Commit 173bf5b1 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 963

parent 1d01bfcb

ChangeLog.txt

+12 −1
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2018-12-26  Martin C. Frith  <Martin C. Frith>



	* src/tantan.cc:

	Make tantan repeat-finding faster

	[44199bff9cef] [tip]



	* doc/Makefile, doc/last-parallel.txt, doc/last-split.txt, doc/last-

	tutorial.txt:

	Update the documents a bit

	[6727ae8b7a12]



2018-12-10  Martin C. Frith  <Martin C. Frith>



	* doc/last-dotplot.txt, scripts/last-dotplot:

	Add last-dotplot --maxseqs option

	[ed0fb9b1eb40] [tip]

	[ed0fb9b1eb40]



	* src/split/last-split.cc:

	Make last-split -n keep E-values

doc/Makefile

+1 −0
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@@ -15,6 +15,7 @@ ${DOCS}: last-doc.css Makefile 


# Ugh!  Is there a better way?

RST_CSS = `locate html4css1.css | tail -n1`

#RST_CSS = html4css1.css



RSTFLAGS = --initial-header-level=2 --no-compact-lists	\

--no-compact-field-lists --option-limit=0 --no-doc-info

doc/last-parallel.html

+2 −2
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@@ -364,11 +364,11 @@ parallel-fasta &quot;lastal mydb&quot; &lt; queries.fa &gt; myalns.maf 
</pre>

<p>Instead of this:</p>

<pre class="literal-block">

lastal -Q1 -D100 db q.fastq | last-split &gt; out.maf

lastal -Q1 db q.fastq | last-split &gt; out.maf

</pre>

<p>try this:</p>

<pre class="literal-block">

parallel-fastq &quot;lastal -Q1 -D100 db | last-split&quot; &lt; q.fastq &gt; out.maf

parallel-fastq &quot;lastal -Q1 db | last-split&quot; &lt; q.fastq &gt; out.maf

</pre>

<p>Instead of this:</p>

<pre class="literal-block">

doc/last-parallel.txt

+2 −2
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@@ -53,11 +53,11 @@ try this:: 


Instead of this::



  lastal -Q1 -D100 db q.fastq | last-split > out.maf

  lastal -Q1 db q.fastq | last-split > out.maf



try this::



  parallel-fastq "lastal -Q1 -D100 db | last-split" < q.fastq > out.maf

  parallel-fastq "lastal -Q1 db | last-split" < q.fastq > out.maf



Instead of this::

doc/last-split.html

+3 −3
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@@ -334,7 +334,7 @@ format), and the genome is in &quot;genome.fasta&quot; (in fasta format). We 
can do the alignment like this:</p>

<pre class="literal-block">

lastdb -uNEAR -R01 db genome.fasta

lastal -Q1 -D100 db q.fastq | last-split &gt; out.maf

lastal -Q1 db q.fastq | last-split &gt; out.maf

</pre>

</div>

<div class="section" id="spliced-alignment-of-rna-reads-to-a-genome">
@@ -397,7 +397,7 @@ matches.</p> 
<h2>Going faster by parallelization</h2>

<p>For example, split alignment of DNA reads to a genome:</p>

<pre class="literal-block">

parallel-fastq &quot;lastal -Q1 -D100 db | last-split&quot; &lt; q.fastq &gt; out.maf

parallel-fastq &quot;lastal -Q1 db | last-split&quot; &lt; q.fastq &gt; out.maf

</pre>

<p>This requires GNU parallel to be installed

(<a class="reference external" href="http://www.gnu.org/software/parallel/">http://www.gnu.org/software/parallel/</a>).</p>
@@ -558,7 +558,7 @@ middle of the query, we can do &quot;spliced&quot; alignment without considering 
splice signals or favouring cis-splices:</p>

<pre class="literal-block">

lastdb -uNEAR -R01 db genome.fasta

lastal -Q1 -D100 db q.fastq | last-split -c0 &gt; out.maf

lastal -Q1 db q.fastq | last-split -c0 &gt; out.maf

</pre>

</div>

</div>