FLAG: 1
refSeqFile = ../data/Cvirginica_v300/Cvirginica_v300.fa.
bamFileName = ../output/02.10-bismark-deduplication/CF08-CM05-Larvae_dedup.sorted.bam.
snpFileName = ../output/12-snp-calling-BS-Snper/per-sample/CF08-CM05-Larvae.candidates.txt.
methCgFileName = ../output/12-snp-calling-BS-Snper/per-sample/CF08-CM05-Larvae.CpG.tab.
methChgFileName = ../output/12-snp-calling-BS-Snper/per-sample/CF08-CM05-Larvae.CHG.tab.
methChhFileName = ../output/12-snp-calling-BS-Snper/per-sample/CF08-CM05-Larvae.CHH.tab.
vQualMin = 15.
nLayerMax = 1000.
vSnpRate = 0.100000.
vSnpPerBase = 0.020000.
mapqThr = 20.
Init chrome name-len array completed, total 684741128 bp of 11 chromosomes.
11 chromes loaded.
Init chrome name-idx hash table completed.
Init chrome seq array completed.
Meth process begins...
Chrome updated to NC_035780.1!
Chrome updated to NC_035781.1!
Chrome updated to NC_035782.1!
Chrome updated to NC_035783.1!
Chrome updated to NC_035784.1!
Chrome updated to NC_035785.1!
Chrome updated to NC_035786.1!
Chrome updated to NC_035787.1!
Chrome updated to NC_035788.1!
Chrome updated to NC_035789.1!
Chrome updated to NC_007175.2!
Meth process ends...
SNP process begins...
100000 records have been dealed.
200000 records have been dealed.
SNP process ends...
SNP process completed.