Bases: TASSELpy.java.lang.Object.Object
Provides DNA read depth data for a genotype data
Methods
| castTo(pyType) | Casts this object to another java/python type |
| clone(*args) | Creates and returns a copy of this object |
| depth(*args) | Returns total depth for given taxon and site |
| depthAllSitesByte(*args) | Returns allele depths for all alleles and sites for a taxon in byte format |
| depthForAllele(*args) | Returns depth count for given allele at given taxon and site |
| depthForAlleleByte(*args) | Returns depth count as byte for given allele at given taxon and site |
| depthForAlleles(*args) | Returns depth count for each diploid allele at the given taxon and site The array of depths is sizes as determined by NUMBER_NUCLEOTIDE_ALLELES (6) and it is ordered as in NUCLEOTIDE_ALLELES (A, C, G, T, +(insertion), - (deletion)) The depths from 0 to 127 are recorded exactly. |
| depthForSite(*args) | Returns total depth of all alleles and taxa for given site |
| depthForTaxon(*args) | Returns total depth of all alleles and sites for given taxon |
| equals(*args) | Indicates whether some other object is “equal to” this one |
| getArray(size) | Gets an empty wrapped java array that can accept the type of the wrapped |
| getClass(*args) | Returns the runtime class of this Object. |
| getDblArray(rows[, cols]) | Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e. |
| hashCode(*args) | Returns a hash code vlaue for the object |
| toString(*args) | Returns a string representation of the object |
| wrap_existing_array(arr_instance) | Wraps a java array of this class’s type |
Returns total depth for given taxon and site
| Signature: | depth (int taxon, int site) |
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| Parameters: |
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| Returns: | total depth |
| Return type: | int |
Returns allele depths for all alleles and sites for a taxon in byte format (negative values are logs)
| Signature: | depthAllSitesByte (int taxon) |
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| Parameters: | taxon (int) – taxon |
| Returns: | Allele depths for all alleles and sites |
| Return type: | byte[][] |
Returns depth count for given allele at given taxon and site
| Signature: | depthForAllele (int taxon, int site, int allele) |
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| Parameters: |
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| Returns: | Count |
| Return type: | int |
Returns depth count as byte for given allele at given taxon and site
| Signature: | depthForAlleleByte (int taxon, int site, int allele) |
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| Parameters: |
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| Returns: | Count as byte |
| Return type: | byte |
Returns depth count for each diploid allele at the given taxon and site The array of depths is sizes as determined by NUMBER_NUCLEOTIDE_ALLELES (6) and it is ordered as in NUCLEOTIDE_ALLELES (A, C, G, T, +(insertion), - (deletion)) The depths from 0 to 127 are recorded exactly. Depths above 127 are stored as approximate logs (equation), and they are represented by negative numbers
| Signature: | depthForAlleles (int taxon, int site) |
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| Parameters: |
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| Returns: | Array of counts |
| Return type: | int[] |