xref: /dports/biology/sra-tools/sra-tools-2.11.0/CHANGES.md

# NCBI External Developer Release:


## SRA Toolkit 2.11.0
**March 15, 2021**

  **fasterq-dump**: does not exit with 0 any more if the given path 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 formatting of HTTP requests for 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
  **sra-tools**: created a script to fix names of downloaded sra files
  **sra-tools**: created a script to move downloaded sra run files into proper directories
  **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


## SRA Toolkit 2.10.9
**December 16, 2020**

  **align, vdb**: fixed situation where network access could drastically slow down reading references
  **build**: added configure option to produce build in output directory relative to sources
  **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 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
  **vdb**: prefetch is used for test
  **vfs**: allow to find local files when remote repository is disabled
  **vfs**: not to call names.cgi but SDL when resolving runs and reference sequences


## SRA Toolkit 2.10.8
**June 29, 2020**

  **kproc, fasterq-dump**: fixed problem with seg-faults caused by too small stack used by threads
  **kdbmeta**: allow to work with remote runs
  **kdb, vdb, vfs, sra-tools**: fixed bug preventing use of path to directory created by prefetch if it ends with '/'
  **vfs, sra-tools, ngs-tools**: report an error when file was encrypted for a different ngc file
  **prefetch**: print error message when cannot resolve reference sequence
  **vfs, prefetch**: download encrypted phenotype files with encrypted extension
  **vdb, sra-docker**: config can auto-generate LIBS/GUID when in a docker container


## SRA Toolkit 2.10.7
**May 20, 2020**

  **sratools**: fixed issue with some runs not working correctly and fixed typo in fasterq-dump command line
  **kns, sra-tools, ngs-tools**: added new header to HTTP requests to communicate VDB version


## SRA Toolkit 2.10.6
**MAY 18, 2020**

  **align, sra-tools, ngs-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 having a single 'root' node
  **kns, sra-tools, ngs-tools**: added new header to HTTP requests to communicate SRA version
  **kns, sra-tools**: close socket when accessing GCP files
  **kns, sra-tools, ngs-tools**: introduced a additional configurable network retry loop
  **krypto, sra-tools, vfs**: fixed decryption when password contains # symbol
  **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**: restored possibility to cache WGS references to user repository
  **sra-tools, vfs**: fixed working with runs having WGS reference sequences


## SRA Toolkit 2.10.5
**April 1, 2020**

  **build, sratools**: fixed a potential build problem in libutf8proc
  **ncbi-vdb, ngs, ngs-tools, sra-tools**: all Linux builds now use g++ 7.3 (C++11 ABI)
  **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


## SRA Toolkit 2.10.4
**February 26, 2020**

  **kns, sra-tools:**: fixed errors when using ngc file


## SRA Toolkit 2.10.3
**February 18, 2020**

  **sraxf, fasterq-dump, fastq-dump, sam-dump**: fixed a problem resulting in a segmentation fault


## 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**: 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
  **prefetch, vfs**: allow to specify file type to resolve
  **prefetch, vfs**: allow to use "prefetch --type all" to request download of all file types
  **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**: 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
  **sratools, vdb-config**: dbGaP page removed
  **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**: fixed bug in -X ( hex ) mode
  **vdb-dump, vfs**: addressed obscure bug preventing access to a single external reference
  **vdb-validate**: fixed handling of empty cells affecting certain databases


## SRA Toolkit 2.10.1
**December 16, 2019**

  **sra-tools**: changed version to match that of _ncbi-vdb_


## 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**: fixed crash when run with --output-file option
  **prefetch**: updated prefetch help text
  **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
  **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)
  **test**: created a standard way to detect ascp availability
  **tui, vdb-config**: new look and cloud specific options in 'vdb-config -i'
  **vdb**: make greater use of data returned by latest name resolver
  **vdb-validate**: referential integrity checker prints out completion message, if it printed out any progress
  **vfs**: added possibility to set resolver version from configuration
  **vfs**: allow to use SDL as remote service


## SRA Toolkit 2.9.6
**March 18, 2019**

  **prefetch**, **vfs**: fixed regression that prevented re-download of incomplete files


## SRA Toolkit 2.9.5
**March 6, 2019**

  **prefetch**: fixed regression that caused download of incomplete files


## SRA Toolkit 2.9.4-1
**March 4, 2019**

  **sra-tools, vfs**: fixed regression introduced in 2.9.4 release thas caused delay when starting sra tools


## 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
  **sra-tools, vfs**: added support of realign objects


## SRA Toolkit 2.9.3
**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


## SRA Toolkit 2.9.2-2
**September 26, 2018**

  **read-filter-redact**: Fixed to update HISTORY metadata


## SRA Toolkit 2.9.2
**July 23, 2018**

  **kfg, vfs**: Introduced enhanced handling of download-only NGC files that lack read/decrypt permissions


## SRA Toolkit 2.9.1-2
**July 17, 2018**

  **bam-load**: fixed a bug preventing early termination on error


## SRA Toolkit 2.9.1-1
**June 26, 2018**

  **prefetch**: restored download of dependencies when running "prefetch 'local file'"


## SRA Toolkit 2.9.1
**June 15, 2018**

  **build**: 'make install' ignore ROOT environment variable
  **build**: sra-toolkit GUI is now integrated into the regular build
  **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, 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
  **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.


## SRA Toolkit 2.9.0
**February 23, 2018**

  **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
  **bam-load**: renamed an internal function to avoid a name conflict
  **bam-load, fastq-load**: updated to use better thread termination signaling
  **bam-load, sra-stat**: Updated sra-stat to extract statistics of alterations made by loaders for inclusion in its report
  **build**: Created a script that allows to add a new volume to existing repository
  **build**: Fixed configure allowing to run it on Perl with version >= v5.26 that has "." removed from @INC
  **build**: added "smoke tests"
  **build**: recognize version of libhdf5 that does not allow static linking and do not try to use it
  **build, doc**: added wiki page: Building-from-source-:--configure-options-explained
  **build, ncbi-vdb, sra-tools**: the installation script now saves configuration files if they were modified by the user
  **build, sra-tools**: "make runtests" now invokes "make all"
  **build, vdb-sql**: modified build to avoid vdb-sql in absence of libxml2
  **fastq-dump**: minor change to help text
  **fastq-dump, vdb**: Fixed crashing of fastq-dump when dumping multiple runs with -split-3 option specified
  **fastq-load**: preserves spot names when the platform is Illumina
  **kfg**: added searching of configuration files in ../etc/ncbi/ relative to the binaries
  **kfg, prefetch**: set limit of Aspera usage to 450m
  **kfg, prefetch, remote-fuser, vfs**: Updated resolving of cache location of non-accession objects
  **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
  **latf-load**: now processing multi-line sequences and qualities
  **latf-load**: pacbio spot names with a range are now processed correctly
  **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)
  **vfs**: Name resolving service was updated and switched to protocol version 3.0


## SRA Toolkit 2.8.2
**March 6, 2017**

  **blast**: Updated blast library to be able to process runs having empty rows
  **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**: **bam-load**: changed memcpy to memmove when regions overlap - seems to corrupt data on centos7
  **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
  **build, ncbi-vdb, sra-tools**: installation will back up old configuration files if they differ from the ones being installed
  **cg-load**: added loading of CG File format v2.4
  **kns**: SRA tools respect standard set of environment variables for proxy specification
  **kns**: updated mbedtls library to version 2.4.1
  **ncbi-vdb, ngs, ngs-tools, sra-tools**: eliminated memcpy from sources due to potential for overlap
  **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


## SRA Toolkit 2.8.1-2
**January 19, 2017**

  **prefetch**: fixed download of dbGaP files via HTTP


## SRA Toolkit 2.8.1
**December 22, 2016**

  **bam-load**: the result code updated to indicate empty slice rather than EOF
  **kfg**: added possibility to create an empty KConfig object that does not try to load any file
  **latf-load**: fixed an occasional crash on Ubuntu
  **latf-load, test**: test script no longer executes failing tests for unimplemented features
  **prefetch**: uses KStream rather than KHttpFile - it fixed environments with proxies non supporting HTTP Range
  **sam-dump**: use of --seqid options creates now headers consistent with sam-lines
  **test-sra**: added ability to print http response headers


## 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
  **build**: fixed a bug in 'configure' when in could not find source files in repository saved with non-standard name
  **cg-load**: added loading of CG File format v2.4


## 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
  **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
  **build, sra-tools**: Now makefile copies default.kfg file when it is updated
  **build, sra-tools**: separate decryption package was removed - decryption tools are included as part of sratoolkit.
  **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
  **kns**: replaced all direct uses of sleep() within code to enforce standardization upon mS.
  **kproc, ncbi-vdb**: Fixed KCondition to generate timeout error on Windows when timeout exhausted
  **latf-load**: now handles column values up to 64MB long
  **ngs**: Fixed all crashes when using null as string in ngs-java APIs
  **ngs**: NGS_ReferenceGetChunk() will now return chunks potentially exceeding 5000 bases
  **ngs**: fixed potential concurrency issues at exit, when called from Java
  **ngs**: ngs-java and ngs-python auto-download (of native libraries) now works through HTTPS
  **ngs**: read fragments of length 0 are now ignored
  **ngs, ngs-tools, ref-variation**: added class ngs-vdb::VdbAlignment, featuring method IsFirst()
  **ngs-engine**: improved diagnostic messages
  **ngs-tools**: Fixed Makefiles to keep supporting "./configure; make" build of sra-search, alongside CMake-based build.
  **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**: updated tests to not fail outside of NCBI
  **test-sra**: test-sra prints network information
  **test-sra**: test-sra prints version of ncbi-vdb or ngs-sdk dynamic library
  **vdb**: improved parameter checking on VDatabaseOpenTableRead()
  **vdb**: new function: "VDBManagerDeleteCacheOlderThan()"
  **vdb**: problem with buffer-overrun when compressing random data fixed
  **vdb**: remote/aux nodes have been removed from configuration
  **vdb-dump**: does not ignore table-argument on plain table any more, has to be SEQUENCE on plain tables if used


## SRA Toolkit 2.7.0
**June 12, 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
  **build, sra-tools**: Running make and make install in sra-tools repository prepares all configuration files required to access NCBI repository
  **doc, ncbi-vdb**: created a Wiki page illustrating how to use the API to set up logging
  **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**: Fixed a bug when KHttpRequestPOST generated an incorrect Content-Length after 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
  **sam-dump**: updated to append asterisks to quality field of SAM output when corrupt original BAM has secondary alignment is shorter than the primary.
  **search**: now supports multi-threaded search
  **sra-search**: now supports sorted output
  **sra-tools**: added possibility to build rpm package in sra-toolkit
  **sra-tools**: fixed exit codes for a number of applications in response to command line options
  **vdb-dump**: added tests to verify vdb-dump operation on nested databases
  **vdb-validate**: A new checks were added for SEQUENCE table
  **vdb**: fixed a bug in VCursorFindNextRowIdDirect where it returned a wrong rowId
  **vdb**: fixed a bug in the code used to iterate over blobs where rowmap expansion cache would reset iteration to initial row instead of respecting sequence
  **vfs**: environment variable VDB_PWFILE is no longer used


## 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

## SRA Toolkit 2.6.2
**April 20, 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.
  **build**: Allow to build sra-tools on systems without static c++ library
  **check-corrupt, vdb-validate**: Added a new set of checks that can be triggered by using one of two "--sdc:" cmd options
  **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
  **kdb**: Fixed VTableDropColumn, so that it can drop static columns
  **kfs, kns, ngs, sra-tools**: Fixed thread safety issues for both cache and http files
  **kget**: has a new option --full to match wget in speed. added examples.sh
  **kproc**: Fixed KQueue to wake waiters when sealed, fixed KSemaphore to wake waiters when canceled
  **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**: filters out duplicates in the rows that it generates
  **sam-dump**: produces BX-tags if preserved in SRA file by bam-load
  **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.
  **sra-tools**: [https://github.com/ncbi/sra-tools/issues/27](https://github.com/ncbi/sra-tools/issues/27) : contains short and long examples of how to configure sra-tools build
  **var-expand**: a tool for batch variation expansion
  **vdb-config**: now handles standard options such as --option-file
  **vdb-validate**: Added code to continue with the next row when column has discontiguous blobs