-
Notifications
You must be signed in to change notification settings - Fork 294
/
ChangeLog
3662 lines (2654 loc) · 148 KB
/
ChangeLog
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
2016-11-15 Nicole Kingsley <nbkingsley@ucdavis.edu>
* tests/{test_normalize_by_median.py,test_scripts.py}:
Replaced two lines that created a file and stored test data with one
line that calls the utils.copy_test_data function to complete the
same task.
2016-11-15 Daniel Standage <daniel.standage@gmail.com>
* docs/dev/scripts-and-sandbox.rst: Added documentation for reserved flags
for command line scripts.
2016-11-15 Titus Brown <titus@idyll.org>
* khmer/{_cpy_counttable,_cpy_hashgraph.hh,cpy_nodetable.hh,_khmer.cc,
khmer/__init__.py}: new Counttable and Nodetable CPython types, plus
renaming of CountingHash to CountGraph and Hashbits to Nodegraph;
refactoring of CPython hierarchy to separate graph methods from table
methods.
* lib/hashtable.{cc,hh}: pull some more CountingHash/Counttable methods
back to base class; rename.
* lib/hashgraph.{cc,hh}: create new files containing the Countgraph
and Nodegraph classes.
* Makefile, setup.py: updated dependencies for added and removed files.
* lib/Makefile: eliminated lib/counting.{cc,hh} and lib/hashbits.{cc,hh}.
* lib/{labelhash.cc,read_aligner.hh,storage.cc,storage.hh,subset.cc,
subset.hh,test-Colors.cc,test-compile.cc},
examples/c++-api/count-demo.cc - renamed CountingHash and Hashbits.
* tests/test_cpython_hierarchy.py - some preliminary tests for new CPython
inheritance hierarchy.
* tests/{test_nodegraph,test_countgraph}.py - added creation tests of
'tablesizes' passed into Nodegraph and Countgraph constructors.
2016-11-15 Luiz Irber <khmer@luizirber.org>
* khmer/__init__.py,tests/test_functions.py: Fix get_n_primes_near_x to
always return integers.
2016-11-14 Tim Head <betatim@gmail.com>
* khmer/_khmer.cc,lib/read_parsers.hh: Expose khmer's Read type fully to
the python side.
* scripts/{extract-paired-reads.py,filter-abund-single.py,filter-abund.py,
sample-reads-randomly.py,split-paired-reads.py,trim-low-abund.py}: Switch to
using ReadParser to speed up scripts.
* tests/test_read_handling.py,tests/test_scripts.py: Remove streaming tests
that use a FIFO.
2016-11-14 Shannon EK Joslin <sejoslin@ucdavis.edu>
*khmer/tests/test_countgraph.py: Refactor test code to use load_countgraph #1474
*khmer/tests/test_nodegraph.py: Refactor test code to use load_nodegraph and load_countgraph #1474
2016-11-14 Tim Head <betatim@gmail.com>
* .travis.yml: whitelist `master` branch to allow build-on-push without
building every push for a PR twice.
2016-11-11 Titus Brown <titus@idyll.org>
* doc/requirements.txt: set autoprogram version requirements to something
that works on python 2.7, in order to fix ReadTheDocs builds.
2016-11-10 Camille Scott <camille.scott.w@gmail.com>
* lib/assembler.{hh,cc}: add JunctionCountAssembler implementation.
* lib/kmer_filters.{hh,cc}: add get junction_count_filter function.
* khmer/{__init__.py,_khmer.cc}: add LinearAssembler,
SimpleLabeledAssembler, and JunctionCountAssembler to CPython interface.
* tests/test_assembly.py: minor refactoring, & tests for
JunctionCountAssembler and newly exposed C++ functions.
* sandbox/streaming-assembly-simple.py: demo script for streaming assembly.
* Makefile: update debug flags.
* lib/{counting.hh,hashtable.{hh,cc},hllcounter.hh,labelhash.hh,
read_aligner.hh,subset.{hh,cc}}: minor cleanup.
* tests/test_sandbox_scripts.py: minor cleanup.
2016-11-07 Luiz Irber <khmer@luizirber.org>
* Makefile: add --ignore-installed flag to pip install (fix installation
on conda environments.
* doc/requirements.txt: change hard requirement to 'newer than', avoid
installing a quite old setuptools version.
2016-11-04 Tim Head <betatim@gmail.com>
* Make khmer's Read type accessible from the python API.
2016-11-03 Titus Brown <titus@idyll.org>
* lib/{counting.cc,counting.hh,hashbits.cc,hashbits.hh,hashtable.cc,
hashtable.hh,storage.cc,storage.hh}: extracted in-memory storage details
into Storage/Bitstorage/ByteStorage classes.
* khmer/_khmer.cc,lib/{assembler.cc,assembler.hh,subset.cc,
subset.hh,labelhash.cc,labelhash.hh,traversal.cc,traversal.hh}: renamed
Hashtable to Hashgraph.
* setup.py,lib/Makefile: added storage.{cc,hh} to build.
2016-10-31 Titus Brown <titus@idyll.org>
* lib/{counting.hh,hashbits.hh,hashtable.hh}: factor out global functions
_hash and _revhash into Hashtable methods hash_dna and unhash_dna.
* khmer/_khmer.cc, lib/{hashtable.cc,read_aligner.cc,subset.cc}: update
Hashtable code to use new hash_dna and unhash_dna methods.
2016-10-31 Camille Scott <camille.scott.w@gmail.com>
* khmer/__init__.py, khmer/_khmer.cc, tests/test_functions.py: Expose
reverse_complement to Python.
* lib/{traversal.cc, traversal.hh}: Add two new Traverser classes,
AssemblerTraverser and NonloopingAT, to do the traversal portions of
assembly.
* lib/{assembler.cc, assembler.hh}, khmer/_khmer.cc: New code files
containing the LinearAssembler and LabeledLinearAssembler classes which wrap
AssemblerTraverser and NonloopingAT, respectively, and expose a contig
assembly interface.
* lib/{hashtable.cc, hashtable.hh, labelhash.cc, labelhash.hh}: Move
assembler API to the new assembler.hh.
* lib/{kmer_filters.hh, kmer_filters.cc}: Helper filter-functions for the
AssemblerTraversers.
* lib/kmer_hash.hh: Helper functions for the Kmer class.
* lib/{alphabets.hh, alphabets.cc}: Global DNA alphabets.
* tests/test_assembly.py: Tests for the assembler API.
2016-10-28 Daniel Standage <daniel.standage@gmail.com>
* lib/hashtable.cc,tests/test_nodegraph.py: fix bug in assemble_linear_path
that returns seed k-mer even if it is not present in the DBG.
2016-10-13 Camille Scott <camille.scott.w@gmail.com>
* Wrap IO functions in with an extra catch to handle the gcc
basic_ios_failure bug.
2016-10-03 Tim Head <betatim@gmail.com>
* .travis.yml: adjust setup for exclusive use of travis (jenkins is retiring)
2016-10-02 Titus Brown <titus@idyll.org>
* khmer/{utils.py,thread_utils.py,trimming.py}: introduce new function,
clean_input_reads, that does consistent read cleaning; update ReadBundle
and trimming to make use of new cleaned_seq attribute.
* scripts/{normalize-by-median.py,trim-low-abund.py}: refactor to use
cleaned_seq attribute properly; this fixed a bug in normalize-by-median.py
that led to ignoring lowercase 'actgn'.
* doc/dev/development.rst: update developer documentation for new
cleaned_seq attribute and ReadBundle behavior.
* tests/test_script_output.py: update md5 signatures for output to reflect
corrected behavior.
* tests/test_functions.py: add test for broken_paired_iter uppercase
behavior.
* tests/test_read_handling.py: update tests for ReadBundle.
2016-10-01 Titus Brown <titus@idyll.org>
* khmer/trimming.py,scripts/{filter-abund-single.py,filter-abund.py,
trim-low-abund.py}: extracted similar trimming code and refactored.
* khmer/utils.py,tests/test_read_handling.py: change ReadBundle.trimmed_reads
to trimmed_seqs; fix associated tests.
* tests/test_functions.py: updated tests to use screed.Record instead of
namedtuple classes.
2016-10-01 Titus Brown <titus@idyll.org>
* lib/hashtable.{cc,hh}: added assemble_linear_path function & helpers.
* khmer/_khmer.cc: CPython API for assemble_linear_path.
* tests/test_nodegraph.py: tests for new assemble_linear_path behavior.
* khmer/khmer_args.py, tests/test_script_arguments.py: fix some lingering
PEP 8 errors.
* lib/kmer_hash.hh: added string -> string _revcomp function.
2016-09-30 Daniel Standage <daniel.standage@gmail.com>
* scripts/trim-low-abund.py, khmer/utils.py, doc/dev/development.rst: moved
ReadBundle class to utils
* tests/test_read_handling.py, tests/test-data/unclean-reads.fastq: tests
related to ReadBundle
2016-09-29 Tim Head <betatim@gmail.com>
* khmer/khmer_args.py, tests/test_functions.py,
tests/test_script_arguments.py: fix up formatting
2016-09-26 Ali Aliyari <aaliyari@ucdavis.edu>
* khmer/khmer_args.py: prevent -N from being set to more than 20 (override by -f)
* tests/test_script_arguments.py added test functions for the above change
2016-09-26 Luiz Irber <khmer@luizirber.org>
* khmer/khmer_args.py: Update HLL citation to point to preprint.
2016-09-23 Tim Head <betatim@gmail.com>
* khmer/_khmer.cc, lib/counting.{cc,hh}, lib/hashbits.{cc,hh},
lib/hashtable.hh, lib/hllcounter.{cc,hh}, lib/kmer_hash.cc,
tests/khmer_tst_utils.py, tests/test_functions.py: move away from using
HashIntoType as synonym to uint64.
2016-09-21 Tim Head <betatim@gmail.com>
* .travis.yml: add python 3.5 to the build matrix and allow fast finishing
2016-09-20 Titus Brown <titus@idyll.org>
* khmer/utils.py: fixed bug in broken_paired_reader when short reads
are discarded and require_paired is set; improved read pair error reporting.
* tests/test_functions.py: added tests for broken_paired_reader fix.
* tests/khmer_tst_utils.py: de-nested exceptions for better error reporting
from tests.
2016-09-09 Daniel Standage <daniel.standage@gmail.com>
* lib/read_parsers.{cc,hh}: rename SeqAnParser to FastxParser.
2016-09-09 Tim Head <betatim@gmail.com>
* tests/test_filter_abund.py: remove for loops introduce to the test suite.
2016-09-01 Tim Head <betatim@gmail.com>
* khmer/khmer_args.py: added check_argument_range to check an integer
command-line argument is within a given range.
* scripts/{normalize-by-median.py, filter-abund.py, filter-abund-single.py}
now use check_argument_range for the cutoff parameter.
* tests/test_normalize_by_median.py: modified
test_normalize_by_median_no_bigcount.
2016-09-01 Tim Head <betatim@gmail.com>
* scripts/filter-abund-single.py: Add support for variable coverage trimming
2016-08-31 Tim Head <betatim@gmail.com>
* Fixed several source code style issues in python and cpp.
* Makefile: removed setup.py from the list of files passed to astyle
2016-08-30 Tim Head <betatim@gmail.com>
* Fix coverage reporting on OSX and rename nosetests.xml to pytests.xml
2016-08-29 Daniel Standage <daniel.standage@gmail.com>
* doc/dev/getting-started.rst: updated dev environment setup instructions to
include installation of 'enchant' library, and dropped Arch linux install
instructions.
2016-08-26 Daniel Standage <daniel.standage@gmail.com>
* tests/test_scripts.py: fix PEP8 errors missed with previous PR (due to CI
issues)
* Makefile: make the pep8 target less verbose by removing the --show-pep8
option
2016-08-26 Ryan Shean <rcs333@uw.edu>
* tests/{test_countergraph.py, test_filter_abund.py,
test_normalize_by_median.py, test_read_handling.py,
test_sandbox_scripts.py, test_scripts.py}: updated to use
copy_test_data function
2016-07-18 Titus Brown <titus@idyll.org>
* khmer/_khmer.cc: fixed ReadPairIterator exception return error messages.
2016-07-03 Titus Brown <titus@idyll.org>
* lib/{hashtable.cc, hashtable.hh}: added get_kmer_hashes_as_hashset to
graphs.
* khmer/_khmer.cc: updated CPython API to add get_kmer_hashes_as_hashset.
* tests/test_countgraph.py: added test for get_kmer_hashes_as_hashset.
2016-06-27 Titus Brown <titus@idyll.org>
* doc/requirements.txt: updated sphinx-autoprogram requirement for building
documentation, to point at released version.
2016-06-26 Titus Brown <titus@idyll.org>
* khmer/_khmer.cc, tests/test_nodegraph.py: 'add' is now a synonym for
graph.count(kmer).
* khmer/thread_utils.py: update verbose_loader function to take 'verbose'
argument.
* scripts/{abundance-dist-single.py, abundance-dist.py,
filter-abund-single.py, filter-abund.py, load-into-counting.py,
normalize-by-median.py,trim-low-abund.py}: updated to
respect -q/--quiet.
* tests/test_filter_abund.py: tests for '-q'.
* scripts/partition-graph.py: fix typo in args help message.
2016-06-26 Titus Brown <titus@idyll.org>
* khmer/_khmer.cc, lib/{hashtable.cc, hashtable.hh},
tests/test-data/simple-genome.fa, tests/test_nodegraph.py: added functions
'find_high_degree_nodes' and 'traverse_linear_path' to hashtables/graphs.
* lib/kmer_hash.cc: minor change to use object member _seq instead of
constructor argument seq in KmerIterator.
* lib/kmer_hash.hh: added const to Kmer::get_string_rep(...) signature.
* sandbox/extract-compact-dbg.py: new sandbox script to
extract compact De Bruijn graphs (with linear paths contracted).
* tests/test_sandbox_scripts.py: added tests for the extract-compact-dbg.py
script.
2016-06-26 Titus Brown <titus@idyll.org>
* lib/khmer.hh,lib/{labelhash.cc,labelhash.hh}: removed label pointer-based
indirection from labelhash code.
* khmer/_khmer.cc: updated CPython API to match new behavior.
* tests/test_labelhash.py: renamed to match new API; no changes in test
logic.
2016-06-17 Daniel Standage <daniel.standage@gmail.com>
* scripts/filter-abund-single.py: add -o/--outfile option.
* tests/test_script_output.py: move `_calc_md5` function for calculating
file MD5 hashes to test utils module (tests/khmer_tst_utils.py).
* tests/{test_filter_abund.py,test_scripts.py): move filter_abund tests to
dedicated test script, add minimal test for new -o option.
* tests/test-data/paired-mixed-witherror.fa.pe: add data file in support of
new test.
* .gitignore: add .cache/ directory, which appears to be an artifact of the
py.test framework.
2016-06-17 Daniel Standage <daniel.standage@gmail.com>
* scripts/filter-abund-single.py: add -o/--outfile option.
* tests/test_script_output.py: move `_calc_md5` function for calculating file
MD5 hashes to test utils module (tests/khmer_tst_utils.py).
* tests/{test_filter_abund.py,test_scripts.py): move filter_abund tests to
dedicated test script, add minimal test for new -o option.
* tests/test-data/paired-mixed-witherror.fa.pe: add data file in support of
new test.
* .gitignore: add .cache/ directory, which appears to be an artifact of the
py.test framework.
2016-05-25 Titus Brown <titus@idyll.org>
* scripts/trim-low-abund.py: switched to watermark-based reporting to
isolate a hard-to-trigger undefined variable error in reporting.
* tests/test_scripts.py: added a test for basic reporting functionality.
2016-05-16 Titus Brown <titus@idyll.org>
* khmer/_khmer.cc: define new khmer_HashSet_Type and khmer_HashSet_Object;
lots of associated cleanup of k-mer <-> C++ interface; added
Hashtable::neighbors; added Hashtable::hash and Hashtable::reverse_hash;
CPython 'hashtable.count(...)' function now takes either hash or string.
* lib/{kmer_hash.cc, kmer_hash.hh}: added some function overloads so that
_hash(...) could take strings as arguments without conversion; added
Kmer::set_from_unique_hash convenience function.
* lib/{hashtable.cc, hashtable.hh}: minor cleanup;
* lib/{read_aligner.cc, subset.cc}: minor refactoring.
* lib/{traversal.cc, traversal.hh}: made 'filter' argument to traverse*
functions optional; added 'traverse' function for combine traversal.
* tests/test_hashset.py: tests for new HashSet class.
* tests/test_countgraph.py: tests for new hash/reverse_hash functions,
and 'count' behavior.
* tests/test_nodegraph.py: tests for new neighbors function.
* khmer/__init__.py: import new HashSet type from _khmer.
* scripts/{do-partition.py, make-initial-stoptags.py,
partition-graph.py},tests/{test_labelhash.py, test_subset_graph.py}:
refactor existing code to use HashSet object.
* tests/test_counting_single.py: add printout to assert.
2016-05-16 Luiz Irber <khmer@luizirber.org>
* Makefile,jenkins-build.sh,setup.cfg,tests/khmer_tst_utils.py,
tests/test_{countgraph,counting_single,hll,labelhash,nodegraph,
normalize_by_median,read_aligner,read_handling,read_parsers,sandbox_scripts,
scripts,version}.py: replace nose with pytest, update configuration.
2016-05-16 Luiz Irber <khmer@luizirber.org>
* lib/hashtable.cc: fix bug with substr
* tests/test_countgraph.py: add test to trigger the substr bug.
2016-05-11 Titus Brown <titus@idyll.org>
* scripts/trim-low-abund.py: refactor to use generators; add --diginorm
option to include digital normalization in trim-low-abund functionality.
* tests/test_script_output.py: added md5sum hashing tests to pin down
functionality in trim-low-abund.py and normalize-by-median.py; verified
that refactoring does not alter existing functionality.
* tests/test-data/simple-genome-reads.fa: supporting file for md5sum
tests.
* tests/test-data/README.rst: a new README for describing test files,
how to generate them, and their uses.
* tests/test_scripts.py: added additional tests for trim-low-abund.py
functionality and error cases.
2016-05-11 Titus Brown <titus@idyll.org>
* tests/test_read_parsers.py: fixed syntax error introduced by previous
merge.
2016-05-08 Michael R. Crusoe <crusoe@ucdavis.edu>
* scripts/{do-partition,partition-graph}.py,oxli/partition.py: pulled up
duplicate `worker` partition function into a reusable place.
2016-05-08 Michael R. Crusoe <michael.crusoe@gmail.com>
* .dictionary, pylintrc: added `pylint` configuration that checks spelling
in Python files. Added dictionary of project specific words.
* khmer/__init__.py, scripts/readstats.py, setup.py: Fixed typos.
* Makefile: line-wrapped; bumped up `pep8` version; beefed up `cppcheck`
target to correctly list the defines and includes for the current platform
which eliminates false positives; `*.pyc` files are now cleaned from the
`sandbox` as well as the `dist` directory. Added `cppcheck-long` target to
also examine the seqan headers. Fed the dynamically constucted list of
includes to Doxygen. Added simultaneous OS X, Debian, and Ubuntu
compatibility to many targets. Added helper target to print the value of
any variable via `make print-VARNAME`. Fixed the `make coverage-report`
target. pep257 is now called pydocstyle
* third-party/seqan/core/include/seqan/basic/debug_test_system.h,
third-party/seqan/ChangeLog: silenced bogus import
* doc/dev/coding-guidelines-and-review.rst,.github/PULL_REQUEST_TEMPLATE.md:
reformulated checklist to list action followed by a motivating question.
* doc/dev/release.rst: added author management to release checklist
* lib/counting.{cc,hh},sandbox/find-high-abund-kmers.py,
sandbox/README.rsr: removed the unused function
CountingHash::collect_high_abundance_kmers and the nonfunctional sandbox
script that called it.
* lib/kmer_hash.hh: make KmerFactory's default contrustor explicit to avoid
auto-casting optimizations.
* */*.py: a multitude of pylint inspired cleanups and bug fixes. Some
checks silenced in place.
2016-05-08 Michael R. Crusoe <michael.crusoe@gmail.com>
* README.rst: add depsy badge
2016-05-08 Michael R. Crusoe <michael.crusoe@gmail.com>
* setup.py,sandbox/{readaligner_pairhmm_train.py,
Makefile.read_aligner_training}: switch to BAM parsing using simplesam
2016-05-06 Titus Brown <titus@idyll.org>
* khmer/_khmer.cc, lib/{counting.cc,counting.hh,hashbits.cc,hashbits.hh,
hashtable.cc,hashtable.hh,subset.cc,subset.hh},
sandbox/{fasta-to-abundance-hist.py,find-high-abund-kmers.py
hi-lo-abundance-by-position.py,stoptag-abundance-hist.py,
abundance-hist-by-position.py},
tests/{test_countgraph.py,test_counting_single.py,test_filter.py,
test_nodegraph.py,test_subset_graph.py}: removed unused functions,
sandbox scripts, and tests for many functions. Specifically,
consume_fasta_and_tag_with_stoptags, identify_stop_tags_by_position and
identify_stoptags_by_position,
count_and_transfer_to_stoptags, traverse_from_tags,
filter_if_present, consume_fasta_and_traverse,
collect_high_abundance_kmers, fasta_dump_kmers_by_abundance,
fasta_count_kmers_by_position, output_fasta_kmer_pos_freq,
compare_partitions/compare_to_partition, join_partitions_by_path,
is_single_partition, and find_unpart function.
* sandbox/README.rst: updated for removed sandbox scripts.
2016-04-29 Luiz Irber <khmer@luizirber.org>
* jenkins-build.sh: add codecov coverage upload tool.
2016-02-17 Daniel Standage <daniel.standage@gmail.com>
* ./github/CONTRIBUTING.md,.github/PULL_REQUEST_TEMPLATE.md: auto-populate
pull requests with checklist using GitHub's new template feature
* doc/dev/coding-guidelines-and-review.rst: update developer docs with
compensatory changes
2016-02-15 Kevin Murray <spam@kdmurray.id.au>
* scripts/load-into-counting.py: Insert khmer's version into .info files
2015-11-30 Luiz Irber <khmer@luizirber.org>
* lib/Makefile: add missing hllcounter.hh header to KHMER_HEADERS.
2015-11-14 Luiz Irber <khmer@luizirber.org>
* lib/subset.cc: check iterator before decrementing in
repartition_largest_partition
2015-10-25 Titus Brown <titus@idyll.org>
* scripts/normalize-by-median.py,tests/test_normalize_by_median.py: test
and fix for close of --output file after first input file.
2015-10-19 Michael R. Crusoe <crusoe@ucdavis.edu>
* versioneer.py,khmer/_version.py,setup.py,setup.cfg: upgrade Versioneer to
version 0.15+dev, Mon Jun 29 2015 99d5d9341830945f7080537ddd3bbd79c4aa1732
* doc/conf.py, lib/Makefile: update method of retrieving current version
* lib/get_version.py: no longer needed, removed
2015-10-05 Michael R. Crusoe <crusoe@ucdavis.edu>
* lib/magic: add file extensions, one media type, and a better comment
* khmer/__init__.py: Replace an errant 'Presence table' with 'node graph'
2015-09-28 Lisa Cohen <ljcohen@ucdavis.edu>
* tests/test_read_handling.py: created new file with interleave-reads,
split-paired-reads, and extract-paired-reads functions
* tests/test_scripts.py: removed functions mentioned above
2015-09-19 Titus Brown <titus@idyll.org>
* scripts/filter-abund.py: fixed bug with -o and --gzip used together.
* tests/test_scripts.py: added test for fixed bug.
* sandbox/count-kmers.py: added executable bit.
2015-09-17 Camille Scott <camille.scott.w@gmail.com>
* scripts/interleave-reads.py: Added --no-reformat flag
to disable format checking and renaming of headers
* tests/{test_scripts.py, test-data/paired.malformat*}: Tests
and test data for --no-reformat flag.
2015-09-11 Russell Y. Neches <ryneches@ucdavis.edu>
* lib/hashbits.hh: added get_raw_tables to Hashbits
* khmer/_khmer.cc: added get_raw_tables to Hashbits
* tests/test_nodegraph.py: added test for Nodegraph.get_raw_tables
2015-09-11 Camille Scott <camille.scott.w@gmail.com>
* lib/hashbits.cc: Make hasbits::update_from() correctly update
_occupied_bins.
* lib/test_nodegraph.py: Test Nodegraph.n_occupied() after update.
2015-09-07 Michael R. Crusoe <crusoe@ucdavis.edu>
* doc/roadmap.rst: Updated for 2.0 release.
* README.rst: drop unstable badges; fix links
* doc/index.rst: point at getting help guide
2015-09-05 Michael R. Crusoe <crusoe@ucdavis.edu>
* tests/test_scripts.py: make the script version test more specific; double
check that script in question is from the 'khmer' project based upon the
second line of the file.
2015-09-04 Michael R. Crusoe <crusoe@ucdavis.edu>
* tests/khmer_tst_utils.py: look in "EGG-INFO" for scripts before checking
the PATH
2015-09-04 Michael R. Crusoe <crusoe@ucdavis.edu>
* doc/release-notes/release-2.0.md: release notes for 2.0
* doc/user/install.txt: correct second invocation of nosetests to match the
first.
* setup.py: update the authors list for PyPI.
* doc/user/known-issues.rst: remove three fixed issues; add a new one
* doc/whats-new-2.0.rst: update to match the release notes
* doc/release-notes/*.rst: refresh using `make convert-release-notes'
2015-09-02 Michael R. Crusoe <crusoe@ucdavis.edu>
* *: complete audit of license headers
* LICENSE: listings of some of the third-party licenses
* bink.ipynb,lib/graphtest.cc,lib/primes.hh: deleted unused files
* sandbox/assemstats.py: updated screed install instructions
2015-09-02 Michael R. Crusoe <crusoe@ucdavis.edu>
* *: finish undoing the `load-graph.py` rename
2015-09-02 Micheal R. Crusoe <crusoe@ucdavis.edu>
* doc/requirements.txt: Update URL to sphinxcontrib-autoprogram tarball
2015-08-31 Michael R. Crusoe <crusoe@ucdavis.edu>
* khmer/thread_utils.py: Use the robust test for paired reads from
khmer.utils; drop `is_pair()`
* tests/test_threaded_sequence_processor.py: Update to use Screed Record
objects.
2015-08-28 Michael R. Crusoe <crusoe@ucdavis.edu>
* doc/whats-new-2.0.rst: Many updates from `diff`ing the `--help` output of
version 1.4.1 vs now.
* Makefile: build the project if needed when making a PDF
* doc/index.rst: fixed inter-doc links to be relative
* doc/user/blog-posts.rst: replaced link to 88m-reads.fa.gz with a working
URL
* doc/user/{choosing-table-sizes,guide}.rst: disambiguated :option:
references so that they link properly.
* scripts/README.txt: removed unhelpful file
* scripts/normalize-by-median.py: replace `--force-single` with
`--force_single`. Added help text for `--cutoff`.
2015-08-27 Titus Brown <titus@idyll.org>
* doc/dev/getting-started.rst: fixed a few misspellings.
2015-08-26 Michael R. Crusoe <crusoe@ucdavis.edu>
* tests/test_scripts.py: removed the unused `_DEBUG_make_graph` function in
favor of other debugging methods like `ipdb`. Added
test_do_partition_no_big_traverse and test_extract_paired_reads_unpaired.
2015-08-24 Michael R. Crusoe <crusoe@ucdavis.edu>
* khmer/khmer_args.py: Replaced sanitize_epilog() with santize_help() that
reflows the text of ArgParse descriptions and epilog while preserving the
formatting. Enhanced removal of Sphinx directives by replacing double
backticks with the double quote character.
* scripts/*.py: Renamed sanitize_epilog to sanitize_help; leading newlines
from triple-quoted epilogs removed; formatting made consistent;
sanitize_help and ComboFormatter added where it was missing; a couple
script specific epilog reformatting (for use of `:doc:` and a
hyperlink).
* scripts/{count-median,filter-abund-single}.py: Fixed printing of output
file name to do so instead of printing information about the file handle.
* scripts/count-median.py: Added missing command so that example given
actually works.
* scripts/filter-abund-single.py: Removed redundant printing of output file
names.
* scripts/normalize-by-median.py: Removed unused option "-d" from an example
command (left over from the "--dump-frequency" era).
* scripts/{partition-graph.py,do-partition.py}: Fixed erasure of the queue
module name in the worker functions, which is necessary for basic
functionality.
* scripts/{do-partition,abundance-dist,abundance-dist-single,
extract-long-sequences}.py: Added an example command to the epilog.
* tests/khmer_tst_utils.py: Added 'name' attribute to make the fake
sys.stdout more like a read stdout object.
* oxli/__init__.py: removed redundant and unused help text
* scripts/{abundance-dist,annotate-partitions,count-median,
extract-long-sequences,extract-paired-reads,extract-partitions,
fastq-to-fasta,filter-abund,filter-stopgaps,interleave-reads,
load-into-graph,merge-partitions,normalize-by-median,partition-graph,
readstats,sample-reads-randomly,split-paired-reads}.py: made "--version"
and the citation header consistent across the scripts.
* tests/test_scripts.py: added tests for the "--version" and citation
header behavior.
* tests/test_normalize_by_median.py: updated test for 'quiet' mode as
citation header still prints to STDERR.
* setup.py,tests/test_scripts.py: turned off the "oxli" script for v2.0.
2015-08-17 Michael R. Crusoe <crusoe@ucdavis.edu>
* Makefile: remove BASH shell designation that appears to be incompatible
with OS X Mavericks & virtualenv; refactored out BASH-isms for those whose
default shell isn't BASH (Debian, and others).
* lib/test-read-aligner.cc,read_aligner_test.sh: removed unused test files
found during search for other shell scripts with BASHisms.
2015-08-18 Michael R. Crusoe <crusoe@ucdavis.edu>
* *: reverted load-into-counting.py -> load-into-countgraph.py and
load-graph.py -> load-into nodegraph.py rename.
* CITATION: unescaped URL
* doc/user/guide.rst: added `:program:` and `:option:` directives as
needed; replaced references to `strip-and-split-for-assembly` with
`extract-paired-reads`. Updated instructions to use `--unpaired-reads` with
`normalize-by-median.py` instead of second round of diginorm.
2015-08-18 Titus Brown <titus@idyll.org>
* doc/index.rst: update introductory text.
* doc/user/biblio.rst: update bibliography link descriptions and text.
* doc/_static/labibi.css: reference new location of base CSS
2015-08-14 Luiz Irber <khmer@luizirber.org>
* scripts/unique-kmers.py: Rename option --stream-out to --stream-records.
* tests/test_streaming_io.py: Fix unique-kmers tests, use new option.
* khmer/_khmer.cc, lib/hllcounter.cc: Rename some variables for consistency.
2015-08-13 Jacob Fenton <bocajnotnef@gmail.com>
* scripts/extract-partitions.py: refactored much of the processing into
generators
* tests/test_scripts.py: added test
2015-08-12 Jacob Fenton <bocajnotnef@gmail.com>
* doc/dev/{codebase-guide,coding-guidelines-and-review,development,
for-khmer-developers,getting-started,release,scripts-and-sandbox,
binary-file-formats}.rst,doc/{index,introduction,whats-new-2.0,
contributors}.rst,doc/user/{blog-posts,choosing-table-sizes,galaxy,
getting-help,guide,install,known-issues,partitioning-big-data,
scripts}.rst,CITATION: Cleaned up documentation
* scripts/*.py, khmer/khmer_args.py: added epilog sanitation
* scripts/{load-into-counting,load-graph,load-into-countgraph,
load-into-nodegraph}.py, tests/{test_scripts,test_normalize_by_median,
test_streaming_io,test_countgraph}: renamed load-into-counting ->
load-into-countgraph, load-graph -> load-into-nodegraph, fixed tests to not
bork
2015-08-12 Luiz Irber <khmer@luizirber.org>
* khmer/_khmer.cc: Fix a GCC string initialization warning.
2015-08-12 Michael R. Crusoe <crusoe@ucdavis.edu>
* CITATION, doc/{index,introduction,user/scripts}.rst, khmer/khmer_args.py:
formatting fixes and new citation for the software as a whole
* Makefile: PDF building hints, tweaked dependencies, update coverity URL,
new target to generate author list for the paper citation
* sort-authors-list.py: helper script for the above
* doc/conf.py: don't generate a module index
* doc/contributors.rst: formatting, remove references to old lab
* doc/dev/coding-guidelines-and-review.rst: add C++ version standard
* doc/dev/getting-started.rst: ccache, git-merge-changelog, and advanced
commit squashing
* doc/user/biblio.rst: added links to khmer citation collections
* doc/user/examples.rst: linked to online version of example scripts
* doc/user/guide.rst: commented out empty section, added BSD note
* lib/counting.{cc},lib/*.hh: c++11 fixes: remove unneeded trailing
semicolons
* scripts/*.py: line-wrap & scrub output
* setup.py: turn optimizations back on and -pedantic
* .mailmap: additional tweaks to author list
2015-08-11 Kevin Murray <spam@kdmurray.id.au>
* lib/Makefile: Fix SONAME and ABI versioning to sync with Debian standard
practice.
2015-08-10 Camille Scott <camille.scott.w@gmail.com>
* lib/traversal.{cc,hh}: Add new files with unified traversal machinery.
Introduce Traverser class to handle finding neighbors and appropriate
bitmasking.
* khmer/_khmer.cc,lib/{counting,hashbits,hashtable,labelhash,subset}.{cc,hh}:
Updated relevant instances of HashIntoType and KMerIterator to use new Kmer
and KmerIterator, respectively.
* lib/Makefile: Add -std=c++11 flag.
* Makefile: Update -std=c++11 flag in libtest target.
* lib/hashtable.{cc,hh}: Update calc_connected_graph_size to use Traverser.
Change kmer_degree to use functions from traversal.cc. Remove redundant
count_kmers_with_radius in favor of calc_connected_graph_size. Update
traverse_from_kmer to use Traverser. Hashtable subclasses KmerFactory.
* lib/{hashtable.hh,kmer_hash.{cc,hh}}: Move KmerIterator from hashtable.hh
to kmer_hash.{cc,hh}. Add Kmer class to store forward, reverse, and
uniqified integer representations of k-mers, and to handle string
conversion. Update KmerIterator to emit objects of type Kmer and to subclass
KmerFactory; add doxygen markup.
* lib/khmer.hh: Forward declare Kmer and typedef new Kmer data structures.
* lib/subset.{cc,hh}: Move constructor definition to .cc file. Remove
queue_neighbors in favor of new traversal machinery. Update find_all_tags,
sweep_for_tags, and find_all_tags_truncate_on_abundance to use Traverser.
* setup.py: Add traversal.{cc,hh} to deps.
2015-08-10 Luiz Irber <khmer@luizirber.org>
* scripts/unique-kmers.py: use consume_fasta again.
* khmer/_khmer.cc: expose output_records option on HLLCounter consume_fasta.
* lib/hllcounter.{cc,hh}: implement output_records option in consume_fasta.
* lib/read_parsers.{cc,hh}: add Read method write_to, useful for outputting
the read to an output stream.
* doc/whats-new-2.0.rst: Add unique-kmers description.
2015-08-09 Jacob Fenton <bocajnotnef@gmail.com>
* khmer/khmer_args.py: pep8
* scripts/{interleave-reads,load-graph}.py: Removed unreachable code
* tests/test-data/{paired-broken.fq.badleft,paired-broken.fq.badright,
paired-broken.fq.paired.bad}: added test data files
* tests/{test_normalize_by_median,test_scripts}.py: added tests
2015-08-07 Titus Brown <titus@idyll.org>
* khmer/_khmer.cc,lib/hashbits.{cc,hh}: removed overlap functionality;
eliminated n_entries() as redundant with hashsizes(); removed arguments to
n_occupied(); removed get_kadian_count.
* lib/{hashbits.cc,counting.cc,khmer.hh},tests/test_hashbits.py: updated
save/load of countgraph/nodegraph structures to save _n_occupied.
* lib/{hashtable.hh,counting.hh,hashbits.hh}: promoted n_occupied() to
Hashtable class; fixed CountingHash unique_kmers calculation.
* lib/counting.{cc,hh}: removed get_kadian_count() and moved
n_unique_kmers(); updated countgraph writing to save n_occupied.
* khmer/__init__.py: modified extract_nodegraph_info and
extract_countgraph_info to read in & return n_occupied;
* sandbox/bloom-count-intersection.py,scripts/count-overlap.py,
tests/test-data/overlap.out: removed overlap scripts and test files.
* doc/user/scripts.rst: removed count-overlap.py documentation.
* tests/test_scripts.py: removed count-overlap.py tests.
* sandbox/README.rst: updated with removal of bloom-count-intersection.py.
* tests/test-data/normC20k20.ct: updated file contents to reflect new
format containing _n_occupied.
* tests/test_countgraph.py: removed get_kadian_count tests; added save/load
tests.
* tests/test_counting_single.py: remove n_entries() tests; replace
n_entries() calls with hashsizes() call.
* tests/test_functions.py: updated tests for new extract_*_info functions.
* tests/test_nodegraph.py: update htable etc. to nodegraph; added a
save/load test for n_occupied() on nodegraph.
* tests/{test_normalize_by_median,test_scripts}.py: fixed unique kmers
tests.
2015-08-07 Michael R. Crusoe <crusoe@ucdavis.edu>
* scripts/*.py,tests/*.py,sandbox/*.py,khmer/*.py,oxli/*.py:
many function and variable renames:
counting_hash, countinghash, hashtable->countgraph;
CountingHash->Countgraph
hashbits->nodegraph; Hashbits->Nodegraph;
check_space_for_hashtable->check_space_for_graph;
hash_args->graph_args
* khmer/_khmer.cc: remove unused 'new_hashtable' method; match renames
* TODO: removed several items
* doc/dev/scripts-and-sandbox.rst: fixed hashbang
2015-08-04 Jacob Fenton <bocajnotnef@gmail.com>
* khmer/khmer_args.py, oxli/functions.py: migrated estimation functions out
oxli and into khmer_args
* oxli/build_graph.py, tests/test_oxli_functions.py,
sandbox/{estimate_optimal_hash,optimal_args_hashbits}.py,
scripts/{normalize-by-median,unique-kmers}.py: changed to not break on
location change
* tests/{test_normalize_by_median,test_scripts}.py: added tests for
automatic arg setting
* tests/test_script_arguments: changed to play nice with unique_kmers as an
argument
2015-08-04 Titus Brown <titus@idyll.org> and Camille Scott
<camille.scott.w@gmail.com>
* khmer/utils.py: added UnpairedReadsError exception.
* scripts/{extract-paired-reads,split-paired-reads}.py: changed --output-dir
argument short form to use '-d'.
* scripts/{split-paired-reads.py} added -0 <filename> to allow orphans; made
'-p'/'--force-paired' default & removed from script.
* scripts/{normalize-by-median,filter-abund,trim-low-abund}.py: changed
long form of '-o' to be '--output'.
* tests/{test_scripts,test_streaming_io}.py: updated and added tests for
new behavior.
2015-08-03 Jacob Fenton <bocajnotnef@gmail.com>
* doc/dev/coding-guidelines-and-review.rst: added codespell as a possible
spelling tool
2015-08-03 Jacob Fenton <bocajnotnef@gmail.com>
* Makefile: added oxli to pep257 make target, made clean target wipe out all
.pyc files in scripts/* and tests/* and oxli/*
2015-08-03 Jacob Fenton <bocajnotnef@gmail.com>
* tests/test_counting_single.py: removed redundant test
2015-08-01 Jacob Fenton <bocajnotnef@gmail.com> and Titus Brown
<titus@idyll.org>
* scripts/normalize-by-median.py,khmer/khmer_logger.py: added logging
framework, prototyped in normalize-by-median; added -q/--quiet to
* tests/test_normalize_by_median.py: associated tests.
* khmer/khmer_args.py: Made info function use logging functions.
* tests/khmer_tst_utils.py: removed info reporting in runscript from 'out'
returned.
2015-08-01 Jacob Fenton <bocajnotnef@gmail.com>
* khmer/kfile.py: added infrastructure for doing compressed output
* khmer/thread_utils.py: switched threaded_sequence_processor to make use of
write_record
* scripts/{extract-long-sequences,extract-paired-reads,
extract-partitions,fastq-to-fasta,filter-abund-single,filter-abund,
interleave-reads,normalize-by-median,sample-reads-randomly,
split-paired-reads,trim-low-abund}.py: added output compression
* tests/{test_functions,test_scripts,test_normalize_by_median}.py: added
tests
* scripts/{load-graph,partition-graph,find-knots.py,
make-initial-stoptags}.py,oxli/build_graph.py: made load-graph no longer
add .pt to graph outfiles, changed partition-graph to not expect .pt's
* doc/whats-new-2.0.rst: doc'd changes to load-graph and partition-graph
* doc/dev/scripts-and-sandbox.rst: updated scripts/ requirements.
2015-08-01 Sherine Awad <drmahmoud@ucdavis.edu>
* sandbox/multi-rename.py: updated output of long FASTA sequences to
wrap text at 80 characters.
* tests/test_sandbox_scripts.py: Added a test for multi-rename.py.
2015-07-31 Kevin Murray <spam@kdmurray.id.au>
* lib/Makefile,Makefile,lib/*.pc.in,lib/test-compile.cc: Misc debian-based
compatibility changes
* lib/get_version.py: Add crunchbang, chmod +x
2015-07-29 Michael R. Crusoe <crusoe@ucdavis.edu>
* khmer/_khmer.cc: add more CPyChecker inspired fixes
* lib/*.{cc,hh}: clean up includes and forward declarations
2015-07-29 Luiz Irber <khmer@luizirber.org>
* Makefile: Adapt Makefile rules for py3 changes.
* jenkins-build.sh: Read PYTHON_EXECUTABLE and TEST_ATTR from environment.
2015-07-29 Amanda Charbonneau <charbo24@msu.edu>
* scripts/fastq-to-fasta.py: Changed '-n' default description to match
behaviour
2015-07-29 Luiz Irber <khmer@luizirber.org>
* tests/test_{scripts,streaming_io}.py: Fix the build + add a test
2015-07-28 Titus Brown <titus@idyll.org>
* tests/test_streaming_io.py: new shell cmd tests for streaming/piping.
* tests/khmer_tst_utils.py: refactor/replace runtestredirect(...) with
scriptpath(...) and run_shell_cmd(...).
* scripts/test_scripts.py: remove test_interleave_reads_broken_fq_4 for
only one input file for interleave-reads.py; replace runscriptredirect call
with run_shell_cmd.
* scripts/interleave-reads.py: force exactly two input files.
* scripts/split-paired-reads.py: fix print statement; clarify output.
* scripts/{normalize-by-median.py,sample-reads-randomly.py,
trim-low-abund.py}: if stdin is supplied for input, check that -o
specifies output file.
* scripts/filter-abund.py: if stdin is supplied for input, check that -o
specifies output file; switched -o to use argparse.FileType.
* scripts/extract-long-sequences.py: switched -o to use argparse.FileType.
* scripts/{abundance-dist,count-median}.py: added '-' handling for output.
* khmer/kfile.py: change 'check_input_files' to no longer warn that
'-' doesn't exist'.
* tests/test-data/paired.fq.2: removed extraneous newline from end.
* tests/{test_normalize_by_median,test_script_arguments,test_scripts}.py:
added tests for new code.
* scripts/oxli: added script for running tests in development directory.
* khmer/{__init__,khmer_args}.py,tests/{test_normalize_by_median,
test_script_arguments}.py: refactored out use of AssertionError by not
throwing plain Exceptions when a ValueError or RuntimeError would do.
* oxli/__init__.py: give default help instead of an error when `oxli` is
called with no arguments.
* tests/test_{normalize_by_median,sandbox_scripts,scripts,streaming_io}.py:
always check status code if calling `runscripts` with `fail_ok=True`.
2015-07-28 Luiz Irber <khmer@luizirber.org>
* sandbox/unique-kmers.py: moved to scripts.
* scripts/unique-kmers.py: fix import bug and initialize to_print earlier.
* tests/test_scripts.py: add tests for unique-kmers.py.
* doc/user/scripts.rst: added unique-kmers.py to script page
2015-07-28 Jacob Fenton <bocajnotnef@gmail.com>
* scripts/abundance-dist.py: disallowed forcing on the input file check for
the counting table file
2015-07-28 Michael R. Crusoe <crusoe@ucdavis.edu>
* .mailmap, Makefile: generate a list of authors
2015-07-28 Kevin Murray <spam@kdmurray.id.au>
Titus Brown <titus@idyll.org>
* khmer/utils.py: added fix for SRA-style FASTQ output.
* tests/test_scripts.py: tested against a broken version of SRA format.
* tests/test-data/paired-broken4.fq.{1,2}: added test files.
2015-07-28 Michael R. Crusoe <crusoe@ucdavis.edu>
Titus Brown <titus@idyll.org>
* lib/read_aligner.{cc,hh},tests/{test_read_aligner.py,
test-data/readaligner-{default,k12}.json},khmer/__init__.py: refactor,
read aligner parameters are now configurable & save/load-able. Can do
whole-genome variant finding.
* khmer/_khmer.cc,tests/test_read_aligner.py: ReadAligner.align_forward
method added
* sandbox/correct-errors.py -> sandbox/correct-reads.py: total rewrite
* sandbox/error-correct-pass2.py: new script
* sandbox/readaligner_pairhmm_train.py: new script
* tests/test_sandbox_scripts.py, doc/release-notes/release-1.4.rst:
spelling fixes, import re-arrangement
* sandbox/{Makefile.read_aligner_training,readaligner_pairhmm_train.py}:
Added script to train the aligner
2015-07-27 Titus Brown <titus@idyll.org>
* khmer/khmer_args.py,CITATION: added entry for PeerJ paper on
semi-streaming to citations.
* scripts/{abundance-dist-single.py,abundance-dist.py,count-median.py,
count-overlap.py,filter-abund-single.py,load-into-counting.py}: changed
default behavior to output data in CSV format and report total k-mers.
* tests/test_scripts.py: updated/removed tests for CSV.
* doc/whats-new-2.0.rst: added information about change in columnar output,
along with other minor corrections.
* scripts/normalize-by-median.py: corrected epilog.
* khmer/thread_utils.py,
sandbox/{calc-best-assembly.py,extract-single-partition.py},
scripts/{count-median.py,extract-long-sequences.py,extract-paired-reads.py,
extract-partitions.py,fastq-to-fasta.py,
interleave-reads.py,normalize-by-median.py,readstats.py,
sample-reads-randomly.py,split-paired-reads.py,trim-low-abund.py},
tests/{test_normalize_by_median.py,test_scripts.py}: remove explicit
'parse_description' from screed open calls.
* khmer/_khmer.cc,lib/Makefile,lib/hashtable.{cc,hh},setup.py: removed
WITH_INTERNAL_METRICS and trace_logger/perf_metrics references.
* lib/perf_metrics.{cc,hh},lib/trace_logger.{cc,hh}: removed unused files.