Mercurial > repos > chrisd > coverage_sampler

changeset 7:d43960f50fc1 draft

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planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit a5d62efa31bd5cd41ce400f51a59efb2284e1151-dirty
author chrisd
date Tue, 28 Jun 2016 23:07:45 -0400
parents 59c6a5729ce0
children 1fdee48eab64
files README.md
diffstat 1 files changed, 0 insertions(+), 36 deletions(-) [+]
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--- a/README.md	Tue Jun 28 22:49:28 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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-Coverage Sampler: A simple tool for calculating the amount of a gene that is covered by a sample of alignments.
-
-#### Installation
-```
-git clone https://github.com/cdeanj/coverage_sampler
-cd coverage_sampler
-make
-./csa
-```
-
-#### Usage
-Usage: csa [options]
-
-Options:
-
-    -ref_fp    STR/FILE	    ref file path
-    -sam_fp    STR/FILE	    sam file path
-    -min       INT      	starting sample level
-    -max       INT	        ending sample level
-    -skip      INT	        amount of sample levels to skip
-    -t         INT	        gene fraction threshold
-    -samples   INT	        iterations per sample level
-    -out_fp    STR/FILE	    output file path
-
-#### Output
-
-The output is a tab delimited text file with five columns
-```
-Level   Iteration   Gene Id Gene Fraction   Hits
-```
-
-* Level: the sampling percent alignments were taken at
-* Iteration: the ith iteration of the current sample level
-* Gene Id: the reference sequence having a gene fraction greater than the threshold
-* Gene Fraction: the number of bases covered by the sample of alignments
-* Hits: the number of alignments that had bases cover the reference sequence