Mercurial > repos > charles_s_test > seqsero2
diff libs/sratoolkit.2.8.0-centos_linux64/CHANGES @ 3:38ad1130d077 draft
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
author | charles_s_test |
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date | Mon, 27 Nov 2017 11:21:07 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/libs/sratoolkit.2.8.0-centos_linux64/CHANGES Mon Nov 27 11:21:07 2017 -0500 @@ -0,0 +1,135 @@ +# =========================================================================== +# +# 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<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