[med-svn] [Git][med-team/last-align][upstream] New upstream version 1111
Nilesh Patra
gitlab at salsa.debian.org
Fri Sep 25 21:52:50 BST 2020
Nilesh Patra pushed to branch upstream at Debian Med / last-align
Commits:
3cdbac34 by Nilesh Patra at 2020-09-26T02:11:46+05:30
New upstream version 1111
- - - - -
7 changed files:
- ChangeLog.txt
- − data/RY8-7.seed
- + data/RY8-8.seed
- doc/last-seeds.html
- doc/last-seeds.txt
- src/CyclicSubsetSeedData.hh
- src/version.hh
Changes:
=====================================
ChangeLog.txt
=====================================
@@ -1,8 +1,15 @@
+2020-09-23 Martin C. Frith <Martin C. Frith>
+
+ * data/RY8-7.seed, data/RY8-8.seed, test/last-test.out, test/last-
+ test.sh:
+ Improve RY8 seeding
+ [300db7059c0c] [tip]
+
2020-09-15 Martin C. Frith <Martin C. Frith>
* src/dna_words_finder.cc, src/dna_words_finder.hh:
Try to appease C++ compilers
- [367e48c99f55] [tip]
+ [367e48c99f55]
* src/GappedXdropAligner.cc, src/GappedXdropAligner.hh,
src/GappedXdropAligner2qual.cc, src/GappedXdropAligner3frame.cc,
=====================================
data/RY8-7.seed deleted
=====================================
@@ -1,27 +0,0 @@
-# This DNA seeding scheme reduces run time and memory use, by only
-# seeking seeds at ~1/8 of positions in each sequence [from Table 3 of
-# MC Frith, L Noé, G Kucherov].
-
-#abbreviation RY8
-
-#lastal -r6 -q18 -a21 -b9
-
-R A G
-Y C T
-
-RRRYRRR
-RRRYRYR
-RRYRRYR
-RRYYRRR
-RRYYRRY
-RRYYRYR
-RRYYYRR
-RRYYYYR
-RYRYYRR
-RYYYRYR
-RYYYYYR
-RYYYYYY
-YRYYRYR
-YRYYYRR
-YRYYYYR
-YYRYYRR
=====================================
data/RY8-8.seed
=====================================
@@ -0,0 +1,42 @@
+# This DNA seeding scheme reduces run time and memory use, by only
+# seeking seeds at ~1/8 of positions in each sequence.
+
+#abbreviation RY8
+
+#lastal -r6 -q18 -a21 -b9
+
+R A G
+Y C T
+
+RRRRRRRY
+RRYRRRYY
+RYRRRRYR
+RYRRRRYY
+RYRRRYRY
+YRRRRRRY
+YRRRRRYR
+YRRRRRYY
+YRRRYRRY
+YRRYRRYR
+YRRYRRYY
+YRYRRRYY
+YRYRRYRY
+YRYRRYYR
+YRYRRYYY
+YRYRYRYY
+YYRRRRYR
+YYRRRRYY
+YYRRRYRY
+YYRRRYYR
+YYRRRYYY
+YYRRYRYR
+YYRRYRYY
+YYRRYYRY
+YYRRYYYR
+YYRRYYYY
+YYRYRYYR
+YYRYRYYY
+YYRYYRYY
+YYYRYYYR
+YYYRYYYY
+YYYYYYYR
=====================================
doc/last-seeds.html
=====================================
@@ -517,11 +517,10 @@ YYYYRY
<p>It sets this lastal default:
-r6 -q18 -a21 -b9</p>
</div>
-<div class="section" id="ry8-7-abbreviation-ry8">
-<h2>RY8-7 (abbreviation: RY8)</h2>
+<div class="section" id="ry8-8-abbreviation-ry8">
+<h2>RY8-8 (abbreviation: RY8)</h2>
<p>This DNA seeding scheme reduces run time and memory use, by only
-seeking seeds at ~1/8 of positions in each sequence [from Table 3 of
-MC Frith, L Noé, G Kucherov].
+seeking seeds at ~1/8 of positions in each sequence.
It uses this seed alphabet:</p>
<pre class="literal-block">
R A G
@@ -529,22 +528,38 @@ Y C T
</pre>
<p>And these patterns:</p>
<pre class="literal-block">
-RRRYRRR
-RRRYRYR
-RRYRRYR
-RRYYRRR
-RRYYRRY
-RRYYRYR
-RRYYYRR
-RRYYYYR
-RYRYYRR
-RYYYRYR
-RYYYYYR
-RYYYYYY
-YRYYRYR
-YRYYYRR
-YRYYYYR
-YYRYYRR
+RRRRRRRY
+RRYRRRYY
+RYRRRRYR
+RYRRRRYY
+RYRRRYRY
+YRRRRRRY
+YRRRRRYR
+YRRRRRYY
+YRRRYRRY
+YRRYRRYR
+YRRYRRYY
+YRYRRRYY
+YRYRRYRY
+YRYRRYYR
+YRYRRYYY
+YRYRYRYY
+YYRRRRYR
+YYRRRRYY
+YYRRRYRY
+YYRRRYYR
+YYRRRYYY
+YYRRYRYR
+YYRRYRYY
+YYRRYYRY
+YYRRYYYR
+YYRRYYYY
+YYRYRYYR
+YYRYRYYY
+YYRYYRYY
+YYYRYYYR
+YYYRYYYY
+YYYYYYYR
</pre>
<p>It sets this lastal default:
-r6 -q18 -a21 -b9</p>
=====================================
doc/last-seeds.txt
=====================================
@@ -210,12 +210,11 @@ And these patterns::
It sets this lastal default:
-r6 -q18 -a21 -b9
-RY8-7 (abbreviation: RY8)
+RY8-8 (abbreviation: RY8)
-------------------------
This DNA seeding scheme reduces run time and memory use, by only
-seeking seeds at ~1/8 of positions in each sequence [from Table 3 of
-MC Frith, L Noé, G Kucherov].
+seeking seeds at ~1/8 of positions in each sequence.
It uses this seed alphabet::
R A G
@@ -223,22 +222,38 @@ It uses this seed alphabet::
And these patterns::
- RRRYRRR
- RRRYRYR
- RRYRRYR
- RRYYRRR
- RRYYRRY
- RRYYRYR
- RRYYYRR
- RRYYYYR
- RYRYYRR
- RYYYRYR
- RYYYYYR
- RYYYYYY
- YRYYRYR
- YRYYYRR
- YRYYYYR
- YYRYYRR
+ RRRRRRRY
+ RRYRRRYY
+ RYRRRRYR
+ RYRRRRYY
+ RYRRRYRY
+ YRRRRRRY
+ YRRRRRYR
+ YRRRRRYY
+ YRRRYRRY
+ YRRYRRYR
+ YRRYRRYY
+ YRYRRRYY
+ YRYRRYRY
+ YRYRRYYR
+ YRYRRYYY
+ YRYRYRYY
+ YYRRRRYR
+ YYRRRRYY
+ YYRRRYRY
+ YYRRRYYR
+ YYRRRYYY
+ YYRRYRYR
+ YYRRYRYY
+ YYRRYYRY
+ YYRRYYYR
+ YYRRYYYY
+ YYRYRYYR
+ YYRYRYYY
+ YYRYYRYY
+ YYYRYYYR
+ YYYRYYYY
+ YYYYYYYR
It sets this lastal default:
-r6 -q18 -a21 -b9
=====================================
src/CyclicSubsetSeedData.hh
=====================================
@@ -5,7 +5,7 @@ const struct {
{"RY16", "RY16-8"},
{"RY32", "RY32-10"},
{"RY4", "RY4-6"},
-{"RY8", "RY8-7"},
+{"RY8", "RY8-8"},
};
const struct {
@@ -147,26 +147,42 @@ YYYRRY\n\
YYYYRY\n\
"},
-{"RY8-7", "\
+{"RY8-8", "\
#lastal -r6 -q18 -a21 -b9\n\
R A G\n\
Y C T\n\
-RRRYRRR\n\
-RRRYRYR\n\
-RRYRRYR\n\
-RRYYRRR\n\
-RRYYRRY\n\
-RRYYRYR\n\
-RRYYYRR\n\
-RRYYYYR\n\
-RYRYYRR\n\
-RYYYRYR\n\
-RYYYYYR\n\
-RYYYYYY\n\
-YRYYRYR\n\
-YRYYYRR\n\
-YRYYYYR\n\
-YYRYYRR\n\
+RRRRRRRY\n\
+RRYRRRYY\n\
+RYRRRRYR\n\
+RYRRRRYY\n\
+RYRRRYRY\n\
+YRRRRRRY\n\
+YRRRRRYR\n\
+YRRRRRYY\n\
+YRRRYRRY\n\
+YRRYRRYR\n\
+YRRYRRYY\n\
+YRYRRRYY\n\
+YRYRRYRY\n\
+YRYRRYYR\n\
+YRYRRYYY\n\
+YRYRYRYY\n\
+YYRRRRYR\n\
+YYRRRRYY\n\
+YYRRRYRY\n\
+YYRRRYYR\n\
+YYRRRYYY\n\
+YYRRYRYR\n\
+YYRRYRYY\n\
+YYRRYYRY\n\
+YYRRYYYR\n\
+YYRRYYYY\n\
+YYRYRYYR\n\
+YYRYRYYY\n\
+YYRYYRYY\n\
+YYYRYYYR\n\
+YYYRYYYY\n\
+YYYYYYYR\n\
"},
{"YASS", "\
=====================================
src/version.hh
=====================================
@@ -1 +1 @@
-"1110"
+"1111"
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/commit/3cdbac3452b3ef83836d9ba8d7eeaf9695368c15
--
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/commit/3cdbac3452b3ef83836d9ba8d7eeaf9695368c15
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