Commit 93f448c6 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 938

parent 84ec4ca8

ChangeLog.txt

+35 −1
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2018-05-14  Martin C. Frith  <Martin C. Frith>



	* scripts/last-dotplot, scripts/last-postmask, test/102.maf, test

	/last-postmask-test.out, test/last-postmask-test.sh, test/last-

	split-test.out, test/last-split-test.sh:

	postmask: fix bug for unusual alignment headers

	[65969d4d464d] [tip]



	* scripts/last-dotplot, scripts/last-map-probs, scripts/last-postmask,

	scripts/last-train, scripts/maf-convert, scripts/maf-swap:

	Make last-train find LAST programs more robustly

	[8a4fadbe6080]



2018-05-07  Martin C. Frith  <Martin C. Frith>



	* scripts/last-postmask, scripts/last-train, scripts/maf-convert,

	scripts/maf-join, scripts/maf-swap:

	Modernize the Python code

	[b1c09fdd12fe]



	* doc/last-tuning.txt, doc/lastal.txt, doc/lastdb.txt,

	src/LastalArguments.cc, src/LastalArguments.hh, test/last-test.out,

	test/last-test.sh:

	Change lastal -x & -z options

	[b09d82479c91]



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

	Make last-train use last-postmask

	[2755c8f0dc79]



	* scripts/last-postmask, test/last-postmask-test.out:

	postmask: bugfix for strand-asymmetric scores

	[9caca45429d8]



2018-04-20  Martin C. Frith  <Martin C. Frith>



	* doc/Makefile, doc/lastal.txt, doc/maf-cut.txt, scripts/maf-cut:

	Add maf-cut utility

	[482845444bcd] [tip]

	[482845444bcd]



2018-04-18  Martin C. Frith  <Martin C. Frith>

doc/.htaccess

+1 −1
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@@ -5,4 +5,4 @@ IndexIgnore last-map-probs.txt last-matrices.txt last-pair-probs.txt 
IndexIgnore last-papers.txt last-parallel.txt last-postmask.txt

IndexIgnore last-repeats.txt last-seeds.txt last-split.txt last-train.txt

IndexIgnore last-tuning.txt last-tutorial.txt last.txt lastal.txt lastdb.txt

IndexIgnore maf-convert.txt
 
IndexIgnore maf-convert.txt maf-cut.txt

doc/last-train.html

+6 −1
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@@ -334,7 +334,7 @@ final score parameters, in a format that can be read by <a class="reference exte 
option</a>.</p>

<p>You can also pipe sequences into last-train, for example:</p>

<pre class="literal-block">

zcat queries.fasta.gz | last-train mydb

bzcat queries.fasta.bz2 | last-train mydb

</pre>

<div class="section" id="options">

<h2>Options</h2>
@@ -377,6 +377,11 @@ e.g. score(A→G) = score(G→A).</td></tr> 
optimize the parameters for low-similarity alignments,

similarly to the BLOSUM matrices.</td></tr>

<tr><td class="option-group">

<kbd><span class="option">--postmask=<var>NUMBER</var></span></kbd></td>

<td>By default, last-train ignores alignments of mostly-lowercase

sequence (by using <a class="reference external" href="last-postmask.html">last-postmask</a>).

To turn this off, do <tt class="docutils literal"><span class="pre">--postmask=0</span></tt>.</td></tr>

<tr><td class="option-group">

<kbd><span class="option">--sample-number=<var>N</var></span></kbd></td>

<td>Use N randomly-chosen chunks of the query sequences.  The

queries are chopped into fixed-length chunks (as if they were

doc/last-train.txt

+5 −1
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@@ -20,7 +20,7 @@ option <lastal.html#score-options>`_. 


You can also pipe sequences into last-train, for example::



  zcat queries.fasta.gz | last-train mydb

  bzcat queries.fasta.bz2 | last-train mydb



Options

-------
@@ -46,6 +46,10 @@ Training options 
         Ignore alignments with > PID% identity.  This aims to

         optimize the parameters for low-similarity alignments,

         similarly to the BLOSUM matrices.

  --postmask=NUMBER

         By default, last-train ignores alignments of mostly-lowercase

         sequence (by using `last-postmask <last-postmask.html>`_).

         To turn this off, do ``--postmask=0``.

  --sample-number=N

         Use N randomly-chosen chunks of the query sequences.  The

         queries are chopped into fixed-length chunks (as if they were

doc/last-tuning.html

+18 −6
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@@ -370,7 +370,7 @@ alphabetically earliest.</p> 
<div class="section" id="lastdb8-lastal8">

<h2>lastdb8 &amp; lastal8</h2>

<p>If your reference has more than about 4 billion letters, 8-byte LAST

<em>may</em> be beneficial.  Ordinary (4-byte) LAST cannot directly handle so

may be beneficial.  Ordinary (4-byte) LAST cannot directly handle so

much data, so it splits it into volumes, which is inefficient.  8-byte

LAST can handle such data without voluming, but it uses more memory.</p>

<p>8-byte LAST combines well with lastdb option -w or -W, which reduce
@@ -401,15 +401,27 @@ high-identity matches.</p> 
<p>This option (gapless alignment culling) can make lastal <strong>faster</strong> but

<strong>less sensitive</strong>.  It can also <strong>reduce redundant output</strong>.  For

example, -C2 makes it discard alignments (before gapped extension)

whose query coordinates lie in those of 2 or more stronger alignments.</p>

whose query coordinates lie in those of 2 or more stronger alignments.

This works well for aligning long, repeat-rich, indel-poor sequences

(e.g. mammal chromosomes) without repeat-masking.</p>

</div>

<div class="section" id="lastal-x">

<h3>lastal -x</h3>

<div class="section" id="lastal-z">

<h3>lastal -z</h3>

<p>This option can make lastal <strong>faster</strong> but <strong>less sensitive</strong>.  It

sets the maximum score drop in alignments, in the gapped extension

phase.  Lower values make it faster, by quitting unpromising

extensions sooner.  The default aims at best accuracy.  For example,

use -x50% to specify 50% of the default value.</p>

extensions sooner.  The default aims at best accuracy.</p>

<p>You can set this option in several ways: perhaps the most intuitive is

via maximum gap length.  For example, -z10g sets the maximum score

drop such that the longest possible gap length is 10.</p>

</div>

<div class="section" id="lastal-x">

<h3>lastal -x</h3>

<p>This option (preliminary gapped extension) can make lastal <strong>faster</strong>

but <strong>less sensitive</strong>.  For example, -x2g makes it extend gapped

alignments with a maximum gap length of 2, discard those with score

below the gapped score threshold, then redo the survivors with the

final max score drop (z).</p>

</div>

<div class="section" id="id2">

<h3>lastal -M</h3>