Ecosyste.ms: Issues

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GitHub / SamStudio8/gretel issues and pull requests

#41 - float division by zero error

Issue - State: open - Opened by Saannah almost 2 years ago

#40 - Could not create iterator for region 'megahit_contigs.fa:1-603'

Issue - State: closed - Opened by kangxiongbin over 3 years ago - 8 comments

#39 - Question about how to deal with missing bridges between SNPs

Issue - State: closed - Opened by gavinmdouglas over 3 years ago - 2 comments

#38 - Upstream Protocol

Issue - State: closed - Opened by bjtully over 3 years ago - 1 comment

#37 - Issue loading vcf file

Issue - State: closed - Opened by GoneAwry over 3 years ago - 8 comments

#36 - Documentation does not mention `gretel-snpper`

Issue - State: open - Opened by SamStudio8 almost 4 years ago

#35 - gretel crumbs output

Issue - State: closed - Opened by kbseah about 4 years ago - 3 comments

#34 - Improve error message for no bridge found

Issue - State: open - Opened by jsgounot about 4 years ago - 7 comments
Labels: enhancement

#33 - Non-compressed VCF should emit warning (or just drop pyVCF)

Issue - State: open - Opened by SamStudio8 about 4 years ago - 1 comment
Labels: usability

#32 - IndexError when adding observations to Hansel

Issue - State: closed - Opened by SamStudio8 about 5 years ago - 16 comments

#31 - Huge temporary files when running gretel on very large contigs

Issue - State: open - Opened by SamStudio8 about 5 years ago - 7 comments
Labels: bug, enhancement, usability

#30 - Temporary file, output sequence, indexerror

Issue - State: closed - Opened by mherold1 about 5 years ago - 2 comments

#29 - Failing at SNP #0 at position 0, questions for understanding output

Issue - State: closed - Opened by mherold1 about 5 years ago - 10 comments
Labels: question

#28 - gretel --version doesn't work

Issue - State: closed - Opened by tseemann over 5 years ago - 1 comment

#27 - [tracking] Ideas for future work

Issue - State: open - Opened by SamStudio8 over 5 years ago - 3 comments
Labels: enhancement, idea

#25 - Likelihood reported in FASTA

Issue - State: closed - Opened by SamStudio8 almost 7 years ago
Labels: question

#24 - Haplotypes not detected despite strong read support

Issue - State: closed - Opened by Sebdu132 almost 7 years ago - 1 comment
Labels: question

#23 - Overlapping mates should be ignored?

Issue - State: closed - Opened by SamStudio8 almost 7 years ago - 1 comment
Labels: question

#22 - gretel adds spurious SNPs ???

Issue - State: closed - Opened by Sebdu132 almost 7 years ago - 8 comments
Labels: bug

#21 - Hansel and Gretel as conda packages

Issue - State: closed - Opened by johnne almost 7 years ago - 10 comments

#20 - Improve UX for bridging errors [Fixes #14]

Pull Request - State: closed - Opened by SamStudio8 almost 7 years ago

#19 - gretel fails with "Unable to select next branch from"

Issue - State: closed - Opened by johnne almost 7 years ago - 8 comments
Labels: question

#18 - Compatibility with PALADIN

Issue - State: closed - Opened by thh32 about 7 years ago - 2 comments
Labels: question

#17 - Using hansel & gretel on multiple contigs.

Issue - State: closed - Opened by fwhelan about 7 years ago - 7 comments
Labels: question

#16 - Multiple read pairs with same name

Issue - State: closed - Opened by SamStudio8 over 7 years ago - 1 comment
Labels: bug

#15 - fasta output

Issue - State: closed - Opened by linsalrob over 7 years ago - 1 comment
Labels: bug

#13 - Should use reference length (or fail sensibly) if missing -e

Issue - State: closed - Opened by SamStudio8 over 7 years ago
Labels: bug

#12 - Gretel expects the `master.fa` to have just one reference

Issue - State: closed - Opened by SamStudio8 almost 8 years ago

#11 - Reads with a single SNP

Issue - State: closed - Opened by SamStudio8 almost 8 years ago - 1 comment

#10 - Find a happy system for reweighting

Issue - State: open - Opened by SamStudio8 almost 8 years ago - 2 comments
Labels: enhancement, question, idea

#9 - Weight conditional probabilities on their distance

Issue - State: closed - Opened by SamStudio8 almost 8 years ago - 1 comment
Labels: question, idea

#8 - What's an appropriate stopping criterion?

Issue - State: closed - Opened by SamStudio8 about 8 years ago
Labels: question

#7 - Insert detected insertions onto the reference

Issue - State: open - Opened by SamStudio8 about 8 years ago - 1 comment
Labels: question

#6 - [Q] Minimum reweight value

Issue - State: closed - Opened by SamStudio8 about 8 years ago - 1 comment
Labels: question

#5 - Naively call SNPs if no VCF is provided

Issue - State: closed - Opened by SamStudio8 about 8 years ago - 1 comment
Labels: enhancement

#4 - Indels

Issue - State: closed - Opened by SamStudio8 over 8 years ago - 1 comment
Labels: enhancement, question

#3 - Is the intuition for `L` correct?

Issue - State: closed - Opened by SamStudio8 over 8 years ago - 2 comments
Labels: question

#2 - Target ramp

Issue - State: closed - Opened by SamStudio8 over 8 years ago
Labels: question

#1 - Pull some exciting exploitable enzymes out of a metagenome

Issue - State: open - Opened by SamStudio8 over 8 years ago