[med-svn] [Git][med-team/last-align][master] 4 commits: New upstream version 1179
Nilesh Patra
gitlab at salsa.debian.org
Mon Feb 1 10:41:27 GMT 2021
Nilesh Patra pushed to branch master at Debian Med / last-align
Commits:
038e0863 by Nilesh Patra at 2021-02-01T16:02:24+05:30
New upstream version 1179
- - - - -
fbad3bb0 by Nilesh Patra at 2021-02-01T16:02:24+05:30
routine-update: New upstream version
- - - - -
b7d61639 by Nilesh Patra at 2021-02-01T16:02:26+05:30
Update upstream source from tag 'upstream/1179'
Update to upstream version '1179'
with Debian dir bb6788cb7dbe04f19146c9b3d7f77b98dc76aee6
- - - - -
116f344f by Nilesh Patra at 2021-02-01T16:02:34+05:30
routine-update: Ready to upload to unstable
- - - - -
5 changed files:
- ChangeLog.txt
- debian/changelog
- doc/last-tutorial.html
- doc/last-tutorial.txt
- src/version.hh
Changes:
=====================================
ChangeLog.txt
=====================================
@@ -1,10 +1,16 @@
+2021-01-29 Martin C. Frith <Martin C. Frith>
+
+ * doc/last-tutorial.txt:
+ Small doc update
+ [7911cdbc5e60] [tip]
+
2021-01-27 Martin C. Frith <Martin C. Frith>
* doc/Makefile, doc/last-evalues.txt, doc/last-papers.txt, doc/last-
postmask.txt, doc/last-split.txt, doc/last-train.txt, doc/last-
tuning.txt, doc/last-tutorial.txt, doc/last.txt, doc/lastal.txt:
Big doc update
- [ba6a55ed7287] [tip]
+ [ba6a55ed7287]
2021-01-25 Martin C. Frith <Martin C. Frith>
=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+last-align (1179-1) unstable; urgency=medium
+
+ * New upstream version
+
+ -- Nilesh Patra <npatra974 at gmail.com> Mon, 01 Feb 2021 16:02:34 +0530
+
last-align (1178-1) unstable; urgency=medium
* New upstream version
=====================================
doc/last-tutorial.html
=====================================
@@ -445,6 +445,8 @@ range lies in that of a higher-scoring alignment.</p>
<p>Another possibility is to add <a class="reference external" href="last-train.html">last-train</a> option <tt class="docutils literal"><span class="pre">-X1</span></tt>, which treats
matches to <tt class="docutils literal">X</tt> (unknown) amino acids as neutral instead of
disfavored.</p>
+<p>You can reuse <tt class="docutils literal"><span class="pre">last-train</span></tt> output for different alignment tasks, if
+you expect the rates to be roughly the same.</p>
</div>
<div class="section" id="aligning-high-indel-error-long-dna-reads-to-a-genome">
<h2>Aligning high-indel-error long DNA reads to a genome</h2>
@@ -470,7 +472,7 @@ filter lowercase with <a class="reference external" href="last-postmask.html">la
your aim, e.g. slow-and-sensitive seems necessary to find intricate
rearrangements of repeats. Suggested ways to go faster:</p>
<ul>
-<li><p class="first"><a class="reference external" href="https://github.com/mcfrith/last-rna/blob/master/last-long-reads.md">Mask repeats</a>.</p>
+<li><p class="first"><a class="reference external" href="https://github.com/mcfrith/last-rna/blob/master/last-long-reads.md">Mask repeats</a>. This has often worked well.</p>
</li>
<li><p class="first">Add lastal option <tt class="docutils literal"><span class="pre">-k8</span></tt> (or <tt class="docutils literal"><span class="pre">-k16</span></tt> etc). This makes it faster,
by only finding initial matches starting at every 8th (or 16th etc)
@@ -508,9 +510,10 @@ with little effect on accuracy.</p>
<pre class="literal-block">
lastdb -P8 -uNEAR -R01 -C2 mydb genome.fasta
last-train -P8 -Q1 mydb reads.fastq.gz > reads.train
-lastal -P8 -p reads.train mydb reads.fastq.gz | last-split > out.maf
+lastal -P8 -p reads.train mydb reads.fastq.gz | last-split | gzip > out.maf.gz
</pre>
-<p>Most LAST commands accept gzip-compressed (<tt class="docutils literal">.gz</tt>) files.</p>
+<p>Most LAST commands accept <tt class="docutils literal">.gz</tt> compressed files, and you can
+compress output with <tt class="docutils literal">gzip</tt> as above.</p>
<p><a class="reference external" href="lastdb.html">lastdb</a> option <tt class="docutils literal"><span class="pre">-C2</span></tt> makes the alignment a bit faster, but uses more
memory. This has no effect on the results. (You could use it in the
other examples too, but it might not be faster.)</p>
=====================================
doc/last-tutorial.txt
=====================================
@@ -141,6 +141,9 @@ Another possibility is to add last-train_ option ``-X1``, which treats
matches to ``X`` (unknown) amino acids as neutral instead of
disfavored.
+You can reuse ``last-train`` output for different alignment tasks, if
+you expect the rates to be roughly the same.
+
Aligning high-indel-error long DNA reads to a genome
----------------------------------------------------
@@ -171,7 +174,7 @@ You can go faster by sacrificing a bit of sensitivity. It depends on
your aim, e.g. slow-and-sensitive seems necessary to find intricate
rearrangements of repeats. Suggested ways to go faster:
-* `Mask repeats`_.
+* `Mask repeats`_. This has often worked well.
* Add lastal option ``-k8`` (or ``-k16`` etc). This makes it faster,
by only finding initial matches starting at every 8th (or 16th etc)
@@ -213,9 +216,10 @@ Aligning Illumina DNA reads to a genome
lastdb -P8 -uNEAR -R01 -C2 mydb genome.fasta
last-train -P8 -Q1 mydb reads.fastq.gz > reads.train
- lastal -P8 -p reads.train mydb reads.fastq.gz | last-split > out.maf
+ lastal -P8 -p reads.train mydb reads.fastq.gz | last-split | gzip > out.maf.gz
-Most LAST commands accept gzip-compressed (``.gz``) files.
+Most LAST commands accept ``.gz`` compressed files, and you can
+compress output with ``gzip`` as above.
lastdb_ option ``-C2`` makes the alignment a bit faster, but uses more
memory. This has no effect on the results. (You could use it in the
=====================================
src/version.hh
=====================================
@@ -1 +1 @@
-"1178"
+"1179"
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/compare/490be62483e0e3bc27a605996b65fffc7b1168d4...116f344ff8e6238ff04c843ccbb4b31a5409f51f
--
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/compare/490be62483e0e3bc27a605996b65fffc7b1168d4...116f344ff8e6238ff04c843ccbb4b31a5409f51f
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