Commit 7716ed36 authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 956

parent 93f448c6

ChangeLog.txt

+106 −1
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2018-09-10  Martin C. Frith  <Martin C. Frith>



	* scripts/last-map-probs:

	Python3-ify last-map-probs

	[83191e47259e] [tip]



2018-09-07  Martin C. Frith  <Martin C. Frith>



	* src/last-pair-probs.cc:

	Make pair-probs almost work for ref rev strands

	[da8c69023d0a]



	* scripts/last-postmask:

	postmask: fix asymmetric matrix & ref rev strand

	[d4ecf378f967]



2018-09-05  Martin C. Frith  <Martin C. Frith>



	* doc/last-papers.txt, doc/last-train.txt, doc/lastal.txt,

	doc/lastdb.txt:

	Improve the documentation

	[ffb4e02e04b0]



	* scripts/fastq-interleave:

	fastq-interleave: add /1 & /2 to identical names

	[dd61bce162f0]



	* doc/last-train.txt, scripts/last-train, test/last-train-test.out,

	test/last-train-test.sh:

	last-train: train substitutions from fastq!

	[6de96c2afe47]



2018-08-29  Martin C. Frith  <Martin C. Frith>



	* src/lastal.cc:

	Fix lastal -j7 quality-aware expected counts

	[f70bcd86eb83]



2018-08-24  Martin C. Frith  <Martin C. Frith>



	* src/MultiSequence.cc, src/MultiSequence.hh,

	src/MultiSequenceQual.cc, src/last.hh:

	Read fastq faster

	[41800ed89eb8]



2018-08-21  Martin C. Frith  <Martin C. Frith>



	* src/Alignment.cc, src/Centroid.cc, src/Centroid.hh, src/lastal.cc:

	lastal -j7: quality-aware expected counts

	[9e0b0d0c8438]



2018-08-20  Martin C. Frith  <Martin C. Frith>



	* src/Centroid.cc, src/QualityPssmMaker.cc, src/QualityPssmMaker.hh,

	src/lastal.cc:

	Refactor

	[e454003e6a8a]



2018-08-01  Martin C. Frith  <Martin C. Frith>



	* doc/last-split.txt, src/split/last-split-main.cc, src/split/last-

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

	/last-split-test.sh:

	Add last-split --format option

	[db2bd938c9b8]



2018-07-30  Martin C. Frith  <Martin C. Frith>



	* scripts/last-postmask:

	postmask: fix bug for spliced alignments

	[e7da3afc2179]



2018-07-17  Martin C. Frith  <Martin C. Frith>



	* scripts/maf-join:

	Python3-ify maf-join

	[764713f076f0]



	* src/lastal.cc, test/last-test.out, test/last-test.sh:

	Fix crash for bad score matrix

	[318e420407d8]



2018-06-25  Martin C. Frith  <Martin C. Frith>



	* scripts/last-dotplot:

	Make last-dotplot really work with Python3

	[82b69208c878]



2018-05-28  Martin C. Frith  <Martin C. Frith>



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

	scripts/maf-swap, test/last-test.sh, test/maf-swap-test.out, test

	/maf-swap-test.sh:

	Python3-ify: dotplot, train, convert, swap

	[f3f1ec72542f]



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

	Purely cosmetic change to last-train output

	[05d2563d02e0]



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

	test/last-split-test.out:

	Fix postmask header bug introduced in v938

	[76cdd2203460]



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]

	[65969d4d464d]



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

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

doc/last-papers.html

+5 −0
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@@ -389,6 +389,11 @@ LAST-TRAIN</a>. Hamada M, Ono Y, Asai K Frith MC. 
Bioinformatics. 2017 33(6):926-928.</p>

<p>Describes last-train.</p>

</li>

<li><p class="first"><a class="reference external" href="https://ieeexplore.ieee.org/document/8288582/">A Simplified Description of Child Tables for Sequence Similarity

Search</a>.  Frith MC, Shrestha A.  IEEE/ACM Trans Comput Biol

Bioinform. 2018.</p>

<p>Describes how LAST uses child tables.</p>

</li>

</ol>

<div class="section" id="external-methods">

<h2>External methods</h2>

doc/last-papers.txt

+8 −0
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@@ -108,6 +108,14 @@ research to society. 


    Describes last-train.



13. `A Simplified Description of Child Tables for Sequence Similarity

    Search`__.  Frith MC, Shrestha A.  IEEE/ACM Trans Comput Biol

    Bioinform. 2018.



    __ https://ieeexplore.ieee.org/document/8288582/



    Describes how LAST uses child tables.



External methods

----------------

doc/last-split.html

+5 −0
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@@ -573,6 +573,11 @@ lastal -Q1 -D100 db q.fastq | last-split -c0 &gt; out.maf 
<kbd><span class="option">-h</span>, <span class="option">--help</span></kbd></td>

<td>Show a help message, with default option values, and exit.</td></tr>

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

<kbd><span class="option">-f</span>, <span class="option">--format=<var>FMT</var></span></kbd></td>

<td>Choose the output format: MAF+ (the default), or MAF (which

omits the last-split &quot;p&quot; lines).  The format name is not

case-sensitive.</td></tr>

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

<kbd><span class="option">-g</span>, <span class="option">--genome=<var>NAME</var></span></kbd></td>

<td>Do spliced alignment, and read splice signals (GT, AG, etc)

from the named genome.  NAME should be the name of a lastdb

doc/last-split.txt

+5 −0
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@@ -181,6 +181,11 @@ Options 
  -h, --help

         Show a help message, with default option values, and exit.



  -f, --format=FMT

         Choose the output format: MAF+ (the default), or MAF (which

         omits the last-split "p" lines).  The format name is not

         case-sensitive.



  -g, --genome=NAME

         Do spliced alignment, and read splice signals (GT, AG, etc)

         from the named genome.  NAME should be the name of a lastdb