rename covmed to covstats

HISTORY.md

@@ -1,9 +1,11 @@
 v0.1.16-dev
 ===========
 + `indexcov`: report and plot number of mapped and unmapped reads as reported by the index.
-+ `covmed`: report samplename(s) from read groups as well as bam path.
-+ `covmed`: skip first 100K reads to give better estimates of depth.
-+ `covmed`: report percent of bad (QC-Fail|Duplicate) and of umapped reads.
++ `covmed`: rename to `covstats`
++ `covstats`: report samplename(s) from read groups as well as bam path.
++ `covstats`: skip first 100K reads to give better estimates of depth.
++ `covstats`: report percent of bad (QC-Fail|Duplicate) and of umapped reads.
+
 
 v0.1.15
 =======

README.md

@@ -30,7 +30,7 @@ go install github.com/brentp/goleft/cmd/goleft
 
 # Commands
 
-+ [covmed](https://github.com/brentp/goleft/tree/master/covmed#covmed)   : calculate median coverage and insert-size on bams by sampling
++ [covstats](https://github.com/brentp/goleft/tree/master/covstats#covstats)   : estimate coverage and insert-size statistics on bams by sampling
 + [depth](https://github.com/brentp/goleft/tree/master/depth#depth)    : parallelize calls to samtools in user-defined windows
 + depthwed : matricize output from depth to n-sites * n-samples
 + [indexcov](https://github.com/brentp/goleft/tree/master/indexcov#indexcov) : quick coverage estimate using only the bam index

cmd/goleft/goleft.go

@@ -8,7 +8,7 @@ import (
 	"strconv"
 
 	"github.com/brentp/goleft"
-	"github.com/brentp/goleft/covmed"
+	"github.com/brentp/goleft/covstats"
 	"github.com/brentp/goleft/depth"
 	"github.com/brentp/goleft/depthwed"
 	"github.com/brentp/goleft/indexcov"
@@ -24,7 +24,7 @@ type progPair struct {
 var progs = map[string]progPair{
 	"depth":      progPair{"parallelize calls to samtools in user-defined windows", depth.Main},
 	"depthwed":   progPair{"matricize output from depth to n-sites * n-samples", depthwed.Main},
-	"covmed":     progPair{"calculate median coverage on a bam by sampling", covmed.Main},
+	"covstats":   progPair{"coverage stats across bams by sampling", covstats.Main},
 	"indexcov":   progPair{"quick coverage estimate using only the bam index", indexcov.Main},
 	"indexsplit": progPair{"create regions of even coverage across bams/crams", indexsplit.Main},
 	"samplename": progPair{"report samplename(s) from a bam's SM tag", samplename.Main},

covstats/README.md

@@ -0,0 +1,3 @@
+## covstats
+
+get estimates for coverage, instert size, duplicate, from a bam file by sampling read-length and looking at the index.

covmed/covmed.go → covstats/covstats.go

@@ -1,4 +1,4 @@
-package covmed
+package covstats
 
 import (
 	"fmt"

indexcov/README.md

@@ -8,7 +8,7 @@ coverage estimate in seconds per genome.
 The output is scaled to around 1. So a long stretch with values of 1.5 would be a heterozygous duplication.
 This is useful as a quick QC to get coverage values across the genome.
 
-In our tests, we can **estimate depth across a 60X genomes for 30 samples in 30 seconds**.
+In our tests, we can **estimate depth across 60X genomes for 30 samples in 30 seconds**.
 
 Interactive HTML plots of depth are output for each chromosome. **Live examples of the interactive output are available [here](http://indexcov.s3-website-us-east-1.amazonaws.com/)**