SamStudio8 gretel issues

SamStudio8 / gretel

An algorithm for recovering haplotypes from metagenomes

https://gretel.readthedocs.io/en/latest/

MIT License

31 stars 4 forks source link

issues

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Newest Most commented Recently updated Oldest Least commented Least recently updated

float division by zero error

#41 Saannah opened 1 year ago
0
Could not create iterator for region 'megahit_contigs.fa:1-603'

#40 kangxiongbin closed 3 years ago
8
Question about how to deal with missing bridges between SNPs

#39 gavinmdouglas closed 3 years ago
2
Upstream Protocol

#38 bjtully closed 3 years ago
1
Issue loading vcf file

#37 GoneAwry closed 3 years ago
8
Documentation does not mention `gretel-snpper`

#36 SamStudio8 opened 3 years ago
0
gretel crumbs output

#35 kbseah closed 3 years ago
3
Improve error message for no bridge found

#34 jsgounot opened 4 years ago
7
Non-compressed VCF should emit warning (or just drop pyVCF)

#33 SamStudio8 opened 4 years ago
1
IndexError when adding observations to Hansel

#32 SamStudio8 closed 4 years ago
16
Huge temporary files when running gretel on very large contigs

#31 SamStudio8 opened 4 years ago
7
Temporary file, output sequence, indexerror

#30 mherold1 closed 4 years ago
2
Failing at SNP #0 at position 0, questions for understanding output

#29 mherold1 closed 5 years ago
10
gretel --version doesn't work

#28 tseemann closed 5 years ago
1
[tracking] Ideas for future work

#27 SamStudio8 opened 5 years ago
3
Providing start > end should indicate Gretel to return reverse complement haplotypes

#26 SamStudio8 opened 6 years ago
0
Likelihood reported in FASTA

#25 SamStudio8 closed 5 years ago
0
Haplotypes not detected despite strong read support

#24 Sebdu132 closed 5 years ago
1
Overlapping mates should be ignored?

#23 SamStudio8 closed 5 years ago
1
gretel adds spurious SNPs ???

#22 Sebdu132 closed 6 years ago
8
Hansel and Gretel as conda packages

#21 johnne closed 6 years ago
10
Improve UX for bridging errors [Fixes #14]

#20 SamStudio8 closed 6 years ago
0
gretel fails with "Unable to select next branch from"

#19 johnne closed 6 years ago
8
Compatibility with PALADIN

#18 thh32 closed 5 years ago
2
Using hansel & gretel on multiple contigs.

#17 fwhelan closed 6 years ago
7
Multiple read pairs with same name

#16 SamStudio8 closed 5 years ago
1
fasta output

#15 linsalrob closed 7 years ago
1
Lack of clear explanation for a pair of SNPs missing at least one read throwing an error is terrible

#14 SamStudio8 closed 6 years ago
0
Should use reference length (or fail sensibly) if missing -e

#13 SamStudio8 closed 7 years ago
0
Gretel expects the `master.fa` to have just one reference

#12 SamStudio8 closed 5 years ago
0
Reads with a single SNP

#11 SamStudio8 closed 5 years ago
1
Find a happy system for reweighting

#10 SamStudio8 opened 7 years ago
2
Weight conditional probabilities on their distance

#9 SamStudio8 closed 5 years ago
1
What's an appropriate stopping criterion?

#8 SamStudio8 closed 5 years ago
0
Insert detected insertions onto the reference

#7 SamStudio8 opened 7 years ago
1
[Q] Minimum reweight value

#6 SamStudio8 closed 5 years ago
1
Naively call SNPs if no VCF is provided

#5 SamStudio8 closed 5 years ago
1
Indels

#4 SamStudio8 closed 5 years ago
1
Is the intuition for `L` correct?

#3 SamStudio8 closed 5 years ago
2
Target ramp

#2 SamStudio8 closed 5 years ago
0
Pull some exciting exploitable enzymes out of a metagenome

#1 SamStudio8 opened 8 years ago
0