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The NCBI SRA Software Development Kit
Contact: sra@ncbi.nlm.nih.gov
NCBI Release: SRA Toolkit 3.0.10
December 19, 2023
cloud, ngs-tools, sra-tools: accept AWS credentials in CSV format; warn when credentials file cannot be loaded
cloud, ngs-tools, sra-tools: fixed support on instance identity on Amazon Linux 2023
fasterq-dump: does not emit warning when used on a not-kar'ed accession
fasterq-dump: handles tiny accession correctly
kns, ngs-tools, sra-tools, vfs: improved error logging messages
ncbi-vdb, ngs-tools, sra-tools: added binaries for Arm64 (e.g. Apple Silicon)
ngs-tools, sra-tools, vdb, vfs: avoids multiple calls to resolve the same accession
prefetch: prints to stdout
vdb-dump: added support for new platforms
vdb-validate: optional check for correct redaction added
NCBI Internal Release: SRA Toolkit 3.0.8
September 19, 2023
align, bam-load: 'circular' can be set from configuration for fasta references
NCBI Release: SRA Toolkit 3.0.7
August 29, 2023
abi-load, fastq-load, helicos-load, illumina-load, pacbio-load, sff-load, sra, srf-load: fixed loaders to work without predefined schema
align-info, prefetch, vdb, vfs: stopped printing incorrect 'reference not found' messages; reduced number of calls to resolve WGS references; align-info don't resolve references remotely if found locally
bam-load: changed 'secondary' to 'non-primary' in log messages
bam-load, kdb, vdb-validate: index works correctly with only one key
cloud, kns, ngs-tools, sra-tools: fixed support on 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 prevented accession resolution
sra-info: added parameter --rows to spot layout query
sra-info: added query --schema
sra-info: fixed formatting of multiple queries
vdb-dump: new --inspect feature to show column-size and compression ratios
vdb-validate: compensated for loader optimization that caused a segfault
vdb, vdb-validate: fixes a memory leak
NCBI Release: SRA Toolkit 3.0.6
July 10, 2023
bam-load, sra-stat: fixed false detection of CMP_BASE_COUNT mismatch for unaligned runs
cloud, sra-tools: fixed a bug preventing access to GCP user-pay buckets
fasterq-dump: now switches to split-files if asked to include technical reads
sra-info: added query --spot-layout
sratools: better handling for URL command line arguments
sra-tools wiki: new features for fasterq-dump appended
vdb-config: handles path on windows for temp. storage correctly
vdb-copy: return error code in case of invalid/missing input
NCBI Release: SRA Toolkit 3.0.5
May 9, 2023
bam-load: added option "--min-batch-size" to control spot assembly
fasterq-dump: added error reports
fasterq-dump: can now handle native PacBio HDF5-accessions
fasterq-dump: clearer message if the output-file(s) cannot be overwritten or created
fasterq-dump, fastq-dump, sam-dump: fixed parameter handling for ngc file
fasterq-dump: fixed a crash when modifying defline on flat tables
fasterq-dump: new options to output the references of an accession
fasterq-dump: new options to produce FASTA for WGS and REFSEQ-objects
fasterq-dump: new python3 tests against multiple options and accessions
fasterq-dump: now handles PacBio-accession loaded with bam-load
fasterq-dump: read-id is now always correctly populated
fastq-load, SharQ: added new platform Element Aviti
kfg, ngs-tools, sra-tools, vfs: stopped using old names resolver cgi
latf-load: will not randomly print "KQueuePop failed" error at the end of processing
sam-dump, sra-pileup: added error report
sra-info: new tool to report run info
sra-tools: added schemas to reduce warnings
sratools: mismatching lite/normalized cache files from SDL are not used
test-sra: updated to call modern names service; fixed malformed XML
vdb-validate: fixed a potential crash due to memory corruption
vdb-validate: removed warning message about no platform column
NCBI Release: SRA Toolkit 3.0.3
January 3, 2023
sra-stat: fixed regression leading to a crash
NCBI Release: SRA Toolkit 3.0.2
December 12, 2022
prefetch: fixed 'buffer insufficient while converting string within text module' failure on Mac
NCBI Release: SRA Toolkit 3.0.1
November 15, 2022
bam-load: distributing bam-load for Mac stopped
bam-load: reference resolution honors more the configuration information
fasterq-dump: having the same sequence in the sequence-table as well as in the alignment table is tolerated now
fasterq-dump: includes accession in help-text now
kfg: fixed a bug that caused override of user configuration
kfg, sra-tools: removed interactive requirement to configure SRA Toolkit
kfs: fixed bug with long paths
kns, sra-tools: allow to use AWS data with compute environment via proxy
latf-load: fixed a bug causing a potential freeze on reaching a maximum number of errors
ref-variation: added libraries and tools: ngs-vdb, general-writer, ref-variation, sra-search, general-loader, pileup-stats
sam-dump: missing quality score printed as *
sam-dump: new option to output '*' for quality scores
SharQ: supports nanopore FASTQ format
sra-pileup, vfs: fixed crash when working with no-quality run
sra-stat: prints detailed information for detected mismatch of recorded and calculated statistics
sra-tools, vdb: retired vdb-get
sra-tools, vfs: fixed infinite loop when resolving some accessions
test: stopped distribution of Makefiles for NGS C++ examples
vdb: updated zlib version to fix vulnerability
NCBI Release: SRA Toolkit 3.0.0
February 10, 2022
blast: BLAST tools are now distributed by Blast team
build, ngs, sra-tools: ngs project has been moved to sra-tools
fasterq-dump: fails if stdout requested, but there are multiple output streams
fasterq-dump, fastq-dump, sratools: fixed a bug that caused multiple accession to cause the tool to exit with an error
fasterq-dump: fixed problem where files could be deleted if output directory was a symlink
fasterq-dump: now with pre-flight mode
fasterq-dump, vfs: fixed a warning message when processing prefetched protected run
fastq-dump: create correct name when processing protected run
latf-load: added support for interleaved file I/O
latf-load: added support for long barcodes with '+' in them
latf-load: updated spot assembly for reads with # style barcodes
latf-load: updated spot assembly to pair /1 and /2 reads
latf-load: will no longer accept duplicate read names
ngs: clients will not download dynamic libraries anymore
prefetch: fixed checking of dependencies for absolute path
prefetch, vdb: fixed to downloads reference sequences into "Accession-Directory" when zero-quality is preferred
remote-fuser: was retired
sratools: seq-defline and qual-defline options work correctly
sratools: tries harder to find the executable path on macOS
vdb-decrypt: remove "_dbGaP" suffix when decrypting protected run
vdb-dump: exits with non-zero return code when reference sequences are not found
kfs, sra-tools: fixed a bug in handling of long URLs on Windows
NCBI Release: SRA Toolkit 2.11.3
October 25, 2021
fasterq-dump, sratools: fasta and fasta-unsorted parameters work correctly
NCBI Release: SRA Toolkit 2.11.2
October 7, 2021
fasterq-dump: added flexible defline, fasta-unsorted, only-aligned, only-unaligned
fasterq-dump: new output format available: --fasta
fasterq-dump: option -t sets directory of all temp files (including VDB cache)
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
prefetch, vfs: fixed a problem that prevented downloading of files named with special characters
sam-dump: fixed wrong value for SAM RNEXT field for unaligned records
sra-tools, sratools: verbose option displays information about the type of quality scores contained in the files being used
sratools: temporarily changes quality score preference when quality scores are not being used
sra-tools, vdb: environment variable NCBI_TMP_CACHE sets the caching directory, overriding any other setting
vdb-dump: --info produces valid JSON
NCBI Release: SRA Toolkit 2.11.1
August 17, 2021
align, axf, sra-pileup, vdb, vfs: resolve reference sequences within output directory
cloud, kns, sra-tools: fixed problems with compute environment
prefetch: better control of reference sequences
prefetch: fixed failure when protected repository exists
prefetch: fixed infinite loop
prefetch, vdb, vfs: prefetch with "-O" will now correctly place references in output directory
prefetch, vfs: fixed error message 'multiple response SRR URLs for the same service...' when downloading
prefetch: will download any missed dependencies
vdb-dump: using --info with URLs now works correctly
NCBI Release: SRA Toolkit 2.11.0
March 15, 2021
fasterq-dump: does not exit with 0 any more if the given path/accession is not found
fasterq-dump: does not exit with 0 if accession is not found
fasterq-dump: does not fail when requested to dump a run file with non-standard name
fasterq-dump: available on Windows
kfg, prefetch, vfs: resolve WGS reference sequences into "Accession Directory"
kfg, sra-tools, vfs: dropped support of protected repositories
kns, sra-tools: fixed work via proxy
ncbi-vdb, ngs, ngs-tools, sra-tools, vdb: added support for 64-bit ARM (AArch64, Apple Silicon)
prefetch, vfs: fixed download of protected non-run files
prefetch, vfs: fixed segfault during download of JWT cart
prefetch, vfs: respect requested version when downloading WGS files
sra-pileup: now silent if requested slice has no alignments or reference-name does not exist
sratools: added description and documentation of the sratools driver tool to GitHub wiki
sratools: disable-multithreading option removed from help text for tools that do not support it
sratools: does not access remote repository when it is disabled
sra-tools, vfs: recognize sra file names with version
vdb-dump: exits with no-zero value if asked for non existing column
NCBI Release: SRA Toolkit 2.10.9
December 16, 2020
align, vdb: fixed situation where network access could drastically slow down reading references
fasterq-dump: better recognizes pacbio-runs
fasterq-dump: ignore .sra-extension of input-filename in output-filename
fasterq-dump: non-zero return-code if no arguments given
fastq-dump: fasta parameter will complain about invalid argument
kar: added availability to open remote files on cloud
kns, sra-tools, vdb: added a loop to retry failed connections when fetching SRA files
latf-load: added an option to drop read names (--no-readnames), preserve them by default
prefetch: support of ETL - BQS (synthesized quality) runs
sra-docker: documentation for toolkit docker
sratools: driver tool passes all arguments to the driven tool
sratools: fixed bug that prevented the `concatenate-reads` option from working
sratools: fixed typo `split-e` for option `split-3`
sratools: tools can be executed with no arguments
sratools: transport option is now deprecated and silently ignored
sratools: verbosity argument is passed on to driven tool
vdb-config: added a new option to force use of full qualities
vfs: allow to find local files when remote repository is disabled
vfs: call SDL service when resolving runs and reference sequences
NCBI Release: SRA Toolkit 2.10.8
June 25, 2020
kdbmeta: allow to work with remote runs
prefetch: print error message when cannot resolve reference sequence
vfs, prefetch: download encrypted phenotype files with encrypted extension
kdb, vdb, vfs, sra-tools: fixed bug preventing use of path to directory created by prefetch if it ends with '/'
kproc, fasterq-dump: fixed problem with seg-faults caused by too small stack used by threads
vfs, sra-tools, ngs-tools: report an error when file was encrypted for a different ngc file
NCBI Release: SRA Toolkit 2.10.8
June 24, 2020
sratools, sra-tools: fixed issue with some runs not working correctly and fixed typo in fasterq-dump command line
NCBI Release: SRA Toolkit 2.10.7
May 22, 2020
sratools, sra-tools: fixed issue with some runs not working correctly and fixed typo in fasterq-dump command line
kns, ngs-tools, sra-tools: added new header to HTTP requests to communicate VDB version
NCBI Release: SRA Toolkit 2.10.6
May 15, 2020
align, sra-tools: fixed fetching of reference sequences from cloud
align, sra-tools, vfs: fixed resolving of hs37d5 reference sequence
build, sra-tools: installation script works when libmagic is not present
kar: errors fixed in kar utility
kfg, sra-tools: ignore configuration with invalid protected user repository
kns, sra-tools: fixed error message when accessing GCP files
kns, sra-tools: increased tolerance to network timeouts
krypto, sra-tools, vfs: fixed decryption bug
prefetch: allow to resume interrupted download, validate downloaded file
sratools: sra-tools are now available on Windows
sratools, vdb-dump, vfs: fixed vdb-dump <accession of prefetched run>
sra-tools, vdb: improved caching of WGS reference sequences
sra-tools, vfs: fixed use of WGS reference sequences
NCBI Release: SRA Toolkit 2.10.5
April 1, 2020
prefetch: improvements were made to work in environments with bad network connections.
prefetch, sratools: fixed the names of the --min-size and --max-size command line arguments when running prefetch
NCBI Release: SRA Toolkit 2.10.4
February 26, 2020
kns, ngs-tools, sra-tools: fixed errors when using ngc file
NCBI Release: SRA Toolkit 2.10.3
February 13, 2020
sraxf, sam-dump, fasterq-dump, fastq-dump: fixed a problem resulting in a segmentation fault
NCBI Release: SRA Toolkit 2.10.2
January 15, 2020
cloud, kfg, vdb-config: added command line options for cloud configuration
fasterq-dump: fixed bug of random error at startup
kfg, kns, krypto, prefetch, vdb-config, vfs: names service URL was updated to locate.ncbi.nlm.nih.gov
kfg, prefetch, vfs: fixed possibility to prefetch karts with genotype and phenotype files
latf-load: latf-load now preserves read names
prefetch, vfs: allow to specify file type to prefetch
prefetch, vfs: allow to use "prefetch --type all" to request download of all file types
prefetch: accepts JWT cart command line argument
prefetch: accepts JWT cart command line argument plus accession filter
prefetch: fixed crash when run with --output-file option
prefetch: make sure to accept old style kart file; added --cart command line option
prefetch: the download transport has been limited to https and the eliminate-quals option has been temporarily disabled
sra-pileup: printing bases inbetween slices when user-defined ref-name given fixed
sra-stat: can accept any number of reads
srapath: fixed regression when an extra vdbcache URL is printed
srapath: fixed regression when resolving protected data
sratools, vdb-config: dbGaP page removed
sratools: add --perm option to all accessor tools
sratools: added --ngc command line argument
sratools: fastq-dump accepts both -v and --verbose to enable verbose mode
sratools: sratools accept --ngc to specify the ngc file
sratools: sratools accepts -Z for fasterq-dump
sratools: sratools was rewritten as a stand-alone binary
vdb, vdb-config: GUID shown in vdb-config or created if not yet present
vdb, vdb-dump: fixed an error reporting bug
vdb-config: allow multiple saves in interactive mode
vdb-config: disabled possibility to import ngc file
vdb-config: fixed bug in file-select-dialog
vdb-config: wording of public user-repository changed to just user-repository
vdb-dump, vfs: addressed obscure bug preventing access to a single external reference
vdb-dump: fixed bug in -X ( hex ) mode
NCBI Release: SRA Toolkit 2.10.0
August 19, 2019
bam-load: SAM/BAM record sizes are limited only by available memory
fastq-dump: fixed help text
kfg, sra-tools: use trace.ncbi.nlm.nih.gov to call names service
kfg, vdb-config: alternative remote repository URL was added to default configuration
kfs: introduced readahead strategy for cloud storage
klib, vdb: error report is saved to ncbi_error_report.txt
kns: We now use system root CA certs on Unix
kns: introduced configurable controls over network timeouts
prefetch, srapath: support for original submission files in cloud storage
prefetch, srapath, vfs: added possibility to specify data location
prefetch, vdb: adjustments for latest name resolution service
prefetch, vfs: added support of "run accession as directory"
prefetch, vfs: added support of download of reference sequences in "run accession as directory"
prefetch, vfs: fixed regression when prefetch does not download vdbcache
prefetch: fixed crash when run with --output-file option
prefetch: updated prefetch help text
sra-stat: don't print mismatch warning for old runs having a single SEQUENCE table and CMP_BASE_COUNT=BIO_BASE_COUNT while it should be 0
sra-stat: fixed a bug when processing runs having spots with first reads with length 0
srapath, sratools: Added support of "run accession as directory"
sratools: SRA tools are executed by a driver tool called sratools
sratools: installation creates symlinks to invoke some tools via a driver tool (sratools)
tui, vdb-config: new look and cloud specific options in 'vdb-config -i'
vdb-validate: referential integrity checker prints out completion message, if it printed out any progress
NCBI Release: SRA Toolkit 2.9.6-1
May 7, 2019
prefetch: rolled back to version 2.9.3 to fix regression that prevented download of vdbcache files
NCBI Release: SRA Toolkit 2.9.6
March 18, 2019
prefetch, vfs: fixed regression that prevented re-download of incomplete files
NCBI Release: SRA Toolkit 2.9.5
March 6, 2019
prefetch: fixed regression that caused download of incomplete files
NCBI Release: SRA Toolkit 2.9.4-2
March 6, 2019
prefetch: rolled back to version 2.9.3 to fix regression that caused download of incomplete files
NCBI Release: SRA Toolkit 2.9.4-1
March 4, 2019
sra-tools, vfs: fixed regression causing delay when starting sra tools
NCBI Release: SRA Toolkit 2.9.4
January 31, 2019
fasterq-dump: improved handling of temp files in case of multiple instances
fasterq-dump: produces same output as fastq-dump on SRR000001 (empty reads)
fastq-dump: updated typo in error report
ngs, ngs-tools: dump-ref-fasta: added an option to skip non-local references
read-filter-redact: Fixed to update HISTORY metadata
sra-tools, vfs: added support of realign objects
NCBI Release: SRA Toolkit 2.9.2
July 23, 2018
kfg, vfs: introduced enhanced handling of download-only NGC files that lack read/decrypt permissions
NCBI Release: SRA Toolkit 2.9.1-1
June 27, 2018
prefetch: restored download of dependencies when running "prefetch 'local file'"
NCBI Release: SRA Toolkit 2.9.1
June 18, 2018
fasterq-dump: a tool to dump a whole run in fastq by using a simple query engine approach
kar: Reduced memory consumption for extract operations
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
prefetch: allows user to specify output file or directory
prefetch: fixed leaking of file descriptors during ascp download
prefetch: now supports download from URL
prefetch: relays error messages generated by ascp and prints them to prefetch error log.
NCBI Release: SRA Toolkit 2.9.0
February 23, 2018
align: AlignAccessRefSeqEnumeratorNext no longer filters by the index
align: fixed a bug which caused sam-dump to quit with an error under certain conditions
bam-load, sra-stat: Updated sra-stat to extract statistics of alterations made by loaders for inclusion in its report
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
fastq-dump, vdb: Fixed crashing of fastq-dump when dumping multiple runs with -split-3 option specified
fastq-dump: minor change to help text
fastq-load: preserves spot names when the platform is Illumina
kfg, prefetch, remote-fuser, vfs: Updated resolving of cache location of non-accession objects
kfg, prefetch: set limit of Aspera usage to 450m
kns: Accept the same http_proxy specifications as wget
kns: Added possibility to report server's IP address after network error
kns: added mechanism for enabling mbedtls internal logging to reveal more information about failures
kns: fixed a case where an invalid error message resulted from dropped connection
latf-load: now processing multi-line sequences and qualities
latf-load: pacbio spot names with a range are now processed correctly
ncbi-vdb: fixed bug of directory not found on mac
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
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)
vdb: An error caused by a rare condition was fixed
NCBI Release: SRA Toolkit 2.8.2-1
March 14, 2017
vdb-config: fixed regression: vdb-config exited with error when there was no user default path in configuration
NCBI Release: SRA Toolkit 2.8.2
March 6, 2017
blast, build: removed library dependencies that were preventing users from launching these tools
blast, sra-tools: Prepared completely static build of blast tools for windows with HTTPS support
build, ncbi-vdb, sra-tools: installation will back up old configuration files if they differ from the ones being installed
build: created sra-toolkit Debian package
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: updated mbedtls library to version 2.4.1
ncbi-vdb: configure in detects existence of ngs jar file
ngs, sra-search: now supports search on reference
ngs-tools: updated the NCBI download page to incorporate ngs versions into 3rd party package names
prefetch: Fixed error message "path excessive while opening directory" when prefetch is trying to get vdbcache
prefetch: Fixed regression in prefetch-2.8.1 when downloading dbGaP files via HTTP
prefetch: Fixed regression in prefetch-2.8.1 when downloading vdbcache files from dbGaP via HTTP
sam-dump: consistency of sam-dump in fastq-mod improved
sam-dump: consistency of sam-dump in fastq-mode improved
sra-stat: sra-stat does XML-escaping when printing spot-groups
test-sra: extended test-sra to debug user problems with https connections to NCBI
test-sra: test-sra print amount of available disk space in user repositories
vdb-config: vdb-config correctly works when there is non-canonical path in configuration
vdb: increased tenacity in flushing data to disk to accommodate behaviors of file systems such as Lustre.
NCBI Release: SRA Toolkit 2.8.1-3
February 7, 2017
abi-dump, fastq-dump, illumina-dump, sff-dump: fixed generation of bad gzipped output
prefetch: fixed download of dbGaP vdbcache files via HTTP
NCBI Release: SRA Toolkit 2.8.1-2
January 19, 2017
prefetch: fixed download of dbGaP files via HTTP
NCBI Release: SRA Toolkit 2.8.1-1
January 18, 2017
prefetch: rolled back to 2.8.0 ( fails to download dbGaP files via HTTP )
NCBI Release: SRA Toolkit 2.8.1
December 22, 2016
latf-load: fixed an occasional crash on Ubuntu
prefetch: now streams data over http when retrieving entire files
sam-dump: use of --seqid options creates now headers consistent with sam-lines
test-sra: added ability to print http response headers
blastn_vdb, tblastn_vdb: reduced dependency upon external libraries through static linkage
NCBI Release: SRA Toolkit 2.8.0-2
December 8, 2016
bam-load: changed memcpy to memmove when regions overlap - seems to corrupt data on centos7
blastn_vdb, tblastn_vdb : removed library dependencies that were preventing users from launching these tools
cg-load: added loading of CG File format v2.4
NCBI Release: SRA Toolkit 2.8.0
October 7, 2016
HTTPS-ENABLED RELEASE
bam-load: 10x Genomics CB and UB tags are preserved
bam-load: Orphaned secondary alignments will be converted to primary alignments
bam-load: READ_GROUP is populated from 'BC' if 'RG' has no value
bam-load: fixed support for '-V' and '--version' command-line options
blast: Updated BLAST engine to 2.5.0+ version
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
kns: All tools and libraries now support https
latf-load: now handles column values up to 64MB long
prefetch: Fixed prefetch not to print misleading 'unknown integer storage type' error messages
sam-dump: CB and UB tags are now created if loaded via bam-load from 10xSingleCell
sra-tools: presence of ./ncbi (even if empty) subdirectory next to the executable files is no longer required,
unless configuration files are needed.
test-sra: test-sra prints network information
test-sra: test-sra prints version of ncbi-vdb or ngs-sdk dynamic library
vdb-dump: does not ignore table-argument on plain table any more, has to be SEQUENCE on plain tables if used
NCBI Release: SRA Toolkit 2.7.0
July 14, 2016
align, bam-load: Insert-only alignments no longer cause incorrect binning
bam-load: fixed case where WGS accessions where not being read correctly
bam-load: will NOT perform spot assembly using hard clipped secondary alignments, even when 'make-spots-with-secondary' is enabled
WILL perform spot assembly using hard-clipped secondary alignments when 'defer-secondary' is enabled
blast, kfg, ncbi-vdb, sra-tools, vfs: restored possibility to disable local caching
fastdump, sra-tools: new tool to perform fast dumps of a whole run in either fastq or a custom format for one of our customers.
kar: Alter the default ordering of components of an SRA archive for better network performance
kdb, kfs, kns: Added blob validation for data being fetched remotely
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: POST will no longer append a content length value when attempting a 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
pileup-stats: updated commandline parser to eat unprocessed parameters
search: now supports multi-threaded search
sra-search: now supports sorted output
sra-tools: fixed exit codes for a number of applications in response to command line options
vdb-validate: A new checks were added for SEQUENCE table
vfs: environment variable VDB_PWFILE is no longer used
gatk, hisat2: we are now releasing 3rd party tools GATK and Hisat2 that are built to access the NCBI SRA
NCBI External Developer Release: SRA Toolkit 2.6.3
May 25, 2016
bam-load: Corrects an optimization used to compare read lengths when lengths are greater than 255
bam-load: alignments which are below the minimum match count but with at least 1/2 of the aligned bases matching are accepted
bam-load: improved performance of SAM parsing code
bam-load: non-fatal result codes no longer cause the reader thread to quit early
bam-load: will NOT do spot assembly using hard clipped secondary alignments even when make-spots-with-secondary is enabled;
WILL do spot assembly using hard-clipped secondary alignments when defer-secondary is enabled
build: MSVS 2013 toolset (12.0) is now supported across all repositories
vdb: Fixed a bound on memory cache that would never flush under certain access modes
NCBI Release: SRA Toolkit 2.6.2
Apr 21, 2016
align-cache: a tool producing vdbcache that reduces effects of random access and improves speed.
bam-load: Fixed bug in validation code for unsorted bam files
bam-load: If two (or more) local reference names refer to the same global reference, bam-load will record the first one used and report the change.
bam-load: Secondary alignment will be used for spot assembly if the loader is explicitly told to use them
bam-load: The code that had invalid item in index problem was removed in the process of addressing a performance issue.
bam-load: change reporting of fatal warnings into fatal errors
bam-load: changed from an error to a warning if using secondary alignments to create spots
bam-load: low-match secondary alignments are now discarded; low-match primary alignments are logged, and if too many, it will abort the load.
bam-load: records the contents of the BX tag
bam-load: rules for spot assembly were reverted to assembling spots only on primary alignments
blast, build: Improved blast tools: all required libraries are linked statically.
copycat: now runs on Centos 7; no longer uses system-installed magic file
dbgap-mount: Added support for standard options "-L" and "-o", which allow users to determine the logging level and log output file
dbgap-mount: New optional parameter was introduced '-u' which allows user to unmount FUSE/DOKAN volume. Implemented on linux and windows
fastq-load: The (old) fastq-loader will properly report multiple reads on the 454 platform (and still fail).
kar: added '--md5' option to create md5sum compatible auxiliary file
kget: kget has a new option --full to match wget in speed. added examples.sh
latf-load: now allows undescores inside spot group names
latf-load: now loads data produced by fastq-dump
latf-load: updated to support Illumina tag line format with identifier at the front
pileup-stats: added -V (--version) option: prints out the software
pileup-stats: pileup-stats: added version support (options -V or --version)
prefetch: Added --eliminate-quals option which speeds up HTTP download by ignoring QUALITY column`s data
prefetch: Fixed failure when running prefetch.exe "-a<bin|key>" when there is a space after "-a"
prefetch: messages about maximum size of download are made more user-friendly.
prefetch: now will download even when caching is disabled
ref-variation: --input-file option allows to specify input accessions and paths in the file
ref-variation: added "count-strand" option: it controls relative orientation of 3' and 5' fragments.
ref-variation: added -c option to flush output immediately; reporting zero matches
ref-variation: added a way to specify a number of repeats of the query
ref-variation: improved threading management
ref-variation: removed irrelevant warnings reported in some cases in debug version only
sam-dump: Segfault no longer occurs when confronted with large amounts of header lines
sam-dump: added option to produce MD tags
sam-dump: added support for generating 10xgenomics BX tag
sam-dump: filters out duplicates in the rows that it generates
sra-sort: correctly generates spot-id column even in the absence of primary alignments
sra-stat: no longer fails when CS_NATIVE column is not present.
sra-tools, vdb-config: Removed dependency of mac binaries on unnecessary libraries, e.g. libxml2.
var-expand: a tool for batch variation expansion
vdb-config: now handles standard options such as --option-file
vdb-validate: Added a new set of checks that can be triggered by using one of two "--sdc:" cmd options
vdb-validate: Added code to continue with the next row when column has discontiguous blobs