New upstream version 932

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]

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

	* src/ScoreMatrix.cc, src/ScoreMatrix.hh, src/lastal.cc, src/makefile,

	test/last-test.out:

	Use appropriate scores for ambiguous DNA letters

	[75785542d5a0]

2018-04-17  Martin C. Frith  <Martin C. Frith>

	* src/ScoreMatrix.cc, src/ScoreMatrix.hh, test/last-test.out:

	Prettify the score matrix in lastal's header

	[68bd00d2faff]

	* src/ScoreMatrix.cc, src/lastal.cc:

	Refactor

	[d1aa91889332]

	* src/ScoreMatrix.cc, src/ScoreMatrix.hh, src/TantanMasker.cc,

	src/lastal.cc:

	Refactor

	[e22cac29168c]

2018-04-16  Martin C. Frith  <Martin C. Frith>

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

	src/qualityScoreUtil.hh:

	Refactor

	[fb851b8892a5]

2018-03-05  Martin C. Frith  <Martin C. Frith>

	* scripts/last-dotplot, test/last-dotplot-test.out, test/last-dotplot-

	test.sh:

	Fix dotplot --strands bug with cut sequences

	[bc08832db1a1]

	* scripts/last-dotplot, test/last-dotplot-test.out, test/last-dotplot-

	test.sh:

	Fix dotplot crash for sorting by sequence length

	[e1861f956f60]

2018-02-26  Martin C. Frith  <Martin C. Frith>

	* doc/lastdb.txt, src/Alphabet.cc, test/last-test.out, test/last-

	test.sh:

	Convert Us in RNA to Ts

	[e7d7cb7db0a7]

2018-02-13  Martin C. Frith  <Martin C. Frith>

	* doc/lastdb.txt, src/SubsetSuffixArray.hh,

	src/SubsetSuffixArraySort.cc, src/lastdb.cc:

	Multi-thread lastdb's main sort

	[77d8757028c2]

	* src/alp/sls_alignment_evaluer.cpp, test/last-test.out:

	Fix some E-value & last-train fails

	[2c57015b1e89]

2018-01-05  Martin C. Frith  <Martin C. Frith>

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

	src/Centroid.hh:

	Refactor

	[8430dbf5abe7] [tip]

	[8430dbf5abe7]

	* src/Centroid.cc:

	Try to calculate lastal probs a tiny bit faster

last-papers.html last-parallel.html last-postmask.html			\

last-repeats.html last-seeds.html last-split.html last-train.html	\

last-tuning.html last-tutorial.html last.html lastal.html lastdb.html	\

maf-convert.html

maf-convert.html maf-cut.html

all: ${DOCS}

<td><p class="first">Specify a match/mismatch score matrix.  Options -r and -q will

be ignored.  The built-in matrices are described in

<a class="reference external" href="last-matrices.html">last-matrices.html</a>.</p>

<p class="last">Any other NAME is assumed to be a file name.  For an example of

the format, see the matrix files in the data directory.  Any

letters that aren't in the matrix will get the lowest score in

the matrix when aligned to anything.  Asymmetric scores are

allowed: query letters correspond to columns and reference

letters correspond to rows.  Other options can be specified on

lines starting with "#last", but command line options override

them.</p>

<p>Any other NAME is assumed to be a file name.  For an example of

the format, see the matrix files in the data directory.

Asymmetric scores are allowed: query letters correspond to

columns and reference letters correspond to rows.</p>

<p>Any letters that aren't in the matrix get default match/mismatch

scores.  For doubly- and triply-ambiguous bases (such as "W"

meaning A or T), these default scores are derived from the ACGT

scores, and are shown in the header of lastal's output.  Any

other letters get the lowest score in the matrix when aligned to

anything.</p>

<p class="last">Other options can be specified on lines starting with &quot;#last&quot;,

but command line options override them.</p>

</td></tr>

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

<kbd><span class="option">-a <var>COST</var></span></kbd></td>

      `<last-matrices.html>`_.

      Any other NAME is assumed to be a file name.  For an example of

      the format, see the matrix files in the data directory.  Any

      letters that aren't in the matrix will get the lowest score in

      the matrix when aligned to anything.  Asymmetric scores are

      allowed: query letters correspond to columns and reference

      letters correspond to rows.  Other options can be specified on

      lines starting with "#last", but command line options override

      them.

      the format, see the matrix files in the data directory.

      Asymmetric scores are allowed: query letters correspond to

      columns and reference letters correspond to rows.

      Any letters that aren't in the matrix get default match/mismatch

      scores.  For doubly- and triply-ambiguous bases (such as "W"

      meaning A or T), these default scores are derived from the ACGT

      scores, and are shown in the header of lastal's output.  Any

      other letters get the lowest score in the matrix when aligned to

      anything.

      Other options can be specified on lines starting with "#last",

      but command line options override them.

  -a COST

      Gap existence cost.

<kbd><span class="option">-P <var>THREADS</var></span></kbd></td>

<td>Divide the work between this number of threads running in

parallel.  0 means use as many threads as your computer claims

it can handle simultaneously.  Currently, multi-threading is

used for tantan masking only.</td></tr>

it can handle simultaneously.</td></tr>

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

<kbd><span class="option">-m <var>PATTERN</var></span></kbd></td>

<td><p class="first">Specify a spaced seed pattern, for example &quot;-m 110101&quot;.  In this

is equivalent to "-a ACDEFGHIKLMNPQRSTVWY".  Non-alphabet

letters are allowed in sequences, but by default they are

excluded from initial matches and get the mismatch score when

aligned to anything.  If -a is specified, -p is ignored.</td></tr>

aligned to anything.  As a special case, for the DNA alphabet,

Us are converted to Ts.  If -a is specified, -p is ignored.</td></tr>

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

<kbd><span class="option">-i <var>MATCHES</var></span></kbd></td>

<td>This option makes lastdb faster, at the expense of limiting your