Revision history for App-Anchr
0.4.3 2017-10-14T14:28:01Z
- Add command `anchr localcor`
- PARTIAL_COVERED for `anchr cover`
- Add --jvm to trimlong
0.4.2 2017-06-20T13:12:51Z
- Completely rewrite command cover
- Add JSON and Statistics::Descriptive as dep
- Skip duplicated daligner steps in overlap2
- Modify anchorLong pipeline
-
No more anchor.cover.fasta
- environment.json replaced anchor.cover.fasta.covered.yml
0.4.1 2017-06-19T03:11:31Z
- Use jrange in command covered
- Parallelize paf2ovlp with MCE
- minimap and miniasm in .travis.yml
0.4.0 2017-06-15T20:21:55Z
- Add command `anchr paf2ovlp`
- Add command `anchr trimlong`
- Add command `anchr scaffold`
- Remove command `anchr superreads`
- `anchr anchors`
- Swap <k_unitigs.fasta> <pe.cor.fa>
- Add coverage filter
- `anchr cover`
- Same --idt
- Add `--all` in `overlap2`
- Add create_ovlp_line() and parse_paf_line() to Common.pm
- Document .ovlp.tsv
0.3.2 2017-05-21T05:06:24Z
- Get rid of picard and genomeCoverageBed, use bbmap.sh's build in basecov
- No longer depend on bedrolls and picard-tools
- Remove share/anchor.sh
0.3.1 2017-05-20T14:36:23Z
- Make sr_stat.sh fitting environment.json
- Use `faops dazz` as we don't need original names in `anchr contained`
- share/anchor.sh replaced by `anchr anchors`
0.3.0 2017-05-11T01:12:28Z
- No more anchor2
- Can incorporate SE reads
- Separate `quorum` and `kunitigs` out of `superreads`
0.2.1 2017-05-04T16:04:27Z
- Dealing with branching nodes in `anchr merge`
- Skip finished steps in superreads.sh
- Merge pe.anchor2.fa into pe.anchr.fa
0.2.0 2017-05-03T19:27:23Z
- Parallelise the sampling step
- Use json to save enviroments
- Different K values in superreads.sh
- Drop contained k_unitigs
- Merge k_unitigs before anchor.sh
- Add examples from NCBI Pathogen Detection project
0.1.5 2017-04-22T16:04:51Z
- Specify dependency versions
- Improve documents
- Add GAGE-B examples
- Don't trim reads longer than 200 bp in `anchr superreads`
- Add step of tally
0.1.4 2017-03-31T18:58:35Z
- `anchr trim` in cwd
- Treat cyclic nodes as non-overlapped in `anchr merge`
0.1.3 2017-03-20T01:57:35Z
- Add --proportion to contained
- Add --keep to group
- Adjust pipeline and parameters
0.1.2 2017-03-11T09:20:45Z
- `anchr break`
- Don't leave any anchors in overlap2 and group
0.1.1 2017-03-09T09:04:52Z
- Add --max for maximum contained to cover
- Add --all to overlap2
- Dealing branching and cyclic nodes in layout
- Avoid "Invalid cross-device link"
0.1.0 2017-03-05T12:42:53Z
- `anchr layout`
- Merge all read groups of E. coli
- Discard *long reads* multi-matched by anchors
- Filter short reads before dazzname
0.0.19 2017-03-04T05:36:25Z
- Rename `anchr merge` to `anchr contained`
- `anchr orient` can be used in anchors
- Add a new `anchr merge` to merge oriented anchors
- Simplify anchor.sh
0.0.18 2017-03-02T12:24:38Z
- `anchr merge`
- Add parse_ovlp_line(), poa_consensus(), and lcss() to Common.pm
- Move transitive_reduction() and g2gv() to Common.pm
0.0.17 2017-02-26T14:33:14Z
- Add --restrict for `anchr orient`
- Skip anchors match to multiple parts of a long read
- Delete edges with different strands
- Default prefix 'read' for `anchr dazzname`
0.0.16 2017-02-25T08:44:29Z
- `anchr restrict`
- Rename ovlpreplace to replace
0.0.15 2017-02-25T08:06:14Z
- `anchr ovlpreplace`
- Limit max distance of linked anchors
0.0.14 2017-02-24T09:45:25Z
- `anchr group`
- Add serial2name() to Common.pm
- Add GraphViz to dependancies
0.0.13 2017-02-23T15:49:51Z
- `anchr cover`
- Find tempdir easier
0.0.12 2017-02-22T17:56:27Z
- `anchr orient`
- Use tempdir as basename of dazz db
0.0.11 2017-02-21T08:54:07Z
- `anchr overlap2`: calling `daligner` to detect overlaps between two files
- Document paralogs
- Switch to k-unitigs
- Add --start for dazzname
- Use `faops replace` to rename headers in FA files
0.0.10 2017-02-17T08:38:42Z
- Discard any reads with subs
- Use superReadSequences.fasta or k_unitigs.fasta
0.0.9 2017-02-14T20:59:08Z
- Install quorum and picard via Linuxbrew
- Move docs from sra
- Add quast in QA section
- `--noscythe` for trim
- Change quorum parameters
- Turn raw data stat to tables
0.0.8 2017-02-11T21:48:05Z
- `anchr overlap`
- Merge stat 3 and 4 in `sr_stat.sh`
- exec_cmd() in App::Anchr::Common
- Remove dependencies on ~/Scripts/sra
0.0.7 2017-02-11T05:33:40Z
- Keep original orders in `anchr dazzname`
- Merge stat 1 and 2 in `sr_stat.sh`
0.0.6 2017-02-11T00:57:42Z
- `anchr superreads`
0.0.5 2017-02-10T18:19:39Z
- `anchr trim`
0.0.4 2017-02-09T02:02:06Z
- `anchr dazzname`
- `anchr show2ovlp`
0.0.3 2017-02-08T22:59:37Z
- `anchr dep`
0.0.2 2017-02-08T21:11:05Z
- Setup Travis
0.0.1 2017-02-08T20:17:24Z
- Initial version
- `anchr help` works
- No real commands