diff -Nru last-align-830/ChangeLog.txt last-align-869/ChangeLog.txt
--- last-align-830/ChangeLog.txt 2017-01-19 16:54:24.000000000 +0000
+++ last-align-869/ChangeLog.txt 2017-06-20 09:12:50.000000000 +0000
@@ -1,9 +1,205 @@
+2017-06-20 Martin C. Frith
+
+ * doc/last-train.txt, scripts/last-train, test/last-train-test.out,
+ test/last-train-test.sh:
+ Make it easier to feed stdin/pipe to last-train
+ [b73f1146e688] [tip]
+
+ * doc/lastal.txt, src/AlignmentWrite.cc, test/last-test.out:
+ Add raw score to BlastTab+ format
+ [56f960a740a3]
+
+2017-06-15 Martin C. Frith
+
+ * scripts/last-postmask, scripts/last-train:
+ Make last-train read sequence file "-" from stdin
+ [f9ec9c71d72e]
+
+ * doc/last-dotplot.txt, scripts/last-dotplot:
+ Change last-dotplot's verbosity
+ [5182d8528ce9]
+
+ * src/LastEvaluer.cc, src/alp/sls_alignment_evaluer.cpp,
+ src/alp/sls_alignment_evaluer.hpp, src/alp/sls_alp_data.cpp,
+ src/alp/sls_alp_data.hpp:
+ Enable E-values for some unusual scoring schemes
+ [230d1abe4c5d]
+
+2017-06-02 Martin C. Frith
+
+ * doc/last-papers.txt, doc/last-tutorial.txt:
+ Update docs
+ [c15cd2ae062d]
+
+ * scripts/last-dotplot:
+ last-dotplot: get bp-per-pixel faster
+ [6a4915d5b5cb]
+
+ * src/LastalArguments.cc, src/LastdbArguments.cc, src/getoptUtil.hh,
+ src/makefile:
+ Fix parsing of command-line options
+ [9afba231262d]
+
+2017-05-18 Martin C. Frith
+
+ * scripts/last-dotplot:
+ last-dotplot: do e.g. chr7 annotations -> hg19.chr7 only if no
+ ambiguity
+ [a75b439f0cf2]
+
+ * doc/last-dotplot.txt, scripts/last-dotplot:
+ last-dotplot: add genePred and rmsk options
+ [6e8ff424ce2b]
+
+ * scripts/last-dotplot:
+ last-dotplot: refactor
+ [1ecdbf2ddb78]
+
+ * scripts/last-dotplot:
+ last-dotplot: get layer from BED score
+ [93d47bb8527f]
+
+ * scripts/last-dotplot:
+ last-dotplot: start implementing "layers"
+ [5e4e3f2cf68b]
+
+ * scripts/last-dotplot:
+ last-dotplot: parse BED more liberally
+ [d086361eabec]
+
+2017-05-17 Martin C. Frith
+
+ * scripts/last-dotplot:
+ Refactor last-dotplot
+ [09a9d7ef13ae]
+
+2017-05-15 Martin C. Frith
+
+ * scripts/maf-convert:
+ Make maf-convert to tab faster
+ [0d11825c43b2]
+
+ * doc/last-train.txt, scripts/last-train:
+ Add lastal's -C option to last-train
+ [791ec91ac03c]
+
+2017-05-02 Martin C. Frith
+
+ * doc/last-dotplot.txt, scripts/last-dotplot:
+ Add border options to last-dotplot
+ [f3b6c666afad]
+
+ * doc/last-dotplot.txt, scripts/last-dotplot:
+ Add sequence order options to last-dotplot
+ [5b2acb7fdb3e]
+
+ * doc/last-dotplot.txt, scripts/last-dotplot:
+ Tweak last-dotplot's documentation
+ [db0ddc92f2ec]
+
+2017-04-18 Martin C. Frith
+
+ * src/Alignment.cc, src/Centroid.cc, src/Centroid.hh:
+ Refactor
+ [cb934e010567]
+
+ * doc/last-train.txt, scripts/last-train, test/last-train-test.out,
+ test/last-train-test.sh:
+ Improve last-train sampling for long queries, e.g. chromosomes
+ [7c09e0d848f2]
+
+2017-04-04 Martin C. Frith
+
+ * scripts/last-dotplot:
+ Made last-dotplot print width & height.
+ [3ca7aa4b27a8]
+
+ * doc/last-dotplot.txt, scripts/last-dotplot:
+ Added last-dotplot options to show sequence lengths.
+ [1f46ab956351]
+
+ * doc/last-dotplot.txt, scripts/last-dotplot:
+ Added last-dotplot options to show BED features.
+ [16060c00b129]
+
+ * scripts/last-dotplot:
+ Made last-dotplot faster, sometimes.
+ [23de4eb3be1d]
+
+2017-03-09 Martin C. Frith
+
+ * src/alp/sls_basic.hpp, src/split/cbrc_split_aligner.hh:
+ Fixed compile errors with old compilers.
+ [7872fdade23a]
+
+2017-03-07 Martin C. Frith
+
+ * doc/lastal.txt, src/LastalArguments.cc, src/LastalArguments.hh,
+ src/lastal.cc, test/last-test.out, test/last-test.sh:
+ Added lastal -N option to quickly get the first hits per query.
+ [b69999b5cd1b]
+
+ * src/alp/sls_alignment_evaluer.cpp, src/alp/sls_basic.hpp,
+ src/alp/sls_falp_alignment_evaluer.cpp,
+ src/alp/sls_fsa1_pvalues.cpp, src/alp/sls_fsa1_pvalues.hpp,
+ src/alp/sls_pvalues.cpp, src/alp/sls_pvalues.hpp:
+ Bugfix: E-values were occasionally negative.
+ [681c5acdf5ca]
+
+2017-03-02 Martin C. Frith
+
+ * doc/last-dotplot.txt, scripts/last-dotplot:
+ Enabled sequence ranges for last-dotplot.
+ [85a72978fb7d]
+
+ * doc/last-dotplot.txt, scripts/last-dotplot:
+ Added trim options to last-dotplot.
+ [bbc6f00e683b]
+
+ * scripts/last-dotplot:
+ Refactoring.
+ [7b972338fe04]
+
+2017-02-28 Martin C. Frith
+
+ * scripts/last-dotplot:
+ Refactoring.
+ [2c3511fa1734]
+
+ * scripts/last-dotplot:
+ Refactoring.
+ [1b4db1600728]
+
+ * scripts/last-dotplot:
+ Refactoring.
+ [cdb1e40c28e4]
+
+ * doc/last-papers.txt, scripts/last-dotplot:
+ Bugfix: dotplot left border misplaced (for some versions of
+ python/PIL).
+ [1514199bb31b]
+
+2017-02-03 Martin C. Frith
+
+ * doc/lastdb.txt, src/LastdbArguments.cc:
+ Tiny doc/help edits.
+ [ec636cb2fe64]
+
+ * src/split/last-split.cc:
+ Bugfix: rarely, last-split output end-gaps with wrong score/don/acc.
+ [ff7752714cef]
+
+ * scripts/maf-convert, test/90089.maf, test/maf-convert-test.out, test
+ /maf-convert-test.sh:
+ Bugfix(?): made maf-convert to psl trim end-gaps.
+ [c5591feba7a2]
+
2017-01-19 Martin C. Frith
* src/split/cbrc_split_aligner.cc, src/split/cbrc_split_aligner.hh,
src/split/last-split.cc:
Added don and acc to spliced alignment output.
- [138b43db3812] [tip]
+ [138b43db3812]
* src/split/cbrc_split_aligner.cc, src/split/last-split.cc:
Refactoring.
diff -Nru last-align-830/debian/changelog last-align-869/debian/changelog
--- last-align-830/debian/changelog 2017-06-06 05:56:56.000000000 +0000
+++ last-align-869/debian/changelog 2017-08-11 19:17:15.000000000 +0000
@@ -1,3 +1,19 @@
+last-align (869-1) unstable; urgency=low
+
+ * Team upload.
+
+ [ Steffen Moeller ]
+ * [debian/upstream/metadata] Added references to
+ OMICtools, bio.tools, RRID
+
+ [ Sascha Steinbiss ]
+ * New upstream release.
+ * Use python-pil instead of python-imaging as dependency.
+ Closes: #866438
+ * Add needs-recommends to d/t/control to fix autopkgtests.
+
+ -- Sascha Steinbiss Fri, 11 Aug 2017 15:17:15 -0400
+
last-align (830-2) unstable; urgency=low
* Team upload.
diff -Nru last-align-830/debian/control last-align-869/debian/control
--- last-align-830/debian/control 2017-06-06 05:56:56.000000000 +0000
+++ last-align-869/debian/control 2017-08-11 19:17:02.000000000 +0000
@@ -6,7 +6,7 @@
Priority: optional
Build-Depends: debhelper (>= 10),
help2man,
- python-imaging
+ python-pil
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/last-align.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/last-align.git
@@ -18,7 +18,7 @@
${misc:Depends},
parallel
Recommends: python,
- python-imaging
+ python-pil
Description: genome-scale comparison of biological sequences
LAST is software for comparing and aligning sequences, typically DNA or
protein sequences. LAST is similar to BLAST, but it copes better with very
diff -Nru last-align-830/debian/tests/control last-align-869/debian/tests/control
--- last-align-830/debian/tests/control 2017-06-06 05:56:56.000000000 +0000
+++ last-align-869/debian/tests/control 2017-08-11 19:17:15.000000000 +0000
@@ -1,3 +1,3 @@
Tests: run-unit-test
Depends: @
-Restrictions: allow-stderr
+Restrictions: allow-stderr, needs-recommends
diff -Nru last-align-830/debian/upstream/metadata last-align-869/debian/upstream/metadata
--- last-align-830/debian/upstream/metadata 2017-06-06 05:56:56.000000000 +0000
+++ last-align-869/debian/upstream/metadata 2017-08-11 19:11:17.000000000 +0000
@@ -15,3 +15,10 @@
PMID: 20110255
Repository: http://last.cbrc.jp/last/
Webservice: http://lastweb.cbrc.jp/
+Registry:
+ - Name: OMICtools
+ Entry: OMIC_15813
+ - Name: bio.tools
+ Entry: LAST
+ - Name: RRID
+ Entry: SCR_006119
diff -Nru last-align-830/doc/lastal.html last-align-869/doc/lastal.html
--- last-align-830/doc/lastal.html 2016-12-13 13:54:12.000000000 +0000
+++ last-align-869/doc/lastal.html 2017-06-20 09:12:51.000000000 +0000
@@ -412,9 +412,10 @@
because it does not show gap positions. Warning: the other
LAST programs cannot read this format. Warning: "bit score"
is not the same as "score".
-BlastTab+ format is the same as BlastTab, with 2 extra
-columns at the end: length of query sequence and length of
-reference sequence. More columns might be added in future.
+BlastTab+ format is the same as BlastTab, with 3 extra
+columns at the end: length of query sequence, length of
+reference sequence, and (raw) score. More columns might be
+added in future.
For backwards compatibility, a NAME of 0 means TAB and 1 means
MAF.
@@ -669,6 +670,11 @@
extensions, it skips any remaining initial matches starting at
that position.
+-N COUNT |
+Stop after finding COUNT alignments per query strand. This
+makes lastal faster: it quits gapless and gapped extensions as
+soon as it finds COUNT alignments with score ≥ e. |
+
-R DIGITS |
Specify lowercase-marking of repeats, by two digits (e.g. "-R 01"),
with the following meanings.
diff -Nru last-align-830/doc/lastal.txt last-align-869/doc/lastal.txt
--- last-align-830/doc/lastal.txt 2016-12-13 13:53:24.000000000 +0000
+++ last-align-869/doc/lastal.txt 2017-06-20 09:12:31.000000000 +0000
@@ -93,9 +93,10 @@
LAST programs cannot read this format. *Warning:* `"bit score"
is not the same as "score" `_.
- **BlastTab+** format is the same as BlastTab, with 2 extra
- columns at the end: length of query sequence and length of
- reference sequence. More columns might be added in future.
+ **BlastTab+** format is the same as BlastTab, with 3 extra
+ columns at the end: length of query sequence, length of
+ reference sequence, and (raw) score. More columns might be
+ added in future.
For backwards compatibility, a NAME of 0 means TAB and 1 means
MAF.
@@ -311,6 +312,11 @@
extensions, it skips any remaining initial matches starting at
that position.
+ -N COUNT
+ Stop after finding COUNT alignments per query strand. This
+ makes lastal faster: it quits gapless and gapped extensions as
+ soon as it finds COUNT alignments with score ≥ e.
+
-R DIGITS
Specify lowercase-marking of repeats, by two digits (e.g. "-R 01"),
with the following meanings.
diff -Nru last-align-830/doc/lastdb.html last-align-869/doc/lastdb.html
--- last-align-830/doc/lastdb.html 2016-12-13 13:54:12.000000000 +0000
+++ last-align-869/doc/lastdb.html 2017-02-03 10:23:29.000000000 +0000
@@ -387,7 +387,7 @@
Soft-mask lowercase letters. This means that, when we compare
these sequences to some other sequences using lastal, lowercase
letters will be excluded from initial matches. This will apply
-to lowercase letters in both sets of sequences. | |
+to lowercase letters in both sets of sequences.
-u NAME |
Specify a seeding scheme. The -m option will then be ignored.
diff -Nru last-align-830/doc/lastdb.txt last-align-869/doc/lastdb.txt
--- last-align-830/doc/lastdb.txt 2016-12-13 13:53:24.000000000 +0000
+++ last-align-869/doc/lastdb.txt 2017-02-03 10:23:08.000000000 +0000
@@ -59,7 +59,7 @@
-c Soft-mask lowercase letters. This means that, when we compare
these sequences to some other sequences using lastal, lowercase
letters will be excluded from initial matches. This will apply
- to lowercase letters in both sets of sequences.
+ to lowercase letters in *both* sets of sequences.
-u NAME
Specify a seeding scheme. The -m option will then be ignored.
diff -Nru last-align-830/doc/last-dotplot.html last-align-869/doc/last-dotplot.html
--- last-align-830/doc/last-dotplot.html 2015-12-07 16:11:02.000000000 +0000
+++ last-align-869/doc/last-dotplot.html 2017-06-15 06:18:55.000000000 +0000
@@ -342,10 +342,10 @@
last-dotplot -1 'chr[!U]*' -2 'chr[!U]*' alns alns.png
-Option "-1" selects sequences from the 1st genome, and "-2" selects
-sequences from the 2nd genome. 'chr[!U]*' is a pattern that
-specifies names starting with "chr", followed by any character except
-U, followed by anything.
+Option "-1" selects sequences from the 1st (horizontal) genome, and
+"-2" selects sequences from the 2nd (vertical) genome. 'chr[!U]*' is
+a pattern that specifies names starting with "chr", followed by any
+character except U, followed by anything.
@@ -376,6 +376,11 @@
last-dotplot -1 'chr?' -1 'chr??' alns alns.png
+You can also specify a sequence range; for example this gets the first
+1000 bases of chr9:
+
+last-dotplot -1 chr9:0-1000 alns alns.png
+
Options
@@ -388,11 +393,14 @@
-h, --help
Show a help message, with default option values, and exit. |
+-v, --verbose |
+Show progress messages & data about the plot. |
+
-1 PATTERN, --seq1=PATTERN |
-Which sequences to show from the 1st genome. |
+Which sequences to show from the 1st (horizontal) genome. |
-2 PATTERN, --seq2=PATTERN |
-Which sequences to show from the 2nd genome. |
+Which sequences to show from the 2nd (vertical) genome. |
-x WIDTH, --width=WIDTH |
Maximum width in pixels. |
@@ -400,20 +408,114 @@
-y HEIGHT, --height=HEIGHT
Maximum height in pixels. |
+-c COLOR, --forwardcolor=COLOR |
+Color for forward alignments. |
+
+-r COLOR, --reversecolor=COLOR |
+Color for reverse alignments. |
+
+--sort1=N |
+Put the 1st genome's sequences left-to-right in order of: their
+appearance in the input (0), their names (1), their lengths (2). |
+
+--sort2=N |
+Put the 2nd genome's sequences top-to-bottom in order of: their
+appearance in the input (0), their names (1), their lengths (2). |
+
+--trim1 |
+Trim unaligned sequence flanks from the 1st (horizontal) genome. |
+
+--trim2 |
+Trim unaligned sequence flanks from the 2nd (vertical) genome. |
+
+--border-pixels=INT |
+Number of pixels between sequences. |
+
+--border-color=COLOR |
+Color for pixels between sequences. |
+
+
+
+
+ Text options
+
+
+
+
+
+
-f FILE, --fontfile=FILE |
TrueType or OpenType font file. |
-s SIZE, --fontsize=SIZE |
TrueType or OpenType font size. |
--c COLOR, --forwardcolor=COLOR |
-Color for forward alignments. |
+--lengths1
+Show sequence lengths for the 1st (horizontal) genome. |
--r COLOR, --reversecolor=COLOR |
-Color for reverse alignments. |
+--lengths2
+Show sequence lengths for the 2nd (vertical) genome. |
+
+
+ Annotation options
+ These options read annotations of sequence segments, and draw them as
+colored horizontal or vertical stripes. This looks good only if the
+annotations are reasonably sparse: e.g. you can't sensibly view 20000
+gene annotations in one small dotplot.
+
+
+
+
+
+
+--bed1=FILE |
+Read BED-format
+annotations for the 1st genome. They are drawn as stripes, with
+coordinates given by the first three BED fields. The color is
+specified by the RGB field if present, else pale red if the
+strand is "+", pale blue if "-", or pale purple. |
+
+--bed2=FILE |
+Read BED-format annotations for the 2nd genome. |
+
+--rmsk1=FILE |
+Read repeat annotations for the 1st genome, in RepeatMasker .out
+or rmsk.txt format. The color is pale purple for "low
+complexity" and "simple repeats", else pale red for "+" strand
+and pale blue for "-" strand. |
+
+--rmsk2=FILE |
+Read repeat annotations for the 2nd genome. |
+
+
+
+
+
+ Gene options
+
+
+
+
+
+
+--genePred1=FILE |
+Read gene annotations for the 1st genome in genePred format. |
+
+--genePred2=FILE |
+Read gene annotations for the 2nd genome. |
+
+--exon-color=COLOR |
+Color for exons. |
+
+--cds-color=COLOR |
+Color for protein-coding regions. |
+
+
+
+
Unsequenced gap options
Note: these "gaps" are not alignment gaps (indels): they are regions
@@ -441,6 +543,10 @@
An unsequenced gap will be shown only if it covers at least one whole
pixel.
+
|