readme and nimble

README.md

-# sscocaller
+## sscocaller: Calling crossovers from single-sperm DNA sequencing reads
+
+It takes the large bam file which contains aligned DNA reads from a list of single sperm cells and summarizes allele
+counts for informative SNP markers. A HMM model is applied for haplotypin each sperm and viterbi algorithm is run
+for deriving the inferred haplotype sequence against the list of SNP markers.
+
+## Inputs
+
+- Bam, Reads from single sperm cells with BC tag, eg. single-cell alignment pipeline (cellranger)
+- VCF, variant calling file that contains the list of SNPs provided
+- barcodeFile, the list of cell barcodes
+
+## Outputs
+- Generate per chr allele counts matrices 
+- Sequence of inferred viterbi state (haplotype state) per chr
+
+
+## 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-
 

sscocaller.nimble

+# Package
+
+version       = "0.1.0"
+author        = "Ruqian Lyu"
+description   = "sscocaller: calling crossover events from single-sperm DNA sequencing datasets"
+license       = "MIT"
+srcDir        = "src"
+bin           = @["sscocaller"]
+
+
+# Dependencies
+
+requires "nim >= 1.4.0","docopt","hts >= 0.3.4"
+requires "http://github.com/sdwfrost/rmath.git"
+
+# task test, "run the tests":
+#   exec "nim c  -d:useSysAssert -d:useGcAssert --lineDir:on --debuginfo -r tests/test_groups"
+#   exec "bash tests/functional-tests.sh"

tests/test.sh

+./code/sscocaller --threads 2 --chrom 6 data/AAAGTAGCACGTCTCT-1.raw.bam data/AAAGTAGCACGTCTCT-1.raw.bam.dp3.alt.vcf.gz data/bcAA.tsv ./percell/ccsnp-
+