FLAG: 1
refSeqFile = ../data/Cvirginica_v300/Cvirginica_v300.fa.
bamFileName = ../output/02.10-bismark-deduplication/CF01-CM01-Zygote_dedup.sorted.bam.
snpFileName = ../output/12-snp-calling-BS-Snper/per-sample/CF01-CM01-Zygote.candidates.txt.
methCgFileName = ../output/12-snp-calling-BS-Snper/per-sample/CF01-CM01-Zygote.CpG.tab.
methChgFileName = ../output/12-snp-calling-BS-Snper/per-sample/CF01-CM01-Zygote.CHG.tab.
methChhFileName = ../output/12-snp-calling-BS-Snper/per-sample/CF01-CM01-Zygote.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!
500000 records have been dealed.
Chrome updated to NC_035782.1!
1000000 records have been dealed.
Chrome updated to NC_035783.1!
1500000 records have been dealed.
Chrome updated to NC_035784.1!
2000000 records have been dealed.
Chrome updated to NC_035785.1!
Chrome updated to NC_035786.1!
2500000 records have been dealed.
Chrome updated to NC_035787.1!
Chrome updated to NC_035788.1!
3000000 records have been dealed.
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.
300000 records have been dealed.
400000 records have been dealed.
500000 records have been dealed.
600000 records have been dealed.
700000 records have been dealed.
800000 records have been dealed.
900000 records have been dealed.
1000000 records have been dealed.
1100000 records have been dealed.
1200000 records have been dealed.
1300000 records have been dealed.
1400000 records have been dealed.
1500000 records have been dealed.
1600000 records have been dealed.
1700000 records have been dealed.
1800000 records have been dealed.
1900000 records have been dealed.
2000000 records have been dealed.
2100000 records have been dealed.
2200000 records have been dealed.
2300000 records have been dealed.
2400000 records have been dealed.
2500000 records have been dealed.
2600000 records have been dealed.
2700000 records have been dealed.
2800000 records have been dealed.
2900000 records have been dealed.
3000000 records have been dealed.
3100000 records have been dealed.
3200000 records have been dealed.
3300000 records have been dealed.
SNP process ends...
SNP process completed.