snacktavish/TreeToReads issues and pull requests

#46 - conda instructions

Pull Request - State: closed - Opened by snacktavish about 2 years ago

#45 - Support for threading and additional read simulation parameters

Pull Request - State: open - Opened by ar0ch almost 5 years ago - 7 comments

#44 - random seed in config

Pull Request - State: open - Opened by snacktavish over 5 years ago

#43 - Reproducible results

Issue - State: open - Opened by stevendavis over 5 years ago - 2 comments

#42 - Fix off-by-one error when reporting the number of contigs in the genome.

Pull Request - State: closed - Opened by stevendavis over 5 years ago - 1 comment

#41 - Off-by-one error when reporting the number of contigs in the genome

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

#40 - Improve README formating and document '_indel.fasta' files

Pull Request - State: closed - Opened by ar0ch almost 6 years ago - 1 comment

#39 - Fixes to treetoreads.py

Pull Request - State: closed - Opened by willpitchers almost 6 years ago - 2 comments

#38 - `sys.maxint` and `.sort` deprecations in treetoreads.py

Pull Request - State: closed - Opened by willpitchers about 6 years ago - 3 comments

#37 - Parallelization

Issue - State: open - Opened by lskatz about 7 years ago - 1 comment

#36 - reformated headers

Pull Request - State: closed - Opened by lskatz about 7 years ago

#35 - Multi contig

Pull Request - State: closed - Opened by snacktavish about 7 years ago

#34 - Fix README.md rendering to match new standard

Issue - State: closed - Opened by tseemann over 7 years ago - 1 comment

#33 - Vcf

Pull Request - State: closed - Opened by snacktavish about 8 years ago

#32 - include TTR version number in output files

Issue - State: open - Opened by retimme about 8 years ago - 1 comment

#31 - fix weird line wrapping

Issue - State: open - Opened by snacktavish about 8 years ago

#30 - output VCF of SNPs

Issue - State: open - Opened by snacktavish about 8 years ago - 2 comments

#29 - Newline fix

Pull Request - State: closed - Opened by snacktavish over 8 years ago

#28 - tip labels with underscores

Issue - State: closed - Opened by snacktavish over 8 years ago - 1 comment

#27 - Multicontig

Pull Request - State: closed - Opened by lskatz over 8 years ago

#26 - add indels

Issue - State: closed - Opened by snacktavish over 8 years ago

#25 - Request: a script to figure out input parameters

Issue - State: open - Opened by lskatz almost 9 years ago - 1 comment

#24 - Lowercase nucleotides is an issue

Issue - State: closed - Opened by lskatz almost 9 years ago - 1 comment

#23 - Add ART to the package

Issue - State: open - Opened by snacktavish about 9 years ago

#22 - Create a docker image

Issue - State: closed - Opened by snacktavish about 9 years ago

#21 - file compression for sam and fastq

Pull Request - State: closed - Opened by lskatz about 9 years ago

#20 - Correction to brew install instructions

Issue - State: open - Opened by tseemann about 9 years ago - 2 comments

#19 - Just running treetoreads.py did a whole lot of stuff?

Issue - State: closed - Opened by tseemann about 9 years ago - 3 comments

#18 - Prefer pip2 install for dendropy

Issue - State: closed - Opened by tseemann about 9 years ago

#17 - Don't force /usr/bin/python

Issue - State: closed - Opened by tseemann about 9 years ago - 1 comment

#16 - compression

Issue - State: closed - Opened by lskatz about 9 years ago - 5 comments

#15 - Dockerfile, README updates

Pull Request - State: closed - Opened by crashfrog about 9 years ago

#14 - Write a tutorial

Issue - State: closed - Opened by snacktavish over 9 years ago - 1 comment

#13 - Read nexus tree files

Issue - State: closed - Opened by snacktavish over 9 years ago - 1 comment

#12 - check for dendropy and handle error if absent

Issue - State: closed - Opened by snacktavish over 9 years ago - 1 comment

#11 - config file

Issue - State: closed - Opened by snacktavish over 9 years ago

#10 - Clarify readme

Issue - State: closed - Opened by snacktavish over 9 years ago

#9 - missed some commits

Pull Request - State: closed - Opened by snacktavish over 9 years ago

#8 - license

Pull Request - State: closed - Opened by snacktavish over 9 years ago

#7 - Develop

Pull Request - State: closed - Opened by snacktavish over 9 years ago

#6 - Streamline tests

Issue - State: closed - Opened by snacktavish over 9 years ago

#5 - Add license

Issue - State: closed - Opened by snacktavish over 9 years ago - 4 comments

#4 - Check 10 recomendations

Issue - State: closed - Opened by snacktavish over 9 years ago - 5 comments

#3 - Develop

Pull Request - State: closed - Opened by snacktavish over 9 years ago

#2 - Develop

Pull Request - State: closed - Opened by snacktavish over 9 years ago

#1 - Dockerfile for auto builds; added Numpy dependency to README

Pull Request - State: closed - Opened by crashfrog over 9 years ago - 1 comment

GitHub / snacktavish/TreeToReads issues and pull requests