# =========================================================================== # # 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 SRA Software Development Kit Contact: sra-tools@ncbi.nlm.nih.gov 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" 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