bam list support

[xiekunwhy]

Hi,

Is there an option to support bam list input? if some one have many bam files.

Best,
kun

[lh3]

No such option but I will consider it later

[dwpeng]

Hi,
I fork this repo and implement this feature #1 . branch: bam-list-support with option -i, the progrom can load bam file list.

bam-list.txt

1.bam
# 2.bam  ! filterd, because this line startswith #
3.bam

use option -i bam-files.txt enable bam list support. It is important to note that if '-i' is used,
then the bam file passed directly will be ignored.
The following two ways are supported：

• minipileup ... 1.bam 2.bam
• minipileup -i bam-list.txt ... a.bam b.bam # a.bam and b.bam will be ignored.

[xiekunwhy]

also expect an option to output all positions, including those only 0/0 genotype in all sample.
thank you @dwpeng , I will try it.
Best,
Kun