update readme

README.md

@@ -18,22 +18,22 @@ for deriving the inferred haplotype sequence against the list of SNP markers.
 ## Usage
 Obtain allele counts for cell barcodes listed in barcodeFile at the SNP positions in VCF from the BAM file.
 
-  Usage:
-      sscocaller [options] <BAM> <VCF> <barcodeFile> <out_prefix>
-
-  Options:
-      -t --threads <threads> number of BAM decompression threads [default: 4]
-      -MQ --minMAPQ <mapq> Minimum MAPQ for read filtering [default: 20]
-      -BQ --baseq <baseq>  base quality threshold for a base to be used for counting [default: 13]
-      -CHR --chrom <chrom> the selected chromsome (whole genome if not supplied,separate by comma if multiple chroms)
-      -minDP --minDP <minDP> the minimum DP for a SNP to be included in the output file [default: 1]
-      -maxDP --maxDP <maxDP> the maximum DP for a SNP to be included in the output file [default: 10]
-      -chrName --chrName <chrName> the chr names with chr prefix or not, if not supplied then no prefix
-      -thetaREF --thetaREF <thetaREF> the theta for the binomial distribution conditioning on hidden state being REF [default: 0.1]
-      -thetaALT --thetaALT <thetaALT> the theta for the binomial distribution conditioning on hidden state being ALT [default: 0.9]
-      -cmPmb --cmPmb <cmPmb> the average centiMorgan distances per megabases default 0.1 cm per Mb [default 0.1]
-      -h --help  show help
-
-  Examples
-      ./sscocaller --threads 10 AAAGTAGCACGTCTCT-1.raw.bam AAAGTAGCACGTCTCT-1.raw.bam.dp3.alt.vcf.gz barcodeFile.tsv ./percell/ccsnp-
+Usage:
+    sscocaller [options] <BAM> <VCF> <barcodeFile> <out_prefix>
+
+Options:
+    -t --threads <threads> number of BAM decompression threads [default: 4]
+    -MQ --minMAPQ <mapq> Minimum MAPQ for read filtering [default: 20]
+    -BQ --baseq <baseq>  base quality threshold for a base to be used for counting [default: 13]
+    -CHR --chrom <chrom> the selected chromsome (whole genome if not supplied,separate by comma if multiple chroms)
+    -minDP --minDP <minDP> the minimum DP for a SNP to be included in the output file [default: 1]
+    -maxDP --maxDP <maxDP> the maximum DP for a SNP to be included in the output file [default: 10]
+    -chrName --chrName <chrName> the chr names with chr prefix or not, if not supplied then no prefix
+    -thetaREF --thetaREF <thetaREF> the theta for the binomial distribution conditioning on hidden state being REF [default: 0.1]
+    -thetaALT --thetaALT <thetaALT> the theta for the binomial distribution conditioning on hidden state being ALT [default: 0.9]
+    -cmPmb --cmPmb <cmPmb> the average centiMorgan distances per megabases default 0.1 cm per Mb [default 0.1]
+    -h --help  show help
+
+Examples
+    ./sscocaller --threads 10 AAAGTAGCACGTCTCT-1.raw.bam AAAGTAGCACGTCTCT-1.raw.bam.dp3.alt.vcf.gz barcodeFile.tsv ./percell/ccsnp-