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