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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/sra-sdk">Debian Med / sra-sdk</a>
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<h4>
Commits:
</h4>
<ul>
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<strong><a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/bdf0081d3363e836e27474f0898a55f3ca7562f3">bdf0081d</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-03-04T11:28:37+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.10.4+dfsg</pre>
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#c9512c0b1798e84b5d6a945ad880784dab140a53">
build/Makefile.vers
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<li class="file-stats">
<a href="#4705a68e02a22c6bfea0273af010dd42e1861b4a">
shared/toolkit.vers
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<li class="file-stats">
<a href="#5cd76f234790117309267153be422c6d4e826541">
shared/toolkit.vers.h
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<h4>Changes:</h4>
<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/bdf0081d3363e836e27474f0898a55f3ca7562f3#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># NCBI External Developer Release:</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## SRA Toolkit 2.10.4</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**February 26, 2020**</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"> <span class="gs" style="font-weight: 600;">**kns, sra-tools:**</span>: fixed errors when using ngc file</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## SRA Toolkit 2.10.3</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**February 18, 2020**</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"> <span class="gs" style="font-weight: 600;">**sraxf, fasterq-dump, fastq-dump, sam-dump**</span>: fixed a problem resulting in a segmentation fault </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"></span>
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## SRA Toolkit 2.10.2</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**January 15, 2020**</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"></span>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/bdf0081d3363e836e27474f0898a55f3ca7562f3#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,7 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown">email: sra@ncbi.nlm.nih.gov</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Download</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown">Visit our <span class="p">[</span><span class="nv" style="color: #008080;">download page</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/ncbi/sra-tools/wiki/<span class="idiff left right">Downloads</span></span><span class="p">)</span> for pre-built binaries.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown">Visit our <span class="p">[</span><span class="nv" style="color: #008080;">download page</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/ncbi/sra-tools/wiki/<span class="idiff left right">01.-Downloading-SRA-Toolkit</span></span><span class="p">)</span> for pre-built binaries.</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Change Log</span></span>
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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown">Please check the CHANGES.md file for change history.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,6 +14,14 @@ The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for</td>
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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown">using data in the INSDC Sequence Read Archives.</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### ANNOUNCEMENT:</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown">SRA Toolkit 2.10.3</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown">sraxf, fasterq-dump, fastq-dump, sam-dump: fixed a problem resulting in a segmentation fault</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown">Release 2.10.2 of <span class="sb" style="color: #d14;">`sra-tools`</span> provides access to all the <span class="gs" style="font-weight: 600;">**public and controlled-access dbGaP**</span> of SRA in the AWS and GCP environments _(Linux only for this release)_. This vast archive's original submission format and SRA-formatted data can both be accessed and computed on these clouds, eliminating the need to download from NCBI FTP as well as improving performance.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown">The <span class="sb" style="color: #d14;">`prefetch`</span> tool also retrieves <span class="gs" style="font-weight: 600;">**original submission files**</span> in addition to ETL data for public and controlled-access dbGaP data.</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown">With release 2.10.0 of <span class="sb" style="color: #d14;">`sra-tools`</span> we have added cloud-native operation for AWS and GCP environments _(Linux only for this release)_, for use with the public SRA. <span class="sb" style="color: #d14;">`prefetch`</span> is capable of retrieving original submission files in addition to ETL data.</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown">With release 2.9.1 of <span class="sb" style="color: #d14;">`sra-tools`</span> we have finally made available the tool <span class="sb" style="color: #d14;">`fasterq-dump`</span>, a replacement for the much older <span class="sb" style="color: #d14;">`fastq-dump`</span> tool. As its name implies, it runs faster, and is better suited for large-scale conversion of SRA objects into FASTQ files that are common on sites with enough disk space for temporary files. <span class="sb" style="color: #d14;">`fasterq-dump`</span> is multi-threaded and performs bulk joins in a way that improves performance as compared to <span class="sb" style="color: #d14;">`fastq-dump`</span>, which performs joins on a per-record basis _(and is single-threaded)_.</span>
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<li id="c9512c0b1798e84b5d6a945ad880784dab140a53">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/bdf0081d3363e836e27474f0898a55f3ca7562f3#c9512c0b1798e84b5d6a945ad880784dab140a53"><strong>build/Makefile.vers</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,4 +23,4 @@</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># ===========================================================================</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># SRA-TOOLS and library version</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> 2.10.<span class="idiff left right">2</span></span></pre>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> 2.10.<span class="idiff left right">4</span></span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/bdf0081d3363e836e27474f0898a55f3ca7562f3#4705a68e02a22c6bfea0273af010dd42e1861b4a"><strong>shared/toolkit.vers</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">2.10.<span class="idiff left right">2</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2.10.<span class="idiff left right">4</span></span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define TOOLKIT_VERS 0x020A000<span class="idiff left right">2</span></span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define TOOLKIT_VERS 0x020A000<span class="idiff left right">4</span></span></span></pre>
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