Align bisulfite converted reads

asymmetric filtering

bash biscuit-develop align -v 8 ~/references/hg38/biscuit/hg38.fa -1 CACAAATATACATAAATATATAAATACACATAAATACATATAAATACACA

returns

input 0 chr11 69426259 50 50M * 0 0 CACAAATATACATAAATATATAAATACACATAAATACATATAAATACACA ################################################## NM:i:0 MD:Z:50 ZC:i:24 ZR:i:0 AS:i:50 XS:i:36 YD:A:r

biscuit-develop align -F -v 8 ~/references/hg38_noContig/biscuit/hg38_noContig.fa -1 AAACGAAATTTCACAATATCTAAAATTCCGAACCTCAAATAACCCGCCCG

returns

inputread 16 chr19 54446613 60 50M * 0 0 CGGGCGGGTTATTTGAGGTTCGGAATTTTAGATATTGTGAAATTTCGTTT * NM:i:1 MD:Z:45T4 ZC:i:11 ZR:i:3 AS:i:47 XS:i:23 XL:i:50 YD:A:f