public override void Write(BlamLib.IO.EndianWriter s)
{
s.Write(ulong.MinValue);
Count.Write(s);
Size.Write(s);
OffsetReferences.Write(s);
OffsetStrings.Write(s);
s.Write(uint.MinValue);
}
public override void Read(BlamLib.IO.EndianReader s)
{
s.Seek(4 + 4, System.IO.SeekOrigin.Current);
Count.Read(s);
Size.Read(s);
OffsetReferences.Read(s);
OffsetStrings.Read(s);
s.Seek(1 + 3, System.IO.SeekOrigin.Current);
}
public override bool PrepareOptions()
{
var result = base.PrepareOptions();
long value;
if (OffsetStrings.Any(l => !long.TryParse(l, out value)))
{
ParsingErrors.Add(string.Format("Offsets error {0}.", OffsetStrings.Merge(",")));
}
foreach (var file in this.InputFiles)
{
if (!File.Exists(file))
{
ParsingErrors.Add(string.Format("Input file not exists {0}.", file));
}
}
if (!File.Exists(this.CoordinateFile))
{
ParsingErrors.Add(string.Format("Coordinate file not exists {0}.", this.CoordinateFile));
}
if (!string.IsNullOrEmpty(this.FastaFile) && !File.Exists(this.FastaFile))
{
ParsingErrors.Add(string.Format("Fasta file not exists {0}.", this.FastaFile));
}
if (!string.IsNullOrEmpty(this.ExcludeXml) && !File.Exists(this.ExcludeXml))
{
ParsingErrors.Add(string.Format("Exclude xml file not exists {0}.", this.ExcludeXml));
}
if (!string.IsNullOrEmpty(this.FastqFile) && !File.Exists(this.FastqFile))
{
ParsingErrors.Add(string.Format("Fastq file not exists {0}.", this.FastqFile));
}
if (this.OffsetStrings == null || this.OffsetStrings.Count == 0)
{
this.OffsetStrings = DEFAULT_Offsets.ToList();
}
return(result && ParsingErrors.Count == 0);
}
