forked from GMOD/jbrowse
-
Notifications
You must be signed in to change notification settings - Fork 0
/
release-notes.txt
2378 lines (1788 loc) · 102 KB
/
release-notes.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
{{$NEXT}}
## Minor improvements
* Added the ability to disable sorting on the hierarchical track
selector using the sortHierarchical flag in the trackSelector
config. Thanks to Chris Childers for the suggestion and Colin Diesh
for the implementation (issue #477).
* Made it so that when the user changes the display mode on the
canvas features based tracks, their selection is saved. Thanks to
Jon Hinton for the idea and Colin Diesh for the fix (issue #469).
* Added configurable click event handlers for Wiggle type tracks.
Thanks to Richard Hayes for implementing this feature (issue #489).
* Added the ability to access feature data in customizable callbacks
for the 'View details' pop-ups, and also the ability to customize
the 'About track' page with callbacks. Thanks to Colin Diesh for
the implementation (issue #494).
* Added the ability to load the category attribute from trackMetaData
files to be used for the Hierarchical track selector.
## Bug fixes
* Fixed a bug with VCF tabix file parsing that causes unnecessary
chunkSizeLimit errors. Thanks to Richard Hayes for finding and
debugging this issue (issue #486)!
* Fixed a bug where the Variant popup boxes would not display
complete genotype information in previous 1.11.* versions.
Thanks to Nando for reporting the bug and Colin Diesh for the
bugfix (issue #488).
* Fixed an small error that occured when using variant type tracks
with the REST API.
* Added a bugfix that caused problems scrolling in dialog boxes
for variant type tracks in 1.11.4 (issue #492).
* Fixed the use of the --refs flag on prepare-refseqs.pl. Thanks to
Audrey for finding & fixing this bug (issue #497).
* Added missing template length flag to the Alignments popup dialogs.
Thanks to Kieran Raine for the suggestion and Colin Diesh for the
fix (issue #471).
# Release 1.11.4 2014-05-14 12:04:54 America/Chicago
## Minor improvements
* Added high-resolution rendering for CanvasFeatures, SNPCoverage,
BigWig tracks, and histograms. This allows rendering for canvas-
based tracks to look much sharper on high-resolution displays and
can even look sharper when zooming. The high-resolution rendering
is disabled by default to avoid conflicts with existing instances,
but feel free to test it out by setting "highResolutionMode" in
jbrowse.conf. Thanks to Colin Diesh for the idea and implementation
(issue #456)
* Added the ability to run jbrowse scripts outside of the JBrowse
root directory. Thanks to Chien-Chi Lo for the patch (issue #465).
* Added basic GTF parser that can open files from the File->Open
menu or by using the in-memory adaptor. Big thanks to Andrew Warren
for the contribution (issue #453).
* Added a change to the highlight button to allow the user to more
easily clear highlights. Thanks to Paul Hale for the suggestion
and Colin Diesh for the fix (issue #445).
## Bug fixes
* Fixed help page icons not loading since JBrowse 1.11.2. Thanks to
Colin Diesh for catching the bug and fixing it (issue #460).
* Fixed updating of the y-axis scale when using the resize
quantitative tracks feature. Thanks again to Evan Briones for the
original implementation and Colin Diesh for the fix (issue #461).
* Changed the CanvasFeatures 'View details' pages to display the name
and description of features in the dialog box. Thanks to Colin
Diesh for the fix (issue #463).
* Added a bugfix for non-compliant servers that add a trailing slash
to the URL. Thanks to Colin Diesh for the fix (issue #462).
* Fixed a broken link in the documentation for biodb-to-json.
* Updated setup.sh to maintain compatibility with the latest BioPerl.
Thanks to Thomas Sibley and Scott Cain for helping with this issue
(issue #468).
* Fixed a long standing bug with the coloring of nucleotides on the
SNPCoverage/Alignments2 track. Thanks to Long Le for reporting this
on the mailing list.
* Fixed a long standing bug with the scrollbar in the dialog box on
Chrome and Safari browsers. Thanks to the #dojo irc channel and
and Colin Diesh for helping fix this problem (issue #386).
* Fix a small rendering problem that causes one pixel gap to appear
on Safari due to subpixel rendering issues. Thanks to Colin Diesh
for the preliminary fix (issue #341).
* Fix a bug with CanvasFeatures based tracks loading huge amounts
of data to generate histograms instead of using pre-generated
histograms. Also lowered the maxScreenFeatureDensity default on
the CanvasFeatures tracks so that histograms can be displayed more
readily. Thanks to Daniel Troesser for reporting this issue on the
mailing list and Colin Diesh for the fix (issue #475).
# Release 1.11.3 2014-03-07 13:05:57 EST5EDT
## Minor improvements
* Added a "Zoom to this" item in the default right-click menus for
canvas-based feature tracks. Thanks to Paul Hale for the initial
implementation of this.
* Allow the user to set the document.domain property via jbrowse.conf
which can be helpful especially if jbrowse is embedded in a iframe.
Thanks to Kieran Raine for the idea and Colin Diesh for the bugfix
(issue #440)
* Improved the graphic design of the "Add sequence search" dialog box
to make it clearer how to switch between providing an amino acid
and a nucleotide sequence. Thanks to Kevin Mohamed for the initial
implementation of this (issue #436).
* Expanded the default color set of `Alignments2` tracks to show
different shades of color indications of reads with missing mate
pairs, improperly aligned reads, and reads with mate pairs on
different reference sequences. Thanks to Keiran Raine for
implementing this (issue #443).
* Added support to customize specific parts of the 'View details'
popups using callback functions. Thanks to Kieran Raine for the
idea and Colin Diesh for the implementation (issue #421).
* The File->Open tool will now can add files named `*.coverage.*` or
`*.density.*` as histograms to newly-opened tracks if the file
basenames match. For example, if both `mysample.bam` and
`mysample.coverage.bw` are present, `mysample.coverage.bw` will be
added as a histogram source for `mysample.bam`. Thanks to Keiran
Raine and Alexander Stoddard for suggesting this (issue #423).
## Bug fixes
* Fixed a problem where the feature arrowhead would get stuck in the
middle of the screen at high zoom levels. Thanks to Colin Diesh for
the fix (issue #449).
* Disabled the FASTA download button in the "View details" page on
Safari (issue #412). This feature can't be supported in Safari at
this time, but it is still supported in most other browsers. Rob
Buels and Colin Diesh contributed fixes to this issue.
* Fixed a bug in the client-side GFF3 parser pointed out by Andrew
Warren. Thanks Andrew! (issue #452).
* Fixed the problem of translation frames being switched around at
different zoom levels. Thanks to Kieron Taylor for the bug report
and Colin Diesh for the bugfix (issue #435)
* Fixed a bug where gene features in GFF tracks would not have
arrowhead markers. Thanks to Colin Diesh for finding and fixing
this issue (issue #454)
# Release 1.11.2 2014-02-10 19:11:33 EST5EDT
## Minor improvements
* Added some user interface elements to set the height in pixels of a
single quantitative track, or of all visible quantitative tracks.
Thanks to Evan Briones for implementing this!
* Added a `JBrowse/View/FeatureGlyph/Diamond` glyph that draws
diamond-shaped features instead of boxes. Thanks to OICR Co-op
student Kevin Mohamed for implementing this!
* Reference sequence tracks now display a "no sequence" message
instead of a bunch of blank blocks when the reference sequence
basepairs aren't available. Thanks to Kevin Mohamed for
implementing this (issue #422).
* Persistent session state is now stored on a per-dataset basis,
which improves user experience when switching between multiple
datasets in JBrowse. Thanks to Richard Hayes for pointing this
issue out, and Kevin Mohamed for the fix (issue #410).
* "Hide sites not passing ..." settings in VCF track menus now show
the filter's long description when hovered over. Thanks to Keiran
Raine for suggesting this (issue #420).
* Tweaked display of track labels and added a slight border at the
top edge of each track to make it more clear which track data
belongs to. Thanks to Keiran Raine for suggesting this, and Kevin
Mohamed for the initial implementation (issue #432).
* Added a `--config` option to `flatfile-to-json.pl` that accepts
additional configuration variables that will be merged into the top
level of the track configuration. Thanks to Mikael Brandström
Durling for the initial implementation of this.
## Bug fixes
* `generate-names.pl` now indexes VCF files from track definitions in
`tracks.conf` files. Thanks to Paul Halle for pointing this out
(issue #434).
* Added a missing dependency for the server side formatting tools on
List::MoreUtil 0.28 or higher. Thanks to Cris Lawrence and Keiran
Raine for troubleshooting this!
# Release 1.11.1 2014-01-07 15:48:39 EST5EDT
## Minor improvements
* Alignments2 tracks now include right-click menu items to view the
location of an alignment's mate pair or next segment in a popup or
a new tab. Thanks to Keiran Raine for suggesting this (issue #406).
* Alignments2 tracks now draw gaps and deletions in reads regardless
of zoom level, as long as the alignment is at least 3 pixels wide
in the display. Thanks to Keiran Raine for pointing out the need
for this (issue #403).
* Added support for a `histograms.max` variable for
CanvasFeatures-based tracks that can be used to manually set the
max value of a histogram display. Thanks to Keiran Raine for
pointing out the need for this.
* Added support for drawing clip markers (with their color set by
`histograms.clip_marker_color`) in CanvasFeatures-based
tracks. Thanks to Keiran Raine for pointing out the need for this
(issue #402).
* Canvas-based feature tracks now try to draw histograms, if
available, when the data backend throws a data-overflow error (like
when the BAM backend exceeds the chunkSizeLimit). Thanks to Keiran
Raine for motivating this (issue #405).
* Make it easier to set JS loading baseUrl by moving it into the
initial dojo configuration. Thanks to Jillian Rowe for pointing
out the need for this.
* Enhanced new text-based config syntax to support arrays of values
in a list like:
[trackMetadata]
sources =
+ data/mymeta.csv
+ data/more_meta.csv
## Bug fixes
* When a number is typed into the location box, JBrowse first checks
if it is the name of a feature in the names index, and only
interprets it as a coordinate if it is not found in the names
index. Thanks to Richard Hayes for pointing this out (issue #407).
* Fixed bug that caused client-side GFF3 tracks to appear as
"Loading" forever if the GFF3 is malformed (like malformed GFF3
files that are opened with the File->Open tool).
* Fixed bug in which no default value for
`maxFeatureSizeForUnderlyingRefSeq` was being set, which made
default feature detail popups try to fetch and display a feature's
underlying reference sequence even if it is way too large, unless
the variable was set explicitly in the configuration.
* JBrowse now shows a more understandable error message when trying
to open an uncompressed BAM file. Thanks to Keiran Raine for
pointing this out (issue #404).
* Fixed jbrowse.conf faceted track selector configuration examples
not working as written. Thanks to Cris Lawrence for pointing this
out.
* Fixed a bug in which right-clicking on feature labels in an
HTMLFeatures-based track did not bring up the right-click menu for
a feature. Thanks to Cris Lawrence for pointing this out (issue #408).
# Release 1.11.0 2013-12-19 15:51:37 EST5EDT
## Major improvements
* Introduced density/coverage histogram support for CanvasFeatures,
CanvasVariants, and Alignments2 tracks. These track types now
support an optional `histograms` configuration subsection that can
contain a definition for a second datastore that holds quantitative
data (usually either coverage depth or feature density) to be
displayed when zoomed further out than `featureScale` (or if
`featureScale` is not set, the scale determined by the store's
feature density divided by `maxFeatureScreenDensity`). Thanks to
Richard Hayes for pushing hard for this feature.
* Added a new "Hierarchical" track selector that shows tracks in a
hierarchy of collapsible categories, which is now the default track
selector. To assign categories and subcategories to your tracks,
set `category` or `metadata.category` attributes on each configured
tracks in your `trackList.json`. Thanks to the many users who have
requested this at one time or another.
* JBrowse now supports a new plaintext configuration format that
users of GBrowse will find very familiar, since it is designed to
be very similar to it. This syntax is also much easier to
hand-write than JSON. The JSON configuration syntax is not going
away, and will continue to be supported.
Thanks to Erik Derohanian for the original implementation of this
configuration adaptor, and Richard Hayes and Keiran Raine for
motivating the work to polish and more fully integrate it.
* Variables in configuration files can now be based on the contents
of other variables. For example, setting
"myCustomVariable": "/some/custom/path",
"include": "{myCustomVariable}/conf.json"
will try to include a configuration file located at
"/some/custom/path/conf.json". Interpolation is done as the final
step in configuration loading, so variables can come from anywhere
in the configuration.
* When JBrowse is started, if there are no reference sequences found
in the default `dataRoot`, but the dataset selector is configured,
JBrowse shows a simple list of links to available datasets instead
of the "Congratulations, JBrowse is on the web" page. Thanks to
Saulo Aflitos for the idea and its initial implementation.
* For users wishing to convert existing JSON configuration files to
the new format, there is a new script, `bin/json2conf.pl`, that
does a fair job. Run `bin/json2conf.pl -?` for details on how to
use it.
* Added a new REST backend for name lookup and autocompletion. See
http://gmod.org/wiki/JBrowse_Configuration_Guide#JBrowse_REST_Names_API
for details. Thanks to Erik Derohanian for implementing this, and
Ben Booth for suggesting an API design (issue #267).
* Major performance and scalability improvements for
`generate-names.pl`. Now uses a different algorithm that is faster
and more scalable than before, and no longer relies on BerkeleyDB
for temporary storage. This should also alleviate the need to run
generate-names.pl with `--safeMode` in Perl 5.10 and earlier. In
fact, the `--safeMode argument` to generate-names.pl no longer has
any effect. Thanks to Cris Lawrence for pointing out the
continuing need for more scalability.
## Minor improvements
* Detail popups for CanvasVariants and HTMLVariants tracks now
display the reference sequence itself instead of just "ref" in
genotype displays. Thanks to Cris Lawrence for requesting this.
* Added a "save as FASTA" button to default feature detail popups
that downloads a FASTA file with the displayed piece of reference
sequence (issue #299).
* `chunkSizeLimit` for VCF files now defaults to 1 MiB. It used to
be 15 MiB, which was really far too big for browsers to handle.
* Added support for a `--nameAttributes` argument to
`flatfile-to-json.pl` that takes a comma-separated list of feature
attributes to index for name searching and completions, or 'none'
to not make names searchable.
* Added support for a `nameAttributes` variable in `biodb-to-json.pl`
track configurations that can be set to an array of feature
attribute names to to index for name searching and completions, or
'none' to not make names searchable.
* Add a `--category` argument to bin/wig-to-json.pl that can be used
to set the `metadata.category` of a track.
## Bug fixes
* Fixed a bug in NCList data backed in which feature histograms were
often calculated very incorrectly.
* Fixed a bug in the VCF data backend that caused not all VCF
features to be shown in some files at some zoom levels.
# Release 1.10.12 2013-12-10 16:09:42 EST5EDT
## Minor improvements
* `bam-to-json.pl` and `flatfile-to-json.pl` now support a
`--metadata` argument that can add a `metadata` stanza to track
configurations they generate.
* Multi-valued attributes in feature detail popups are displayed as a
string of boxes, each containing a value, to avoid
misinterpretation. Before, each value was just separated from the
previous one by whitespace. Thanks to Cris Lawrence for pointing
out the need for this.
## Bug fixes
* Re-enabled usage analytics reporting, which had been disabled by a
stray piece of debugging code since the 1.10.7 release.
* Fixed a bug in which the tooltip in canvas-based feature tracks
would sometimes display incorrect label or description text.
# Release 1.10.11 2013-12-03 17:21:20 EST5EDT
## Minor improvements
* Made the sequence track's "zoom in to see sequence" placeholder
take up less vertical space. Thanks to Scott Cain for pointing out
that making it be the same height as it will eventually be when
zoomed in to base level is silly.
* By default highlighting features after searching for them by name
is now turned off. Set the `highlightSearchedRegions` top-level
conf variable to `true` to turn this back on. Turns out, most
people seem not to like this behavior. Thanks to Gregg Helt and
Cris Lawrence for pointing this out.
* `SNPCoverage` tracks now correctly display "skipped" regions in
alignments, such as those produced by TopHat. Thanks to Josh
Orvis, Gustavo Cerquiera, and others for reminders that this was
still an issue.
* `SNPCoverage` tracks now provide per-strand counts of "reference"
reads at each position, like they already were providing for
reads with mismatches.
* `SNPCoverage` tracks now accept a `mismatchScale` configuration
variable that sets the viewing scale (i.e. zoom level, pixels per
bp) above which base-level mismatches will be drawn. Defaults to
1/10. Making this value larger can speed up SNPCoverage tracks for
high-coverage data at the cost of needing to zoom in further to see
mismatches.
* setup.sh now uses `curl` for downloading things instead of `wget`,
since `curl` is more widely available. Thanks to Keiran Raine for
suggesting and implementing this (issue #393).
## Bug fixes
* Fixed a bug in which `generate-names.pl` would sometimes report the
incorrect number of hashing bits in verbose output, and would
sometimes use the number of hashing bits for an existing index even
if that index was being regenerated. Thanks to Richard Hayes for
pointing out the incorrect log output.
* Fix `generate-names.pl` crashing on some older versions of Perl with
an error like `Bareword "POSIX::O_RDONLY" not allowed while "strict
subs" in use`. Thanks to Chris Childers for pointing this out.
* Fix `setup.sh` failing on some older versions of Perl. It now runs
`generate-names.pl` with the `--safeMode` flag.
* Fixed a bug where the value display in SNPCoverage tracks would
sometimes report "NaN%" for the reference when no reads cover a
region.
* Fixed a bug in which activating rubberband zooming using the SHIFT
key while in highlighting mode would cause all the tracks to be
dragged when attempting to highlight a region afterward. Thanks to
Erik Derohanian for pointing out and fixing this (issue #387).
* Fixed the location of the dojo/nls directory in release zipfiles.
Was erroneously in src/nls, supposed to be src/dojo/nls. Thanks to
Matt Bomhoff for pointing this out.
* The in-memory GFF3 parser now copes with a missing newline at the
end of a GFF3 file. Previously, the last line was ignored if it
did not end with a newline character. Thanks to Colin Davenport
for pointing this out (issue #394).
# Release 1.10.10 2013-11-21 09:31:53 EST5EDT
## Minor improvements
* Spacing between tracks is now configurable by setting
`view.trackPadding` in the configuration. Thanks to Chenchen Zhu
for suggesting this (issue #377).
* If reference sequences are defined, but no tracks are yet added,
JBrowse will start normally instead of going to the
"Congratulations, JBrowse is on the web" page.
* `generate-names.pl` now supports a `--compress` option that
compresses the name index files to save server disk space. Thanks
to Richard Hayes for pointing out the need for this (issue #378).
## Bug fixes
* `generate-names.pl` now uses IO::Uncompress::Gunzip instead of
PerlIO::gzip to read compressed VCF files. This fixes a bug in
which only the first few hundred names in a VCF were indexed.
Thanks to Cris Lawrence for pointing this out (issue #380).
* Fixed a bug in which `generate-names.pl` would crash if run with
`--incremental` and no existing names index. Thanks to Richard
Hayes for pointing this out (issue #379).
* Fixed a bug in which `generate-names.pl` would sometimes choose the
wrong number of hash bits when performing incremental updates,
leading to the old data being lost. Thanks to Richard Hayes for
lots of help troubleshooting this.
* Fixed bug where other tracks are visible underneath pinned tracks
when the display is scrolled down. Thanks to Ed Lee for pointing
this out.
* Fixed a bug in which tooltip does not hide after the mouse leaves a
Wiggle track in Safari 5 and 6. Thanks to Charles Girardot for
pointing this out.
* Fixed a bug in which the `main.css` file for plugins was not being
correctly loaded in some installations. Thanks to Matt Bomhoff for
pointing this out.
# Release 1.10.9 2013-11-08 15:22:50 EST5EDT
## Minor improvements
* `generate-names.pl` now supports a `--incremental` or `-i` option
that adds names to an existing index. Thanks to Richard Hayes for
reminding me that this wasn't done yet (issue #373).
* Added a lower-performance, but more backward-compatible indexing
backend to generate-names.pl that can be activated by passing the
`--safeMode` command-line argument. The recent performance
improvements to generate-names.pl have apparently tickled some bugs
that are present in some installations. Thanks to Josie Reinhardt
and GitHub user raj76 for their continued help troubleshooting
this. If you find that name indexing is not working correctly, try
running it again with `--safeMode`, and report to the mailing list
if it helps.
* Added support for using the JBrowse in-memory GFF3 adaptor to
display web-accessible GFF3 files directly. See
docs/tutorial/data_files/volvox.gff3.conf for an example
configuration. Thanks to David Goodstein and Richard Hayes for
motivating this.
## Bug fixes
* `flatfile-to-json.pl` now depends on the latest
Bio::GFF3::LowLevel::Parser 1.8, which fixes a bug in which
features with no ID, Parent, or Derives_from attributes were not
being included in parsed data. Thanks to Gwendoline Andres for
pointing this out.
* Tweak BioPerl-handling code in biodb-to-json.pl to hopefully work
better with BioSQL backends. Thanks to Brian Osborne for pointing
this out.
# Release 1.10.8 2013-10-25 11:13:30 EST5EDT
## Minor improvements
* Added a new `navigateTo` action usable for customizing feature
left-clicks and right-click menus. Thanks to Scott Cain for
requesting this.
* Added a new `feature_range_cache` option for the REST data backend.
If set to true, the REST backend will more aggressively cache
ranges of feature data. Thanks to Daniel Troesser for pointing out
the need for this (issue #369).
* `maker2jbrowse` now, by default, runs `generate-names.pl` to
generate names indexes. Also added a `--no_names_index` option to
turn this off. Thanks to Josie Reinhardt for making me notice this
was missing.
* Tweaked `generate-names.pl` default indexing parameters to
emphasize indexing speed more. Now defaults to a smaller average
file size for the on-disk JSON files it produces, which is much
faster to generate and write (up to 8 or 10x faster). However, the
on-disk index is about 2-2.5x larger overall.
* Removed support for the `--refids` command-line argument to
`prepare-refseqs.pl`, which has probably never really worked.
* Improved `prepare-refseqs.pl` support for Bio::DB::Das::Chado
database backends. Thanks to Gwendoline Andres for helping
troubleshoot this.
## Bug fixes
* Fixed generate-names.pl making incorrect name indexes when using 16
or more bits of hashing (when the number of index entries exceeds
about 4 million). Thanks to Josie Reinhardt for helping
troubleshoot this (issue #370).
* The faceted track selector no longer refuses to display track
unique labels even if they are explicitly included in the
`displayColumns` setting.
# Release 1.10.7 2013-10-15 16:50:00 EST5EDT
## Minor improvements
* Added an optional `stats/regionFeatureDensities` endpoint to the
REST API that makes it possible to provide binned feature counts
that HTMLFeatures tracks can use to display feature histograms.
Thanks to Stuart Watt and Daniel Troesser for pointing out the need
for this (issue #365).
## Bug fixes
* Fixed a bad bug introduced in 1.10.6 in which FASTA files with line
lengths longer than the configured chunk size were not correctly
formatted. Thanks to Jean-Jack Riethoven for pointing this out
(issue #363).
* Fixed a bug introduced in 1.10.6 in which prepare-refseqs.pl would
not respect the --noseq command-line option when using --fasta.
* Fixed bug in which `name` or `seq_id` attributes are required for
reference sequence features. Thanks to Daniel Troesser for
pointing this out.
* Fixed a bug that may have prevented some types of VCF files from
being displayed (error message referring to `inheritedFilters`).
* Fixed a bug in which "Zoom in to see feature" in Sequence tracks
would wrap downwards below track at some zoom levels and window
widths.
* Fixed an off-by-one error in UTR attributes manufactured by the
`impliedUTRs` mechanism of the ProcessedTranscript glyph. Thanks
to Ben Booth for pointing this out (issue #362).
* Fixed a bug in which `score` attributes of features were not being
recorded by `biodb-to-json.pl`. Thanks to HongKee Moon for
pointing this out (issue #364).
* Removed a stray use of Carp::Always in GFF3-processing Perl code
that may have caused problems in some installations.
# Release 1.10.6 2013-10-07 21:06:51 EST5EDT
## Minor improvements
* Made the `impliedUTRs` option for ProcessedTranscript and Gene
glyph still attempt to create UTRs if only '''one''' of the UTRs is
missing from a transcript. Thanks to Ben Booth for pointing out
the need for this.
## Bug fixes
* Fixed bug in which the mouseover value displays for Wiggle and
SNPCoverage tracks would not always be hidden when the mouse leaves
the track.
* Fixed a bad bug that prevented fixed-scale Wiggle and SNPCoverage
tracks from displaying. Thanks to Jean-Jack Riethoven and Michael
Axtell for pointing this out.
# Release 1.10.5 2013-10-03 10:21:37 EST5EDT
## Minor improvements
* Greatly improved the speed and reduced the memory footprint when
running `prepare-refseqs.pl` with the --fasta and --gff options.
* Added an `impliedUTRs` option to the ProcessedTranscript and Gene
glyphs for CanvasFeatures tracks. Thanks to Ben Booth for pointing
out the need for this (issue #348).
* Upgraded flatfile-to-json.pl to use a new version of
Bio::GFF3::LowLevel::Parser for GFF3 parser, which has a lookback
buffer limit that makes it easier to parse large GFF3 files that do
not contain enough '###' directives.
* Further improved the memory footprint and speed of
generate-names.pl. Thanks to Richard Hayes for his continued help
with testing improvements and reporting problems.
* Removed explicit dependency on GD::Image, which is only used by the
old tiled-image generation demo code. This will make dependency
installation easier for many people, at a (very) small cost to
backward compatibility.
## Bug fixes
* Fixed a bad bug that prevented combination tracks from working.
Thanks to Harry Yoo for pointing this out (issue #351).
* Fixed a bug in which one of the temporary files used by
generate-names.pl was not being created in the correct location.
Thanks to Richard Hayes for testing this.
* Fixed a bug in which `generate-names.pl` could sometimes crash when
run with the -v (verbose) switch, or in setup.sh.
* Fixed odd behavior when entering coordinate ranges in the location
box under Safari. Thanks to Keiran Raine for pointing this out
(issue #341).
# Release 1.10.4 2013-09-23 16:16:50 EST5EDT
## Minor improvements
* Rewrote many parts of generate-names.pl, making heavy use of
temporary BerkeleyDB stores (using Perl's DB_File module). This
improves generate-names.pl performance by more than 10x.
* Added a File->Add sequence search track menu item that can make
tracks that show which regions of the reference sequence contain a
given (small) sequence, or match a given regular expression.
Thanks to Daniel Kasenberg for the initial implementation of this
(issue #315).
* Added a CanvasVariants track type, similar to HTMLVariants, which
utilizes the faster CanvasFeatures rendering backend for displaying
variant data.
* Added checkboxes to HTMLVariants and CanvasVariants track menus
that allow filtering displayed features based on the FILTER
attribute in a VCF file. In addition to filtering based on the
presence or absence of PASS, users can filter based on the custom
filters defined in the VCF header. Thanks to Keiran Raine and
Andrew Uzilov for suggesting this (issue #344).
* Added "Hide forward strand" and "Hide reverse strand" checkboxes to
Alignments and Alignments2 track menus that allow alignments on the
forward and/or reverse strands to be hidden.
## Bug fixes
* Fixed a bug that prevented indexing of feature aliases in the names
index when running generate-names.pl.
* Fixed a bug that prevented proper display of the "ibeam" feature
class in HTMLFeatures tracks. Thanks to Ed Lee for pointing this
out.
# Release 1.10.3 2013-09-04 16:22:17 EST5EDT
## Minor improvements
* Added options to Alignments, Alignments2, and SNPCoverage tracks to
allow hiding reads that are duplicates, fail vendor QC, have
missing mate pairs, are secondary alignments, and/or are
supplementary alignments. Thanks to Kieran Raine and Andrew Uzilov
for pointing out the need for this, and for their input on its
design (issue #332).
* Added support for a `variables` configuration for SPARQL data
stores that can be used to specify additional variables for
interpolating into a SPARQL query. Thanks to Toshiaki Katayama for
suggesting this.
* Added the ability for Sequence tracks to display a 6- or 3-frame
translation of the reference sequence. Thanks to Daniel Kasenberg
for implementing this (issue #221).
* Added checkboxes in the track menu of Sequence tracks that allow
users to toggle the display of the forward strand, reverse strand,
and 6-frame translation.
* Added support for an `addStores` variable in the query string of the
URL used to start JBrowse. This variable accepts store
configurations (which are a way to specify data sources separately
from track configurations, so multiple tracks can use the same data
source) in JSON format. For example, to add a store called
"urlbam" that points to a BAM file, you could use the JSON:
`{ "urlbam": { "type": "JBrowse/Store/SeqFeature/BAM", "urlTemplate": "/path/to/my/bamfile.bam" }}`
which, when URI-escaped and put in the query string, looks like:
`addStores=%7B%20%22urlbam%22%3A%20%7B%20%22type%22%3A%20%22JBrowse%2FStore%2FSeqFeature%2FBAM%22%2C%20%22urlTemplate%22%3A%20%22%2Fpath%2Fto%2Fmy%2Fbamfile.bam%22%20%7D%7D`
* Slightly improved performance of generate-names.pl in cases where
--completionLimit is zero. Also improved the POD documentation of
the --completionLimit parameter for generate-names.pl. Thanks to
Richard Hayes for his continued patience.
## Bug fixes
* Fixed some bugs that prevented proper display of BigWig files
larger than 4GB. Thanks to Keiran Raine for pointing this out.
* Fixed a major performance bug that unnecessarily slowed down
display of large BigWig files with Wiggle tracks when `autoscale`
is set to "local".
* Fixed a bug that prevented display of BAM reads that had MD tags
but no associated CIGAR string. Thanks to Keiran Raine for point
this out (issue #330).
* Fixed a bug in which FixedImage tracks (e.g. legacy image-based
Wiggle tracks) never take down the "Loading" message when
displaying on a reference sequence for which no image data has been
provided.
* Fixed a bug that prevented rendering of mismatches, insertions, and
deletions in a BAM read that occurred after a skip. Thanks to Gregg
Helt for noticing this and fixing it (issue #325).
* Fixed a bug in which the SNP frequencies calculated by SNPCoverage
tracks were sometimes incorrect. Thanks to Matthew Conte for
pointing this out (issue #335).
* Fixed a bug in which reference sequences with a start coordinate
other than zero would cause the overview scale track to not be
drawn correctly. Thanks to Gregg Helt for noticing this and
working on an initial fix (issue #324).
* Fixed a bug in which the most recent location visited on a given
reference sequence was not properly being restored from the saved
cookie. Thanks to Gregg Helt for the initial fix for this
(issue #321).
* Fixed a bug in which event handlers and blocks in CanvasFeatures
tracks were not being properly cleaned up. The most prominent
visible consequences of this were duplicate dialog boxes being
opened when clicking on a canvas feature. Thanks to Keiran Raine
for noticing this and making sure it was fixed (issue #329).
* Fixed a bug with flatfile-to-json.pl parsing of GenBank locations.
Thanks to Steve Marshall for pointing this out (issue #323).
* Fixed a bug in which SNPCoverage tracks would not always properly
display error messages when something goes wrong, particularly
under IE 9.
# Release 1.10.2 2013-08-15 13:57:16 EST5EDT
* Added mouse-over 'tooltips' to to CanvasFeatures tracks that show
the a feature's label and description when the mouse hovers over
it. Thanks to Daniel Kasenberg for implementing this.
* Strand arrowheads in CanvasFeatures tracks now attempt to stay
visible on the screen, like they do in HTMLFeatures tracks. Thanks
to Daniel Kasenberg for implementing this.
* Fixed bugs and inefficiencies preventing JBrowse from handling very
dense BigWig files. Thanks to Michael Axtell for pointing this out
(issue #312).
* Fixed a bug in which features were not always laid out correctly in
CanvasFeature tracks when the display mode is set to "compact".
* Fixed a bug causing the text labels of mismatching bases in
Alignments2 tracks (i.e. `Alignments` canvas glyphs) to be slightly
misaligned vertically when feature labels are turned on (they are
off by default for Alignments glyphs).
* Fixed a bug preventing the `defaultTracks` configuration variable
from operating correctly.
# Release 1.10.1 2013-08-06 15:32:21 EST5EDT
* Added support in `maker2jbrowse` for user-defined source tags in
GFF3 output from MAKER. Thanks to Carson Holt for contributing
this fix.
* NCList data stores (actually the array representation used therein)
now store feature attribute names case-insensitively.
* Fixed a bug in which features in canvas-based feature tracks could
not be clicked in Firefox. Thanks to GitHub user mke21 for
pointing this out, and to Daniel Kasenberg for fixing my fix to
work with older versions of Chrome.
* Fixed a bug with client-side GFF3 parsing in which the strand of
features was not being correctly parsed.
* Fixed bug preventing backward-compatibility with 1.2.1-formatted
data. Thanks to Daniel Kasenberg for implementing this.
* Fixed a bug in the Gene glyph that caused the browser to crash if a
gene feature has no subfeatures.
# Release 1.10.0 2013-07-30 14:25:06 EST5EDT
## Major improvements
* Added powerful combination tracks, which can combine data from
multiple other tracks using range, arithmetic, or masking
operations. For example, a BigWig track can be masked to highlight
only regions that lie within features from a BAM track. Or the
intersection of two or more feature tracks can be calculated. To
create a combination track, select "File->Add combination track"
from the menu bar, and then add tracks to the new combination track
by dragging them into it. A huge thanks to OICR co-op students
Julien Smith-Roberge and Daniel Kasenberg for implementing this
powerful feature. It's a very significant accomplishment!
* Added "normal", "compact", and "collapsed" feature layout options
for canvas-based feature tracks (currently just Alignments2
tracks). Thanks to OICR co-op student Daniel Kasenberg for
implementing this!
* Greatly improved the `JBrowse/View/Track/CanvasFeatures` track
type, to the point where it is probably ready for experienced
JBrowse users to use in earnest. It renders features using a
modular glyph system that GBrowse users will find very familiar.
To give it a try, simply change the `type` key in an existing track
configuration to "JBrowse/View/Track/CanvasFeatures" and add a
`glyph` key to set which glyph to use. Glyphs that are currently
implemented are:
* Box - draws a box, optionally with an arrow indicating strandedness.
* Segments - draws a series of boxes connected with a line, for
features with subparts.
* ProcessedTranscript - draws CDS and UTR features, with UTRs a
different color and thinner.
* Gene - draws a group of aligned ProcessedTranscript glyphs for
mRNAs that are subfeatures of a top-level gene feature.
Each of these glyphs have been patterned as near-clones of the
(very popular) analogous glyphs in GBrowse.
* Added a SPARQL data backend to allow displaying features directly
from a SPARQL endpoint. Many thanks to the NDBC/DBCLS BioHackathon
2012 and 2013 participants for suggesting this and helping with
this work! See http://www.biohackathon.org for more on this
fantastic (and I think very important) series of hackathons.
* There is a new "Highlight" button next to the "Go" button that lets
a user quickly and easily highlight a region with the mouse.
* Added the ability to "pin" some tracks to the top of the display,
so that they stay at the top of the pane while the rest of the
tracks are scrolled vertically. Thanks to the WebApollo project
for suggesting this.
* Integrated a `maker2jbrowse` script into the core JBrowse
distribution. You can now visualize your MAKER results in JBrowse
with a single command:
`bin/maker2jbrowse -d /path/to/your/maker/master_datastore_index.log`
Thanks to the MAKER team and Yandell lab for providing the initial
implementation of `maker2jbrowse`.
## Minor improvements
* Added support for an `addFeatures` variable in the query string of
the URL used to start JBrowse. This variable accepts feature data
in JSON format in the form:
`[{ "seq_id":"ctgA", "start": 123, "end": 456, "name": "MyBLASTHit"},...}]`
which, when URI-escaped and put in the query string, looks like:
`addFeatures=%5B%7B%20%22seq_id%22%3A%22ctgA%22%2C%20%22start%22%3A%20123%2C%20%22end%22%3A%20456%2C%20%22name%22%3A%20%22MyBLASTHit%22%7D%5D`
Developers integrating JBrowse into larger project may find this
feature useful for displaying results from other
non-JavaScript-based applications (such as legacy web BLAST tools)
in JBrowse.
Features added to JBrowse in this way are available in a special
data store named `url`, which can be specified in a track
configuration by adding `"store":"url"`.
* Added support for an `addTracks` variable in the query string of
the URL used to start JBrowse. This variable accepts track
configurations in JSON format in the form:
`[{"label":"mytrack","store":"url","type":"JBrowse/View/Track/HTMLFeatures"},...]`
which, when URI-escaped and put in the query string, looks like:
`addTracks=%5B%7B%22label%22%3A%22mytrack%22%2C%22store%22%3A%22url%22%2C%22type%22%3A%22JBrowse%2FView%2FTrack%2FHTMLFeatures%22%7D%5D`
* Added "Save track data" option to Alignments2 tracks. This option
should have been there all along, but somehow slipped through the
cracks. Thanks to Valerie Wong for pointing this out at the 2013
GMOD Summer School!
* Statistics about a track's features are now shown in its "About
this track" dialog, if available.
* Added support for a --reftypes argument to `prepare-refseqs.pl`,
allowing you to search a database for reference sequences based on
the type of the reference sequences, e.g. 'chromosome'. Thanks to
Gaelen Burke at the 2013 GMOD Summer School for pointing out the
need for this, and for assistance in testing the new feature.
* Added a `--gbk` option to `flatfile-to-json.pl` that accepts a
GenBank-format text file as input for loading annotation data.
Thanks to Justin Reese for the initial implementation of this.
* When formatting features with `flatfile-to-json.pl`, multi-valued
feature attributes are now only flattened (renamed foo, foo2, foo3,
etc) for "name", "id", "start", "end", "score", "strand",
"description", and "note" attributes. Formerly, all attributes
were flattened. This improves the default display of features that
have many values for some attributes, such as Dbxrefs or GO terms.
* Further improved scrolling smoothness of HTML-based feature tracks.
* Added a `JBrowse/Store/SeqFeature/FromConfig` feature store adapter
that can display feature data that is specified directly in