Commit 06555f99 authored by Andreas Tille's avatar Andreas Tille

New upstream version 2.8.1

parent b6dd5579

Too many changes to show.

To preserve performance only 1000 of 1000+ files are displayed.

### Verify
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### Subject of the issue
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Provide **screenshots** , **stacktrace** , **logs** where appropriate.
### Your environment
* version of htsjdk
* version of java
* which OS
### Steps to reproduce
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### Expected behaviour
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### Actual behaviour
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### Description
Please explain the changes you made here.
Explain the **motivation** for making this change. What existing problem does the pull request solve?
### Checklist
- [ ] Code compiles correctly
- [ ] New tests covering changes and new functionality
- [ ] All tests passing
- [ ] Extended the README / documentation, if necessary
- [ ] Is not backward compatible (breaks binary or source compatibility)
.DS_Store
._*
*.d
*.db
*.o
*.pyc
/bin64
/build/BUILD.*
/build/COMP.mac
/centos
/ilib64
/lib64
/mac
/Makefile.config.*
/reconfigure
/schema
/test-bin64
/win
*.log
/.cproject
/.project
/.pydevproject
htsjdk.iws
.command_tmp
atlassian-ide-plugin.xml
/htsjdk.version.properties
/test-output
#intellij
.idea/
src/htsjdk.iml
*.iml
*.ipr
*.iws
#gradle stuff
.gradle/
build/
language: java
dist: trusty
sudo: true
before_cache:
- rm -f $HOME/.gradle/caches/modules-2/modules-2.lock
cache:
directories:
- $HOME/.gradle/caches/
- $HOME/.gradle/wrapper/
- $HOME/.m2
jdk:
- oraclejdk8
script: ./gradlew jacocoTestReport testSRA;
after_success:
- echo "TRAVIS_BRANCH='$TRAVIS_BRANCH'";
echo "JAVA_HOME='$JAVA_HOME'";
./gradlew coveralls;
if [ "$TRAVIS_BRANCH" == "master" ]; then
./gradlew uploadArchives;
fi
# ===========================================================================
#
# 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 External Developer Release: SRA Toolkit 2.7.0
July 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
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 External Developer Release: 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: 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 : 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
# NCBI External Developer Release:
## 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