Esempio n. 1
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 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)
Esempio n. 2
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 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)
Esempio n. 3
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    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)
Esempio n. 4
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 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)
Esempio n. 5
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    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)
Esempio n. 6
0
    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)