sstadick perbase issues

sstadick / perbase

Per-base per-nucleotide depth analysis

MIT License

112 stars 14 forks source link

issues

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MacOS build on conda is incompatible with arm (but still gets installed)

#72 patbohn opened 3 weeks ago
2
not all region return when using a bed file

#71 FunGeST opened 5 months ago
0
bgzipped and indexed reference fasta

#70 darked89 opened 5 months ago
0
feat: add citation file

#69 sstadick closed 9 months ago
0
Index out of bounds

#68 ChristopherRichie opened 9 months ago
4
Difference only-depth and base-depth

#67 Akazhiel opened 9 months ago
3
weird encoding for reference name

#66 twaddlac opened 1 year ago
7
WIP: Mate fix efficient

#65 brentp closed 1 year ago
3
from_pileup_mate_aware very inefficient?

#64 brentp opened 1 year ago
2
parameters for sparse data

#63 brentp opened 1 year ago
1
New Tool for Per-Sequence Depths

#62 oschwengers opened 1 year ago
1
enh: filter_read also takes Option<&Alignment>

#61 brentp closed 1 year ago
5
accessing qpos() ?

#60 brentp opened 1 year ago
2
base-depth become extremely slow when calculating highly covered site.

#59 y9c opened 1 year ago
8
Update par_granges_example.rs

#58 y9c closed 1 year ago
7
Missing bam/cram file should return an error code

#57 patbohn opened 1 year ago
2
ubuntu cant find perbase

#56 JMNGLS closed 1 year ago
3
(optional?) Dependencies don't allow perbase to be used or compiled on Ubuntu 18.04.

#55 patbohn closed 1 year ago
3
Add Forward/Reverse mapping counts

#54 25shmeckles opened 2 years ago
2
Panic during base-depth, caused by secondary alignments?

#53 da-i closed 1 year ago
2
Bump crossbeam-deque from 0.8.0 to 0.8.1

#52 dependabot[bot] closed 2 years ago
1
Main

#51 Schaudge closed 2 years ago
0
'Chromosome not found in BAM/CRAM header'

#50 Surar closed 2 years ago
2
Can't use the base -depth function

#49 Surar closed 2 years ago
5
Typos: mergeing -> merging

#48 nh13 closed 2 years ago
0
Update README.md

#47 nh13 closed 2 years ago
0
Support bedGraph output in only-depth

#46 ghuls opened 2 years ago
1
[bugfix] only depth keep zeros

#45 sstadick closed 2 years ago
0
Allow for outputing positions with 0 depth in base-depth

#44 sstadick closed 2 years ago
0
[feature] pre-v0.8.0

#43 sstadick closed 2 years ago
1
Better error message with an invalid bed file

#42 nh13 closed 2 years ago
0
base-depth panicked with a 3-column BED file

#41 nh13 closed 2 years ago
0
[feature] Add bed-format option

#40 sstadick closed 2 years ago
0
Add PGO pass

#39 sstadick opened 3 years ago
0
[feature] Base Quality Filter and BGZIP support

#38 sstadick closed 3 years ago
0
read counter

#37 colindaven closed 3 years ago
2
[feature] Add bgzip support to all subcommands via noodles

#36 sstadick closed 3 years ago
0
Possible to calculate only say INDEL column values?

#35 jelber2 closed 3 years ago
5
Performance and OSX builds

#34 sstadick closed 3 years ago
0
Feature/bound channels

#33 sstadick closed 3 years ago
0
Upgrade htslib version to get fixes for OSX build

#32 sstadick closed 3 years ago
0
Create Benchmarking Suite

#31 sstadick opened 3 years ago
0
How much faster than mosdepth?

#30 brainstorm closed 3 years ago
3
Update README.md

#29 1ndy closed 3 years ago
0
Resume OSX builds

#28 sstadick closed 3 years ago
1
Feature/vcf and maxdepth support

#27 sstadick closed 3 years ago
0
Add tests for > 8000 depth to `base-depth`

#26 sstadick closed 3 years ago
0
Set max depth to max i32

#25 sstadick closed 3 years ago
0
Clean up error messages

#24 sstadick opened 3 years ago
0
Feature/ref base

#23 sstadick closed 3 years ago
0