def __init__(self, cmd="samtools", **kwargs): self.program_name = cmd self.parameters = [ _StaticArgument("merge"), _Switch(["-n", "n"], """The input alignments are sorted by read names rather than by chromosomal coordinates"""), _Switch(["-r", "r"], """Attach an RG tag to each alignment. The tag value is inferred from file names"""), _Switch(["-u", "u"], "Uncompressed BAM output"), _Switch(["-1", "fast_bam"], """Use zlib compression level 1 to compress the output"""), _Switch(["-f", "f"], """Force to overwrite the output file if present"""), _Option(["-h", "h"], """Use the lines of FILE as '@' headers to be copied to out.bam""", filename=True, equate=False, checker_function=lambda x: isinstance(x, str)), _Option(["-R", "R"], "Merge files in the specified region indicated by STR", equate=False, checker_function=lambda x: isinstance(x, str)), _Argument(["output_bam", "out_bam", "out", "output"], "Output BAM file", filename=True, is_required=True), _ArgumentList(["input_bam", "in_bam", "input", "bam"], "Input BAM", filename=True, is_required=True), ] AbstractCommandline.__init__(self, cmd, **kwargs)
def __init__(self, cmd="samtools", **kwargs): self.program_name = cmd self.parameters = [ _StaticArgument("cat"), _Option(["-h", "h"], "Header SAM file", filename=True, equate=False, checker_function=lambda x: isinstance(x, str)), _Option(["-o", "o"], "Output SAM file", filename=True, equate=False, checker_function=lambda x: isinstance(x, str)), _ArgumentList(["input", "input_bam", "bams"], "Input BAM files", filename=True, is_required=True) ] AbstractCommandline.__init__(self, cmd, **kwargs)
def __init__(self, cmd="samtools", **kwargs): self.program_name = cmd self.parameters = [ _StaticArgument("mpileup"), _Switch(["-E", "E"], """Extended BAQ computation. This option helps sensitivity especially for MNPs, but may hurt specificity a little bit"""), _Switch(["-B", "B"], """Disable probabilistic realignment for the computation of base alignment quality (BAQ). BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments"""), _Switch(["-g", "g"], """Compute genotype likelihoods and output them in the binary call format (BCF)"""), _Switch(["-u", "u"], """Similar to -g except that the output is uncompressed BCF, which is preferred for piping"""), _Option(["-C", "C"], """Coefficient for downgrading mapping quality for reads containing excessive mismatches. Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50""", equate=False, checker_function=lambda x: isinstance(x, int)), _Option(["-r", "r"], "Only generate pileup in region STR", equate=False, checker_function=lambda x: isinstance(x, str)), _Option(["-f", "f"], """The faidx-indexed reference file in the FASTA format. The file can be optionally compressed by razip""", filename=True, equate=False, checker_function=lambda x: isinstance(x, str)), _Option(["-l", "l"], """BED or position list file containing a list of regions or sites where pileup or BCF should be generated""", filename=True, equate=False, checker_function=lambda x: isinstance(x, str)), _Option(["-M", "M"], "Cap Mapping Quality at M", equate=False, checker_function=lambda x: isinstance(x, int)), _Option(["-q", "q"], "Minimum mapping quality for an alignment to be used", equate=False, checker_function=lambda x: isinstance(x, int)), _Option(["-Q", "Q"], "Minimum base quality for a base to be considered", equate=False, checker_function=lambda x: isinstance(x, int)), _Switch(["-6", "illumina_13"], "Assume the quality is in the Illumina 1.3+ encoding"), _Switch(["-A", "A"], "Do not skip anomalous read pairs in variant calling."), _Option(["-b", "b"], "List of input BAM files, one file per line", filename=True, equate=False, checker_function=lambda x: isinstance(x, str)), _Option(["-d", "d"], "At a position, read maximally INT reads per input BAM", equate=False, checker_function=lambda x: isinstance(x, int)), _Switch(["-D", "D"], "Output per-sample read depth"), _Switch(["-S", "S"], """Output per-sample Phred-scaled strand bias P-value"""), _Option(["-e", "e"], """Phred-scaled gap extension sequencing error probability. Reducing INT leads to longer indels""", equate=False, checker_function=lambda x: isinstance(x, int)), _Option(["-h", "h"], """Coefficient for modeling homopolymer errors. Given an l-long homopolymer run, the sequencing error of an indel of size s is modeled as INT*s/l""", equate=False, checker_function=lambda x: isinstance(x, int)), _Switch(["-I", "I"], "Do not perform INDEL calling"), _Option(["-L", "L"], """Skip INDEL calling if the average per-sample depth is above INT""", equate=False, checker_function=lambda x: isinstance(x, int)), _Option(["-o", "o"], """Phred-scaled gap open sequencing error probability. Reducing INT leads to more indel calls.""", equate=False, checker_function=lambda x: isinstance(x, int)), _Option(["-p", "p"], """Comma delimited list of platforms (determined by @RG-PL) from which indel candidates are obtained. It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA""", equate=False, checker_function=lambda x: isinstance(x, str)), _ArgumentList(["input_file"], "Input File for generating mpileup", filename=True, is_required=True), ] AbstractCommandline.__init__(self, cmd, **kwargs)