification
kns: updated mbedtls library to version 2.4.1
ngs, sra-search: now supports search on reference
ngs-tools: updated the NCBI download page to incorporate ngs versions into 3rd party package names
October 7, 2016
version: Moved version from 1.0.x to 2.8.0 to be in sync with sra-tools
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, ngs-tools, ref-variation: added class ngs-vdb::VdbAlignment, featuring method IsFirst()
ngs-tools: Fixed Makefiles to keep supporting "./configure; make" build of sra-search, alongside CMake-based build.
test-sra: test-sra prints version of ncbi-vdb or ngs-sdk dynamic library
July 12, 2016
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-tools, sra-search: now uses NGS-VDB extension of NGS
ngs-tools: NGS-VDB extension of NGS is now in place
search: now supports multi-threaded search
sra-search: now supports sorted output
May 25, 2016
build, ngs-tools: 'make test ' will work now when called from ngs-tools
build, ngs-tools: will create all required directories on the first build
build: MSVS 2013 toolset (12.0) is now supported across all repositories
ngs-engine: ncbi-ngs engine was updated: fixed a bug that made NGS read iterator return 0 reads on WGS accessions.
ngs-tools: now uses CMake as the primary build tool
sra-search: now supports near matches and gapped matches.
vdb, ngs-engine: Fixed a bound on memory cache that would never flush under certain access modes