/// <summary>
/// Constructor of SAMAlignedItemCandidateBuilder
/// </summary>
public SAMAlignedItemCandidateGsnapBuilder(ISAMAlignedItemParserOptions options, Dictionary <char, char> mutations = null, char[] validMutations = null)
: base(options)
{
if (mutations == null)
{
this.mutations = new Dictionary <char, char>();
this.mutations['C'] = 'T';
this.mutations['G'] = 'A';
}
else
{
this.mutations = mutations;
}
if (validMutations == null)
{
if (mutations == null)
{
this.validMutations = new HashSet <char>(new char[] { 'C' });
}
else
{
this.validMutations = new HashSet <char>(mutations.Keys);
}
}
else
{
this.validMutations = new HashSet <char>(validMutations);
}
}
/// <summary>
/// Constructor of SAMAlignedItemCandidateBuilder
/// </summary>
/// <param name="engineType">1:bowtie1, 2:bowtie2, 3:bwa</param>
public AbstractSAMAlignedItemCandidateBuilder(int engineType)
{
this._options = new SAMAlignedItemParserOptions()
{
EngineType = engineType,
MaximumMismatch = int.MaxValue,
MinimumReadLength = 0
};
}
public SAMAlignedItemBestScoreCandidateBuilder(ISAMAlignedItemParserOptions options) : base(options)
{
}
public AbstractSAMAlignedItemCandidateBuilder(ISAMAlignedItemParserOptions options)
{
this._options = options;
}
public SAMAlignedItemCandidateFilterBuilder(ISAMAlignedItemParserOptions options, ISAMAlignedItemParsingFilter filter)
: base(options)
{
this._filter = filter;
}
