nhoffman bioy issues - Githubissues

nhoffman / bioy

Tools for NGS sequence analysis and bacterial classification

GNU General Public License v3.0

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New rrndb

#61 crosenth opened 8 years ago
0
Want classifier to emit all queries that were used to make an assignment

#60 tyleraland opened 8 years ago
0
Remove multiple centriods in --max-group-size combined assignments

#59 crosenth closed 6 years ago
0
classifier --split-condensed-assignments double-counts centroids

#58 tyleraland closed 8 years ago
1
Split condensed assignments

#57 crosenth closed 8 years ago
0
054 ref rank

#56 tyleraland closed 8 years ago
2
classifier blast headers

#55 tyleraland opened 8 years ago
0
Include arbitrary rank id,name in details output

#54 tyleraland opened 8 years ago
0
add switch to prevent sets of common condense_ids sharing the same assignment

#53 crosenth closed 8 years ago
0
best N hits

#52 tyleraland closed 8 years ago
2
Classifier assigning part of some sequence names to "root"

#51 tyleraland closed 8 years ago
1
Ion vs miseq

#50 crosenth closed 8 years ago
0
Ssearch strands

#49 crosenth closed 8 years ago
0
require gb rather than just gi -- not yet rigorously tested

#48 crosenth closed 8 years ago
0
limit to one qseqid per classification in --details

#47 nhoffman opened 8 years ago
1
Feature Request, Classifier: keep the best N classification names

#46 tyleraland closed 8 years ago
2
ncbi_fetch: Require "gb" identifier

#45 tyleraland opened 8 years ago
4
fix --version argument switch

#44 crosenth closed 6 years ago
3
don't rely on data/rank_thresholds.csv

#43 nhoffman opened 8 years ago
1
41 hits below threshold

#42 tyleraland closed 9 years ago
0
show classifier hits that were filtered because they were below the classification threshold

#41 tyleraland closed 8 years ago
1
package import fails when installed with pip install --no-deps

#40 nhoffman opened 9 years ago
4
bioy blast unit test

#39 tyleraland opened 9 years ago
1
duplicate lines in specimen map creates duplicate results in details

#38 crosenth closed 9 years ago
0
restoring old (global) coverage calculation

#37 tyleraland closed 9 years ago
1
fails when qseqids are all digits

#36 crosenth closed 9 years ago
0
Dash release candidate in version number gets stripped off

#35 crosenth closed 6 years ago
0
classifier bug when no blast hits

#34 crosenth closed 9 years ago
0
ssearch: optionally search forward and reverse strands

#33 tyleraland closed 9 years ago
0
unknown tax_ids in data/rank_thresholds.csv cause results with those tax_ids to be filtered out

#32 crosenth closed 9 years ago
1
incorrect rank of classification

#31 nhoffman closed 9 years ago
2
combine bioy ssearch and usearch

#30 crosenth closed 6 years ago
0
bioy usearch fieldnames

#29 nhoffman opened 9 years ago
0
Subcommand to list versions of bioy software

#28 tyleraland opened 10 years ago
0
Turn on Travis testing

#27 crosenth closed 6 years ago
2
condensing group tax_ids to size 4: 244%

#26 crosenth closed 9 years ago
1
021 ncbi fetch

#25 tyleraland closed 9 years ago
1
022 blast remotely

#24 tyleraland closed 10 years ago
0
021 ncbi fetch

#23 tyleraland closed 10 years ago
3
Extend bioy blast to perform remote (NCBI) search

#22 tyleraland closed 9 years ago
3
Tool that builds multi-fasta/seqinfo/taxtable from query sequence and its blast results

#21 tyleraland closed 9 years ago
3
019 fix usearch

#20 nhoffman closed 10 years ago
2
'bioy usearch' fails, needs some improvements

#19 nhoffman opened 10 years ago
2
environment variables to define number of processors/threads

#18 nhoffman opened 10 years ago
0
before executing ssearch, check for empty files

#17 tyleraland closed 10 years ago
0
Faster classify

#16 crosenth closed 10 years ago
0
test in tests/test_denoise.py fail (install binary dependencies with dev/bootstrap.sh [muscle, usearch, ssearch])

#15 nhoffman opened 10 years ago
2
requirements.txt should not have editable sources by default

#14 tyleraland closed 10 years ago
1
Fasta2csv

#13 crosenth closed 10 years ago
0
Ssearch coverage addition

#12 tyleraland closed 10 years ago
0