diff --git a/TOOLS/sratoolkit/CHANGES b/TOOLS/sratoolkit/CHANGES index 09940723d60b81c059026e1c013b337f06e675ff..edd0650b2007b8e2245d264979e543e4e51a3935 100644 --- a/TOOLS/sratoolkit/CHANGES +++ b/TOOLS/sratoolkit/CHANGES @@ -26,6 +26,52 @@ The NCBI SRA Software Development Kit Contact: sra@ncbi.nlm.nih.gov +NCBI Release: SRA Toolkit 2.10.9 +December 16, 2020 + + align, vdb: fixed situation where network access could drastically slow down reading references + 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 (synthesized quality) 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 + vfs: allow to find local files when remote repository is disabled + vfs: call SDL service when resolving runs and reference sequences + + +NCBI Release: SRA Toolkit 2.10.8 +June 25, 2020 + + kdbmeta: allow to work with remote runs + prefetch: print error message when cannot resolve reference sequence + vfs, prefetch: download encrypted phenotype files with encrypted extension + kdb, vdb, vfs, sra-tools: fixed bug preventing use of path to directory created by prefetch if it ends with '/' + kproc, fasterq-dump: fixed problem with seg-faults caused by too small stack used by threads + vfs, sra-tools, ngs-tools: report an error when file was encrypted for a different ngc file + + +NCBI Release: SRA Toolkit 2.10.8 +June 24, 2020 + sratools, sra-tools: fixed issue with some runs not working correctly and fixed typo in fasterq-dump command line + + +NCBI Release: SRA Toolkit 2.10.7 +May 22, 2020 + sratools, sra-tools: fixed issue with some runs not working correctly and fixed typo in fasterq-dump command line + kns, ngs-tools, sra-tools: added new header to HTTP requests to communicate VDB version + + NCBI Release: SRA Toolkit 2.10.6 May 15, 2020 align, sra-tools: fixed fetching of reference sequences from cloud diff --git a/TOOLS/sratoolkit/README.md b/TOOLS/sratoolkit/README.md index fc88fa0c446b13af8b5e018a73c5e5e4ff5cedd0..becf46b663f71de595575f3e77fb4b462427f370 100644 --- a/TOOLS/sratoolkit/README.md +++ b/TOOLS/sratoolkit/README.md @@ -14,6 +14,18 @@ The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. ### ANNOUNCEMENT: +NIH has released a request for information (RFI) to solicit community feedback on new proposed Sequence Read Archive (SRA) data formats. Learn more and share your thoughts at https://go.usa.gov/xvhdr. The response deadline is July 17th, 2020. We’d encourage you all to share with your colleagues and networks, and respond if you are an SRA submitter or data user. + +SRA Toolkit 2.10.8 + +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 2.10.5 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) diff --git a/TOOLS/sratoolkit/bin/abi-dump.2 b/TOOLS/sratoolkit/bin/abi-dump.2 index 25a7ba5e5c592dee06fc4cf9585d2d04c31b4072..a2e52970582b59a22e1091ded40a6bde06de4f06 120000 --- a/TOOLS/sratoolkit/bin/abi-dump.2 +++ b/TOOLS/sratoolkit/bin/abi-dump.2 @@ -1 +1 @@ -abi-dump.2.10.6 \ No newline at end of file +abi-dump.2.10.9 \ No newline at end of file diff --git a/TOOLS/sratoolkit/bin/abi-dump.2.10.6 b/TOOLS/sratoolkit/bin/abi-dump.2.10.6 deleted file mode 100755 index 06e8e5bb0d1cc45cf8b97cc13af3497ed1d985ac..0000000000000000000000000000000000000000 Binary files a/TOOLS/sratoolkit/bin/abi-dump.2.10.6 and /dev/null differ diff --git a/TOOLS/sratoolkit/bin/abi-load.2 b/TOOLS/sratoolkit/bin/abi-load.2 index 3c427086824457ff795a36ccf6b2d29ef2071758..bd3bef39272d9bbf482d22a5223d4879693231f0 120000 --- a/TOOLS/sratoolkit/bin/abi-load.2 +++ b/TOOLS/sratoolkit/bin/abi-load.2 @@ -1 +1 @@ -abi-load.2.10.6 \ No newline at end of file +abi-load.2.10.9 \ No newline at end of file diff --git a/TOOLS/sratoolkit/bin/abi-load.2.10.6 b/TOOLS/sratoolkit/bin/abi-load.2.10.6 deleted file 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a/TOOLS/sratoolkit/bin/vdb-config.2 +++ b/TOOLS/sratoolkit/bin/vdb-config.2 @@ -1 +1 @@ -vdb-config.2.10.6 \ No newline at end of file +vdb-config.2.10.9 \ No newline at end of file diff --git a/TOOLS/sratoolkit/bin/vdb-config.2.10.6 b/TOOLS/sratoolkit/bin/vdb-config.2.10.6 deleted file mode 100755 index 8bec72142225e999b9fbda4e7c09bdf14dc42051..0000000000000000000000000000000000000000 Binary files a/TOOLS/sratoolkit/bin/vdb-config.2.10.6 and /dev/null differ diff --git a/TOOLS/sratoolkit/bin/vdb-copy.2 b/TOOLS/sratoolkit/bin/vdb-copy.2 index 730b442f3e06ea1bd59b081ece87f6469b8ae3c9..fbe48a89a36b6e0abc8cde0a267714a74947ecb2 120000 --- a/TOOLS/sratoolkit/bin/vdb-copy.2 +++ b/TOOLS/sratoolkit/bin/vdb-copy.2 @@ -1 +1 @@ -vdb-copy.2.10.6 \ No newline at end of file +vdb-copy.2.10.9 \ No newline at end of file diff --git a/TOOLS/sratoolkit/bin/vdb-copy.2.10.6 b/TOOLS/sratoolkit/bin/vdb-copy.2.10.6 deleted file mode 100755 index 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42a617581fc865907861b725fcdcd31e0dff602a..1944b50c451f6dfe311cd841c09ee74a65d805ca 120000 --- a/TOOLS/sratoolkit/bin/vdb-encrypt.2 +++ b/TOOLS/sratoolkit/bin/vdb-encrypt.2 @@ -1 +1 @@ -vdb-encrypt.2.10.6 \ No newline at end of file +vdb-encrypt.2.10.9 \ No newline at end of file diff --git a/TOOLS/sratoolkit/bin/vdb-encrypt.2.10.6 b/TOOLS/sratoolkit/bin/vdb-encrypt.2.10.6 deleted file mode 100755 index 3a8bff7487d7dd1c001fbbe224df5f2af87a11b3..0000000000000000000000000000000000000000 Binary files a/TOOLS/sratoolkit/bin/vdb-encrypt.2.10.6 and /dev/null differ diff --git a/TOOLS/sratoolkit/bin/vdb-lock.2 b/TOOLS/sratoolkit/bin/vdb-lock.2 index 6e93616556a5495a92c43730cfa1cc16a968ae64..89373bb56f4f5f575544ee52f8f8dac0cccd0110 120000 --- a/TOOLS/sratoolkit/bin/vdb-lock.2 +++ b/TOOLS/sratoolkit/bin/vdb-lock.2 @@ -1 +1 @@ -vdb-lock.2.10.6 \ No newline at end of file +vdb-lock.2.10.9 \ No newline at end of file diff --git a/TOOLS/sratoolkit/bin/vdb-lock.2.10.6 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ffe72d57573c1dbbeddfe6579394cf2269f5aaeb..fda45bd3c43fd4799c7a2b398ebe0e6d36c82112 120000 --- a/TOOLS/sratoolkit/bin/vdb-unlock.2 +++ b/TOOLS/sratoolkit/bin/vdb-unlock.2 @@ -1 +1 @@ -vdb-unlock.2.10.6 \ No newline at end of file +vdb-unlock.2.10.9 \ No newline at end of file diff --git a/TOOLS/sratoolkit/bin/vdb-unlock.2.10.6 b/TOOLS/sratoolkit/bin/vdb-unlock.2.10.6 deleted file mode 100755 index be9c9211d5785598faef9c8faaa6850ee1b67909..0000000000000000000000000000000000000000 Binary files a/TOOLS/sratoolkit/bin/vdb-unlock.2.10.6 and /dev/null differ diff --git a/TOOLS/sratoolkit/bin/vdb-validate.2 b/TOOLS/sratoolkit/bin/vdb-validate.2 index 427f674cc1186ce633cdf158eba3d833edd60af1..ecad4d8ba7e8cb3a413bfbd3194c4a10756e2811 120000 --- a/TOOLS/sratoolkit/bin/vdb-validate.2 +++ b/TOOLS/sratoolkit/bin/vdb-validate.2 @@ -1 +1 @@ -vdb-validate.2.10.6 \ No newline at end of file +vdb-validate.2.10.9 \ No newline at end of file diff --git a/TOOLS/sratoolkit/bin/vdb-validate.2.10.6 b/TOOLS/sratoolkit/bin/vdb-validate.2.10.6 deleted file mode 100755 index ea82f2f54ea5a0628e6a39beb2f37abfa41dabbd..0000000000000000000000000000000000000000 Binary files a/TOOLS/sratoolkit/bin/vdb-validate.2.10.6 and /dev/null differ diff --git a/TOOLS/sratoolkit/schema/ncbi/trace.vschema b/TOOLS/sratoolkit/schema/ncbi/trace.vschema index 0fce1299f7031ea6e44314e76bdaf6108011453e..8b0aab929099a673a989819947d55ef7f07c6e49 100644 --- a/TOOLS/sratoolkit/schema/ncbi/trace.vschema +++ b/TOOLS/sratoolkit/schema/ncbi/trace.vschema @@ -99,8 +99,8 @@ physical NCBI:usamp4 NCBI:usamp4_encoding #1.0 table NCBI:sra:tbl:trace #1 // declare the table = NCBI:SRA:tbl:sra_nopos #2.1.4 // inherit interface AND implementation for (original) SRA model - , NCBI:tbl:base_space #2.0.3 // columns for storing and compressing READ as dna - , NCBI:tbl:phred_quality #2.0.4 // columns for storing and compressing QUALITY as phred + , NCBI:tbl:base_space #3 // columns for storing and compressing READ as dna + , NCBI:tbl:phred_quality #2.0.5 // columns for storing and compressing QUALITY as phred , NCBI:SRA:tbl:stats #1.2.1 // accumulate statistics upon writing , NCBI:SRA:tbl:clip #1.0.2 // clips { diff --git a/TOOLS/sratoolkit/schema/ncbi/wgs-contig.vschema b/TOOLS/sratoolkit/schema/ncbi/wgs-contig.vschema index 515376bd2ef1ac834818f18b77bc525c3aaaefd6..608a2c1782ac983a045f45b5b608fcbb5f665b0a 100644 --- a/TOOLS/sratoolkit/schema/ncbi/wgs-contig.vschema +++ b/TOOLS/sratoolkit/schema/ncbi/wgs-contig.vschema @@ -214,7 +214,7 @@ extern function INSDC:SRA:xread_type */ table NCBI:WGS:tbl:nucleotide #2 = NCBI:tbl:base_space #3 - , NCBI:tbl:phred_quality #2.0.4 + , NCBI:tbl:phred_quality #2.0.5 , NCBI:SRA:tbl:stats #1.2.1 { /* ACCESSION diff --git a/TOOLS/sratoolkit/schema/sra/abi.vschema b/TOOLS/sratoolkit/schema/sra/abi.vschema index 3ec3ecfae1ea00cff19034d2848fadec8c0d7661..a28ca02292173e4dfa7d50acb29fc12849333093 100644 --- a/TOOLS/sratoolkit/schema/sra/abi.vschema +++ b/TOOLS/sratoolkit/schema/sra/abi.vschema @@ -161,7 +161,7 @@ physical NCBI:SRA:swapped_fsamp4 NCBI:SRA:ABI:encoding:SIGNAL #2 table NCBI:SRA:ABI:tbl:v2 #1.0.5 = NCBI:SRA:tbl:sra #2.1.4 , NCBI:tbl:color_space #2.1.0 - , NCBI:tbl:phred_quality #2.0.4 + , NCBI:tbl:phred_quality #2.0.5 , NCBI:SRA:ABI:common #1.0.4 { /* NAME tokenizing and coordinates