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author charles_s_test
date Mon, 27 Nov 2017 11:21:07 -0500
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1 # ===========================================================================
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2 #
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3 # PUBLIC DOMAIN NOTICE
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4 # National Center for Biotechnology Information
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5 #
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6 # This software/database is a "United States Government Work" under the
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7 # terms of the United States Copyright Act. It was written as part of
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8 # the author's official duties as a United States Government employee and
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9 # thus cannot be copyrighted. This software/database is freely available
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10 # to the public for use. The National Library of Medicine and the U.S.
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11 # Government have not placed any restriction on its use or reproduction.
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12 #
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13 # Although all reasonable efforts have been taken to ensure the accuracy
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14 # and reliability of the software and data, the NLM and the U.S.
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15 # Government do not and cannot warrant the performance or results that
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16 # may be obtained by using this software or data. The NLM and the U.S.
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17 # Government disclaim all warranties, express or implied, including
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18 # warranties of performance, merchantability or fitness for any particular
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19 # purpose.
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20 #
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21 # Please cite the author in any work or product based on this material.
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22 #
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23 # ===========================================================================
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24
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25 The NCBI SRA Software Development Kit
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26 Contact: sra-tools@ncbi.nlm.nih.gov
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27
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28
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29 NCBI Release: SRA Toolkit 2.8.0
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30 October 7, 2016
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31
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32 HTTPS-ENABLED RELEASE
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33
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34 bam-load: 10x Genomics CB and UB tags are preserved
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35 bam-load: Orphaned secondary alignments will be converted to primary alignments
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36 bam-load: READ_GROUP is populated from 'BC' if 'RG' has no value
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37 bam-load: fixed support for '-V' and '--version' command-line options
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38 blast: Updated BLAST engine to 2.5.0+ version
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39 kfg, kns: Use environment variables to determine the proxy for a http protocol
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40 kfg, vdb-config: vdb-config-GUI has now option to pick up proxy-setting from environment
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41 kns: All tools and libraries now support https
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42 latf-load: now handles column values up to 64MB long
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43 prefetch: Fixed prefetch not to print misleading 'unknown integer storage type' error messages
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44 sam-dump: CB and UB tags are now created if loaded via bam-load from 10xSingleCell
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45 sra-tools: presence of ./ncbi (even if empty) subdirectory next to the executable files is no longer required,
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46 unless configuration files are needed.
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47 test-sra: test-sra prints network information
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48 test-sra: test-sra prints version of ncbi-vdb or ngs-sdk dynamic library
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49 vdb-dump: does not ignore table-argument on plain table any more, has to be SEQUENCE on plain tables if used
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50
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51
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52 NCBI Release: SRA Toolkit 2.7.0
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53 July 14, 2016
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54
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55 align, bam-load: Insert-only alignments no longer cause incorrect binning
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56 bam-load: fixed case where WGS accessions where not being read correctly
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57 bam-load: will NOT perform spot assembly using hard clipped secondary alignments, even when 'make-spots-with-secondary' is enabled
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58 WILL perform spot assembly using hard-clipped secondary alignments when 'defer-secondary' is enabled
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59 blast, kfg, ncbi-vdb, sra-tools, vfs: restored possibility to disable local caching
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60 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.
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61 kar: Alter the default ordering of components of an SRA archive for better network performance
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62 kdb, kfs, kns: Added blob validation for data being fetched remotely
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63 kfg: When loading configuration files on Windows USERPROFILE environment variable is used before HOME
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64 kfg: modified auxiliary remote access configuration to use load-balanced servers
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65 kns: POST will no longer append a content length value when attempting a retry
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66 ngs, search, sra-search: sra-search was modified to support multiple threads.
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67 ngs-engine, ngs-tools, sra-tools, vfs: The "auxiliary" nodes in configuration are now ignored
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68 pileup-stats: updated commandline parser to eat unprocessed parameters
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69 search: now supports multi-threaded search
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70 sra-search: now supports sorted output
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71 sra-tools: fixed exit codes for a number of applications in response to command line options
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72 vdb-validate: A new checks were added for SEQUENCE table
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73 vfs: environment variable VDB_PWFILE is no longer used
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74 gatk, hisat2: we are now releasing 3rd party tools GATK and Hisat2 that are built to access the NCBI SRA
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75
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76
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77 NCBI External Developer Release: SRA Toolkit 2.6.3
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78 May 25, 2016
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79
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80 bam-load: Corrects an optimization used to compare read lengths when lengths are greater than 255
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81 bam-load: alignments which are below the minimum match count but with at least 1/2 of the aligned bases matching are accepted
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82 bam-load: improved performance of SAM parsing code
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83 bam-load: non-fatal result codes no longer cause the reader thread to quit early
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84 bam-load: will NOT do spot assembly using hard clipped secondary alignments even when make-spots-with-secondary is enabled;
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85 WILL do spot assembly using hard-clipped secondary alignments when defer-secondary is enabled
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86 build: MSVS 2013 toolset (12.0) is now supported across all repositories
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87 vdb: Fixed a bound on memory cache that would never flush under certain access modes
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88
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89
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90 NCBI Release: SRA Toolkit 2.6.2
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91 Apr 21, 2016
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92
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93 align-cache: a tool producing vdbcache that reduces effects of random access and improves speed.
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94 bam-load: Fixed bug in validation code for unsorted bam files
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95 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.
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96 bam-load: Secondary alignment will be used for spot assembly if the loader is explicitly told to use them
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97 bam-load: The code that had invalid item in index problem was removed in the process of addressing a performance issue.
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98 bam-load: change reporting of fatal warnings into fatal errors
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99 bam-load: changed from an error to a warning if using secondary alignments to create spots
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100 bam-load: low-match secondary alignments are now discarded; low-match primary alignments are logged, and if too many, it will abort the load.
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101 bam-load: records the contents of the BX tag
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102 bam-load: rules for spot assembly were reverted to assembling spots only on primary alignments
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103 blast, build: Improved blast tools: all required libraries are linked statically.
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104 copycat: now runs on Centos 7; no longer uses system-installed magic file
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105 dbgap-mount: Added support for standard options "-L" and "-o", which allow users to determine the logging level and log output file
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106 dbgap-mount: New optional parameter was introduced '-u' which allows user to unmount FUSE/DOKAN volume. Implemented on linux and windows
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107 fastq-load: The (old) fastq-loader will properly report multiple reads on the 454 platform (and still fail).
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108 kar: added '--md5' option to create md5sum compatible auxiliary file
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109 kget: kget has a new option --full to match wget in speed. added examples.sh
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110 latf-load: now allows undescores inside spot group names
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111 latf-load: now loads data produced by fastq-dump
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112 latf-load: updated to support Illumina tag line format with identifier at the front
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113 pileup-stats: added -V (--version) option: prints out the software
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114 pileup-stats: pileup-stats: added version support (options -V or --version)
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115 prefetch: Added --eliminate-quals option which speeds up HTTP download by ignoring QUALITY column`s data
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116 prefetch: Fixed failure when running prefetch.exe "-a<bin|key>" when there is a space after "-a"
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117 prefetch: messages about maximum size of download are made more user-friendly.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
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118 prefetch: now will download even when caching is disabled
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
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119 ref-variation: --input-file option allows to specify input accessions and paths in the file
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120 ref-variation: added "count-strand" option: it controls relative orientation of 3' and 5' fragments.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
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121 ref-variation: added -c option to flush output immediately; reporting zero matches
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122 ref-variation: added a way to specify a number of repeats of the query
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
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123 ref-variation: improved threading management
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
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124 ref-variation: removed irrelevant warnings reported in some cases in debug version only
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125 sam-dump: Segfault no longer occurs when confronted with large amounts of header lines
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
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126 sam-dump: added option to produce MD tags
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127 sam-dump: added support for generating 10xgenomics BX tag
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128 sam-dump: filters out duplicates in the rows that it generates
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129 sra-sort: correctly generates spot-id column even in the absence of primary alignments
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130 sra-stat: no longer fails when CS_NATIVE column is not present.
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131 sra-tools, vdb-config: Removed dependency of mac binaries on unnecessary libraries, e.g. libxml2.
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132 var-expand: a tool for batch variation expansion
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133 vdb-config: now handles standard options such as --option-file
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134 vdb-validate: Added a new set of checks that can be triggered by using one of two "--sdc:" cmd options
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135 vdb-validate: Added code to continue with the next row when column has discontiguous blobs