sequenceTools 1.4.0.4 → 1.4.0.5

raw patch · 3 files changed

+11/−2 lines, 3 files

Files

• README.md +9/−0
• sequenceTools.cabal +1/−1
• src-executables/pileupCaller.hs +1/−1

@@ -60,3 +60,12 @@ ## genoStats  A simple tool to get some per-individual statistics from an Eigenstrat or Freqsum-file. Run `genoStats --help` for documentation.++## Scripts+This package also contains several haskell wrapper scripts for the following [ADMIXTOOLS and EIGENSOFT](https://reich.hms.harvard.edu/software) commands: convertf, mergeit, qp3Pop, qpDstat and smartPCA. The original tools require parameter files as input, which I find tedious to use in bioinformatics pipelines. I wrote those wrapper scripts to be able to start the tools with a simple command line option interface.++If you have `stack` installed your system (see above), you should be able to run those scripts on your machine without any difficult setup. Simply clone this repository, navigate to the `scripts` subfolder and invoke any script using standard bash execution, for example++    ./convertf_wrapper.hs++If you start this the first time it may take a while, since `stack` downloads all dependencies and even the script interpreter for you, but after that it should start instantanious. If you want to use the scripts from your path, I suggest to put symbolic links into any folder that is already on your path (for example `~/.local/bin`).

@@ -1,6 +1,6 @@ cabal-version: >=1.10 name: sequenceTools-version: 1.4.0.4+version: 1.4.0.5 license: GPL-3 license-file: LICENSE maintainer: stephan.schiffels@mac.com

@@ -111,7 +111,7 @@     parseTransitionsMissing = OP.flag' TransitionsMissing (OP.long "transitionsMissing" <>         OP.help "mark transitions as missing in the output, but do output the sites.")     parseSingleStrandMode = OP.flag' SingleStrandMode (OP.long "singleStrandMode" <>-        OP.help "At C/T polymorphisms, ignore reads aligning to the forward strand. \+        OP.help "[THIS IS CURRENTLY AN EXPERIMENTAL FEATURE]. At C/T polymorphisms, ignore reads aligning to the forward strand. \         \At G/A polymorphisms, ignore reads aligning to the reverse strand. This should \         \remove post-mortem damage in ancient DNA libraries prepared with the non-UDG single-stranded protocol.")     parseSnpFile = OP.strOption (OP.long "snpFile" <> OP.short 'f' <>