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https://github.com/genome/genome
23 March 2024, 19:04:16 UTC
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Revision Author Date Message Commit Date
e83e763 Travis Abbott 13 September 2012, 20:27:45 UTC allow setting default merge action in merge strategy 13 September 2012, 20:27:45 UTC
7b7ffd4 Travis Abbott 31 August 2012, 18:42:53 UTC add ability to sort ChromPos files like samtools, sniper, etc. 31 August 2012, 18:42:53 UTC
7b67639 Travis Abbott 20 August 2012, 21:52:46 UTC update usage of create-contigs to say vcf instead of bed 20 August 2012, 21:52:46 UTC
7b66998 Travis Abbott 18 August 2012, 23:26:50 UTC another test/bugfix for VariantContig Fixes issue where VariantContig would ask for base 0 in a 1-based fasta. 18 August 2012, 23:26:50 UTC
e54efe3 Travis Abbott 18 August 2012, 21:27:53 UTC re-enable create-contigs integration test 18 August 2012, 21:27:53 UTC
c896eb0 Travis Abbott 18 August 2012, 21:20:03 UTC add tests and fix bugs for create-contigs variants ending on the last base of a sequence caused an exception 18 August 2012, 21:20:03 UTC
27401d5 Travis Abbott 18 August 2012, 20:24:28 UTC more VariantContig test cases 18 August 2012, 20:24:28 UTC
d81ddd6 Travis Abbott 18 August 2012, 20:24:01 UTC convert some ASSERT_EQ(true, ...) to ASSERT_TRUE 18 August 2012, 20:24:01 UTC
478dcf4 Travis Abbott 18 August 2012, 00:52:02 UTC Merge branch 'master' of github.com:genome/joinx 18 August 2012, 00:52:02 UTC
338c38b Ian Ferguson 17 August 2012, 23:00:15 UTC temporarily disabling integration-test CreateContigs 17 August 2012, 23:00:15 UTC
0979558 Ian Ferguson 17 August 2012, 22:52:17 UTC Added VariantContig / CreateContigsCommand 17 August 2012, 22:52:17 UTC
a028c7c Travis Abbott 17 August 2012, 18:01:20 UTC formatting 17 August 2012, 18:01:20 UTC
c95f452 Travis Abbott 10 August 2012, 22:04:26 UTC indel bugfixes and features: vcf-normalize-indels no longer crashes on mixed insertions/deletions vcf-annotate (and more generally, Vcf::Compare::AltIntersect) can now properly intersect equivalent Vcf alts even if they are represented differently. 10 August 2012, 22:04:26 UTC
7ac938b Travis Abbott 23 July 2012, 19:22:13 UTC fix memory leak in SortBuffer 23 July 2012, 19:22:13 UTC
089d452 Travis Abbott 17 July 2012, 22:27:07 UTC bugfix for RT #84118 - vcf-merge bug when merging more than two vcf entries, the old code required that each entry be capable of merging with the one that immediately precedes it, which isn't always the right thing, e.g.: 11111 22 33 These can be merged together even though 3 doesn't want to merge with 2. 17 July 2012, 22:27:07 UTC
428ffa6 Travis Abbott 03 July 2012, 02:37:54 UTC bugfix for RefStatsCommand incorrectly computing CpG region stats 03 July 2012, 02:37:54 UTC
e9ef1ab Travis Abbott 20 June 2012, 22:18:12 UTC Change EntryMetrics to initialize in constructor instead of using a ...::processEntry initializer. There was no benefit to trying to re-initialize the same instance with a different entry (in fact it wasn't even safe to do so), so using a constructor for initialization is preferred. 20 June 2012, 22:18:12 UTC
6902e55 Dave Larson 14 June 2012, 20:32:09 UTC no more segfaultin' when all genotypes are filtered out and there's no per-site filter populated 14 June 2012, 20:32:09 UTC
9ae4ad9 Travis Abbott 07 June 2012, 16:21:41 UTC documentation formatting 07 June 2012, 16:21:41 UTC
f4a462c Travis Abbott 06 June 2012, 22:48:54 UTC fix GenotypeCall ordering and add tests for metrics operators < and = were not well defined in GenotypeCall, but they are now. 06 June 2012, 22:48:54 UTC
9ab1d93 Travis Abbott 31 May 2012, 00:13:35 UTC added comments 31 May 2012, 00:13:35 UTC
eb6d1ec Travis Abbott 30 May 2012, 23:17:04 UTC MakeContigs test program 30 May 2012, 23:17:04 UTC
269c3a9 Travis Abbott 29 May 2012, 22:30:16 UTC fix ordering in vcf-merge (again) when determining sample source priority and the mode is set to filtered or unfiltered, we should only fall back to comparing source order when the filter statuses of the entries in question are equal. 29 May 2012, 22:30:16 UTC
af884c8 Travis Abbott 29 May 2012, 20:45:10 UTC fix ordering in vcf-merge files were being prioritized in the order they enter the merger rather than the source order on the command line, oops. 29 May 2012, 20:45:10 UTC
630cc78 Travis Abbott 26 May 2012, 00:13:48 UTC Merge branch 'master' of github.com:genome/joinx 26 May 2012, 00:13:48 UTC
cb301d1 Travis Abbott 25 May 2012, 20:15:40 UTC Make ConsensusFilter merge filters instead of overwrite 25 May 2012, 20:15:40 UTC
4fb6a67 Travis Abbott 25 May 2012, 20:15:27 UTC remove dead code 25 May 2012, 20:15:27 UTC
63562ab Travis Abbott 24 May 2012, 23:02:14 UTC add missing std::move for move constructor 24 May 2012, 23:02:14 UTC
81e8575 Travis Abbott 24 May 2012, 19:54:32 UTC doc updates for new vcf-merge options (-P, -R) 24 May 2012, 19:54:32 UTC
88cd91a Travis Abbott 24 May 2012, 19:41:42 UTC add --sample-priority option to vcf-merge 24 May 2012, 19:41:42 UTC
df5cebc Travis Abbott 23 May 2012, 20:24:39 UTC Merge branch 'master' of ssh://git/srv/git/joinx 23 May 2012, 20:24:39 UTC
aabec6b Travis Abbott 23 May 2012, 20:23:12 UTC rename GenotypeFormatter -> GenotypeMerger 23 May 2012, 20:23:12 UTC
1891e93 Travis Abbott 23 May 2012, 20:22:26 UTC remove duplicate code 23 May 2012, 20:22:26 UTC
46b4418 Travis Abbott 23 May 2012, 20:21:46 UTC add "isSampleFiltered" method 23 May 2012, 20:21:46 UTC
93724d9 Dave Larson 10 May 2012, 17:50:06 UTC off by one error was killing per-sample Known calculations 10 May 2012, 17:50:06 UTC
3687401 Travis Abbott 08 May 2012, 20:22:13 UTC fix CustomValue("") segfault customvalue objects initialized by "" were leading to a segfault. 08 May 2012, 20:22:13 UTC
67af36e Travis Abbott 07 May 2012, 22:15:05 UTC link boost statically 07 May 2012, 22:15:05 UTC
aa56719 Travis Abbott 07 May 2012, 18:39:50 UTC remove dependency on samtools 07 May 2012, 18:39:50 UTC
7d7717c Travis Abbott 07 May 2012, 17:39:06 UTC allow empty CustomValues, treat like "." 07 May 2012, 17:39:06 UTC
a06e119 Travis Abbott 04 May 2012, 21:46:19 UTC removed make_contigs test program 04 May 2012, 21:46:19 UTC
aab4743 Travis Abbott 04 May 2012, 21:44:35 UTC add consensus filtering to vcf-merge 04 May 2012, 21:44:35 UTC
71d8494 Travis Abbott 20 April 2012, 23:21:01 UTC missed one last initializer list 20 April 2012, 23:21:01 UTC
9024135 Travis Abbott 20 April 2012, 23:20:07 UTC removed more initializer lists 20 April 2012, 23:20:07 UTC
1520324 Travis Abbott 20 April 2012, 23:17:37 UTC get rid of C-style initializer list syntax in some places 20 April 2012, 23:17:37 UTC
ff5870a Travis Abbott 20 April 2012, 23:01:04 UTC build-common updates 20 April 2012, 23:01:04 UTC
eb27e1b Travis Abbott 14 April 2012, 00:29:10 UTC reduce manual memory management a bit 14 April 2012, 00:29:10 UTC
aec8d87 Travis Abbott 02 April 2012, 19:53:11 UTC fix RefStatsCommand help, and handling of -r param RefStats was always printing the reference, even when -r was not specified. Also, its help message was incorrect. 02 April 2012, 19:53:11 UTC
511295e Travis Abbott 30 March 2012, 15:42:53 UTC increase /etc/alternatives priority 30 March 2012, 15:42:53 UTC
eb5c8f7 Travis Abbott 30 March 2012, 15:40:15 UTC add wig2bed and refstats commands for Cyriac 30 March 2012, 15:40:32 UTC
567d47b Dave Larson 29 March 2012, 03:32:29 UTC Merge branch 'master' of ssh://git/srv/git/joinx 29 March 2012, 03:32:29 UTC
8627c4a Dave Larson 29 March 2012, 03:32:22 UTC writing R like C or Perl is bad. 1000X speedup on TsTv and Known callset metrics. 29 March 2012, 03:32:22 UTC
a27591f Travis Abbott 26 March 2012, 21:09:35 UTC allow trailing tabs in vcf entry sample data, for now. 26 March 2012, 21:09:35 UTC
7f33533 Dave Larson 23 March 2012, 15:52:12 UTC added some report generating helper functions 23 March 2012, 15:52:12 UTC
dcab319 Travis Abbott 22 March 2012, 17:10:39 UTC remove silly debugging statement 22 March 2012, 17:10:39 UTC
73672ec Travis Abbott 21 March 2012, 18:55:33 UTC install scripts to /usr/share/joinx<version> 21 March 2012, 18:55:33 UTC
5885c47 Dave Larson 20 March 2012, 02:24:32 UTC added callset summary function and known variant function 20 March 2012, 02:24:32 UTC
3439bba Dave Larson 20 March 2012, 02:23:50 UTC fix header and help documentation 20 March 2012, 02:23:50 UTC
53873f2 Dave Larson 16 March 2012, 18:51:03 UTC R file for graphing or summarizing various aspects of data produced by joinx vcf-report 16 March 2012, 18:51:03 UTC
b1d3514 Dave Larson 16 March 2012, 18:49:57 UTC ../src/exe/joinx/VcfReportCommand.cpp add in per-allele and per-sample novelty reporting based on defined flag(s) in the INFO field 16 March 2012, 18:49:57 UTC
d1270f5 Travis Abbott 23 February 2012, 19:21:59 UTC add vcf-normalize-indels command 23 February 2012, 19:21:59 UTC
57dd76e Travis Abbott 23 February 2012, 18:24:23 UTC Merge branch 'master' of ssh://git/srv/git/joinx 23 February 2012, 18:24:23 UTC
b0d349f Travis Abbott 23 February 2012, 18:23:34 UTC Vcf::Entry::start/stop just report the start/stop of the ref 23 February 2012, 18:23:34 UTC
83bda09 Travis Abbott 22 February 2012, 23:12:16 UTC added AltNormalizer (a start towards indel normalization) 22 February 2012, 23:12:16 UTC
edcfbc7 Dave Larson 22 February 2012, 16:32:11 UTC add in novelty reporting to per-site report 22 February 2012, 16:32:11 UTC
f373378 Dave Larson 22 February 2012, 16:31:52 UTC Fix segfault when determining novelty. 22 February 2012, 16:31:52 UTC
d3593bd Dave Larson 22 February 2012, 15:56:43 UTC Early attempt at determining novelty. Unlikely to be implemented correctly, but doesn't appear to crash. 22 February 2012, 15:56:43 UTC
3a21991 Travis Abbott 20 February 2012, 22:35:41 UTC Merge branch 'master' of ssh://git/srv/git/joinx 20 February 2012, 22:35:41 UTC
3d8130f Travis Abbott 20 February 2012, 22:02:47 UTC add support for vcf entries with 0 alt entries 20 February 2012, 22:02:47 UTC
8d882dc Travis Abbott 18 February 2012, 00:08:49 UTC Fasta class using mmap 18 February 2012, 00:08:49 UTC
f69959d Travis Abbott 16 February 2012, 22:02:56 UTC let vcf-merge merge indels 16 February 2012, 22:03:17 UTC
fa24e67 Travis Abbott 16 February 2012, 22:01:41 UTC remove stray print statement 16 February 2012, 22:03:17 UTC
db6511d Travis Abbott 16 February 2012, 22:01:07 UTC fix input data for vcf-merge integration test One of the files had variants identical to the reference 16 February 2012, 22:03:17 UTC
032c2d6 Travis Abbott 16 February 2012, 19:35:47 UTC remove unused member variable _peekBuf 16 February 2012, 22:03:17 UTC
dcbd668 Travis Abbott 16 February 2012, 17:28:34 UTC bugfix: sometimes we get a null character at eof due to improper checking of boost::iostreams::read's return value in InputStream::peek, sometimes we were pushing a null character back onto the stream. 16 February 2012, 22:03:17 UTC
dc51a44 Dave Larson 16 February 2012, 02:32:02 UTC added header to persite output 16 February 2012, 02:32:02 UTC
4ac354b Dave Larson 16 February 2012, 02:30:22 UTC Merge branch 'master' of ssh://git/srv/git/joinx 16 February 2012, 02:30:22 UTC
698203b Travis Abbott 15 February 2012, 21:43:07 UTC add AlleleMerger to merge equivalent alleles in vcf entries 15 February 2012, 21:43:07 UTC
52a2e25 Travis Abbott 15 February 2012, 17:25:18 UTC add annotation tag to vcf header in vcf-annotate 15 February 2012, 17:25:18 UTC
32bc2d6 Travis Abbott 10 February 2012, 08:21:06 UTC updated build-common 10 February 2012, 08:21:06 UTC
772dab5 Travis Abbott 01 February 2012, 18:51:16 UTC add boost iostreams dependency for packaging 01 February 2012, 18:51:16 UTC
917be92 Travis Abbott 01 February 2012, 17:26:22 UTC change parsing of field 4 of bed entries we typically use this as ref/alt, and downstream tools accept values of 0,-, or * to mean missing (in an indel). So if field 4 starts or ends with 0 or -, change it to * 01 February 2012, 17:26:22 UTC
86e14a1 Travis Abbott 01 February 2012, 17:14:05 UTC normalize missing alt/ref data in Bed to * previously any of 0, -, or * were used to represent missing data 01 February 2012, 17:15:14 UTC
16adad7 Dave Larson 01 February 2012, 17:05:42 UTC cheap fix to always report info on all alts. Underlying mechanics need to be cleaned up. 01 February 2012, 17:05:42 UTC
40ec388 Dave Larson 26 January 2012, 21:55:28 UTC added output of transition and transversion status for each allele 26 January 2012, 21:55:28 UTC
b005a81 Dave Larson 26 January 2012, 21:55:03 UTC added tracking of transition status of each alt allele 26 January 2012, 21:55:03 UTC
69bd17f Dave Larson 26 January 2012, 21:13:49 UTC added in multiple allele frequencies 26 January 2012, 21:13:49 UTC
7dcce6f Dave Larson 26 January 2012, 21:13:02 UTC added calculation of all allele frequencies (not just smallest) 26 January 2012, 21:13:02 UTC
a8cc4de Dave Larson 26 January 2012, 19:24:50 UTC stubbed in output fields and got genotype distribution working properly 26 January 2012, 19:24:50 UTC
f9ab1d7 Dave Larson 26 January 2012, 19:19:03 UTC changed genotype distribution to store by value 26 January 2012, 19:19:03 UTC
d6e021c Dave Larson 26 January 2012, 18:46:17 UTC fixed bad per sample allele distribution accessor 26 January 2012, 18:46:17 UTC
024686e Travis Abbott 25 January 2012, 23:26:26 UTC capitalization in help message 25 January 2012, 23:26:26 UTC
a539ab2 Travis Abbott 25 January 2012, 23:18:40 UTC new command vcf-annotate annotates a vcf file by another vcf (e.g., intersect this file with dbsnp and copy over the specified INFO fields and rsid where there are hits). 25 January 2012, 23:19:26 UTC
2430659 Travis Abbott 25 January 2012, 20:50:27 UTC rename processors/Intersect to processors/IntersectFull 25 January 2012, 23:19:26 UTC
941c747 Travis Abbott 25 January 2012, 20:45:12 UTC CMakeLists entry for TestVcfCompare 25 January 2012, 23:19:26 UTC
d3eb707 Travis Abbott 25 January 2012, 20:44:59 UTC Test for Vcf::Compare 25 January 2012, 23:19:26 UTC
377a16a Travis Abbott 25 January 2012, 20:44:44 UTC make adding info types to vcf headers more straightforward 25 January 2012, 23:19:26 UTC
fabe784 Travis Abbott 25 January 2012, 20:43:51 UTC allow new info fields to be set of VcfEntries also set the number of alternate alleles when parsing CustomValues 25 January 2012, 23:19:25 UTC
5808d3b Travis Abbott 25 January 2012, 20:42:31 UTC add ability to CustomValues #alts For CustomValues representing per-alt CustomTypes, it is important to be able to set the #of alternate alleles! 25 January 2012, 23:19:25 UTC
e4e20d0 Travis Abbott 25 January 2012, 20:35:55 UTC new code to compare alt alleles in vcf entries For two vcf entry objects A and B with equal chrom and position, this code returns as a std::map the set: { (ai => bi) | A.alt()[ai] == B.alt()[bi]} 25 January 2012, 23:19:25 UTC
c8e8b49 Dave Larson 25 January 2012, 21:32:23 UTC added in per site metrics. still needs a lot of work. most of the output is likely to change extensively 25 January 2012, 21:32:23 UTC
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