```r
myobj = processBismarkAln(location = file.list, sample.id = list("1","2","3","4","5","6","7","8","9","10"), assembly = "v3", read.context="CpG", mincov=10, treatment = c(0,0,0,0,0,1,1,1,1,1))
```

```
## Conversion Statistics:
## 
## total otherC considered (>95% C+T): 3515751
## average conversion rate = 94.748540478749
## total otherC considered (Forward) (>95% C+T): 1762968
## average conversion rate (Forward) = 94.723007264251
## total otherC considered (Reverse) (>95% C+T): 1752783
## average conversion rate (Reverse) = 94.77422206061
## 
## Reading methylation percentage per base for sample: 1 
## 
## Conversion Statistics:
## 
## total otherC considered (>95% C+T): 6839341
## average conversion rate = 96.155043396954
## total otherC considered (Forward) (>95% C+T): 3427097
## average conversion rate (Forward) = 96.183173535963
## total otherC considered (Reverse) (>95% C+T): 3412244
## average conversion rate (Reverse) = 96.126790811557
## 
## Reading methylation percentage per base for sample: 2 
## 
## Conversion Statistics:
## 
## total otherC considered (>95% C+T): 7273596
## average conversion rate = 97.347913357828
## total otherC considered (Forward) (>95% C+T): 3647648
## average conversion rate (Forward) = 97.32930391935
## total otherC considered (Reverse) (>95% C+T): 3625948
## average conversion rate (Reverse) = 97.36663416713
## 
## Reading methylation percentage per base for sample: 3 
## 
## 
Read 78.2% of 1112900 rows
Read 1112900 rows and 7 (of 7) columns from 0.061 GB file in 00:00:03
## Conversion Statistics:
## 
## total otherC considered (>95% C+T): 6381045
## average conversion rate = 97.327413998009
## total otherC considered (Forward) (>95% C+T): 3192108
## average conversion rate (Forward) = 97.365882598418
## total otherC considered (Reverse) (>95% C+T): 3188937
## average conversion rate (Reverse) = 97.288907145376
## 
## Reading methylation percentage per base for sample: 4 
## 
## Conversion Statistics:
## 
## total otherC considered (>95% C+T): 8054052
## average conversion rate = 96.956524329087
## total otherC considered (Forward) (>95% C+T): 4034149
## average conversion rate (Forward) = 96.975349196856
## total otherC considered (Reverse) (>95% C+T): 4019903
## average conversion rate (Reverse) = 96.937632748498
## 
## Reading methylation percentage per base for sample: 5 
## 
## Conversion Statistics:
## 
## total otherC considered (>95% C+T): 6417289
## average conversion rate = 97.337628914187
## total otherC considered (Forward) (>95% C+T): 3215419
## average conversion rate (Forward) = 97.363145082118
## total otherC considered (Reverse) (>95% C+T): 3201870
## average conversion rate (Reverse) = 97.312004772303
## 
## Reading methylation percentage per base for sample: 6 
## 
## Conversion Statistics:
## 
## total otherC considered (>95% C+T): 7930348
## average conversion rate = 97.149022090854
## total otherC considered (Forward) (>95% C+T): 3976045
## average conversion rate (Forward) = 97.180623664983
## total otherC considered (Reverse) (>95% C+T): 3954303
## average conversion rate (Reverse) = 97.117246761345
## 
## Reading methylation percentage per base for sample: 7 
## 
## Conversion Statistics:
## 
## total otherC considered (>95% C+T): 7378773
## average conversion rate = 96.75659003169
## total otherC considered (Forward) (>95% C+T): 3693798
## average conversion rate (Forward) = 96.798932937354
## total otherC considered (Reverse) (>95% C+T): 3684975
## average conversion rate (Reverse) = 96.714145743666
## 
## Reading methylation percentage per base for sample: 8 
## 
## Conversion Statistics:
## 
## total otherC considered (>95% C+T): 7047510
## average conversion rate = 97.062417844473
## total otherC considered (Forward) (>95% C+T): 3530383
## average conversion rate (Forward) = 97.065392256551
## total otherC considered (Reverse) (>95% C+T): 3517127
## average conversion rate (Reverse) = 97.05943222188
## 
## Reading methylation percentage per base for sample: 9 
## 
## Conversion Statistics:
## 
## total otherC considered (>95% C+T): 4634962
## average conversion rate = 97.474855946389
## total otherC considered (Forward) (>95% C+T): 2322931
## average conversion rate (Forward) = 97.486769358883
## total otherC considered (Reverse) (>95% C+T): 2312031
## average conversion rate (Reverse) = 97.462886368473
## 
## Reading methylation percentage per base for sample: 10
```