/// <summary>
/// Method to merge higher-indexed item with new constructed contig.
/// Merges consumed contig with new contig. For each sequence in consumed contig,
/// compute sequence and offset to be added to new contig.
/// </summary>
/// <param name="newContig">New contig for merging</param>
/// <param name="globalBest">Best Score, consensus, their offsets</param>
/// <param name="consumedContig">Consumed Contig to be merged</param>
private static void MergeHigherIndexedContig(Contig newContig, ItemScore globalBest, Contig consumedContig)
{
foreach (Contig.AssembledSequence aseq in consumedContig.Sequences)
{
Contig.AssembledSequence newASeq = new Contig.AssembledSequence();
// as the higher-index item, this contig is never reversed or complemented, so:
newASeq.IsReversed = aseq.IsReversed;
newASeq.IsComplemented = aseq.IsComplemented;
// position in the new contig adjusted by alignment of the merged items.
newASeq.Position = globalBest.SecondOffset + aseq.Position;
newASeq.Sequence = SequenceWithoutTerminalGaps(aseq.Sequence);
newContig.Sequences.Add(newASeq);
if (Trace.Want(Trace.AssemblyDetails))
{
ApplicationLog.WriteLine(
"\tseq (rev = {0} comp = {1} pos = {2}) {3}",
newASeq.IsReversed,
newASeq.IsComplemented,
newASeq.Position,
newASeq.Sequence);
}
}
}
/// <summary>
/// Method to merge higher-indexed item with new constructed contig.
/// Merges consumed sequence with new contig. For the consumed sequence,
/// compute new sequence and offset to be added to new contig.
/// </summary>
/// <param name="newContig">New contig for merging</param>
/// <param name="globalBest">Best Score, consensus, their offsets</param>
/// <param name="consumedSequence">Consumed Sequence to be merged</param>
private static void MergeHigherIndexedSequence(Contig newContig, ItemScore globalBest, ISequence consumedSequence)
{
Contig.AssembledSequence newASeq = new Contig.AssembledSequence();
// as the higher-index item, this sequence is never reversed or complemented, so:
newASeq.IsReversed = false;
newASeq.IsComplemented = false;
newASeq.Position = globalBest.SecondOffset;
newASeq.Sequence = SequenceWithoutTerminalGaps(consumedSequence);
newContig.Sequences.Add(newASeq);
if (Trace.Want(Trace.AssemblyDetails))
{
ApplicationLog.WriteLine(
"seq (rev = {0} comp = {1} pos = {2}) {3}",
newASeq.IsReversed,
newASeq.IsComplemented,
newASeq.Position,
newASeq.Sequence);
}
}
/// <summary>
/// Method to merge lower-indexed item with new constructed contig
/// Merges consumed sequence with new contig. For the consumed sequence,
/// compute new sequence and offset to be added to new contig.
/// </summary>
/// <param name="newContig">New contig for merging</param>
/// <param name="globalBest">Best Score, consensus, their offsets</param>
/// <param name="consumedSequence">Consumed Sequence to be merged</param>
private static void MergeLowerIndexedSequence(Contig newContig, ItemScore globalBest, ISequence consumedSequence)
{
Contig.AssembledSequence newASeq = new Contig.AssembledSequence();
// lower-indexed item might be reversed or complemented.
// Retreive information from globalBest
newASeq.IsReversed = globalBest.Reversed;
newASeq.IsComplemented = globalBest.Complemented;
newASeq.Position = globalBest.FirstOffset;
newASeq.Sequence = SequenceWithoutTerminalGaps(consumedSequence);
newContig.Sequences.Add(newASeq);
if (Trace.Want(Trace.AssemblyDetails))
{
ApplicationLog.WriteLine(
"seq (rev = {0} comp = {1} pos = {2}) {3}",
newASeq.IsReversed,
newASeq.IsComplemented,
newASeq.Position,
newASeq.Sequence);
}
}
/// <summary>
/// Method to merge lower-indexed item with new constructed contig.
/// Merges consumed contig with new contig. For each sequence in consumed contig,
/// compute sequence and offset to be added to new contig.
/// </summary>
/// <param name="newContig">New contig for merging</param>
/// <param name="globalBest">Best Score along with offsets information</param>
/// <param name="consumedContig">Contig to be merged</param>
private static void MergeLowerIndexedContig(Contig newContig, ItemScore globalBest, Contig consumedContig)
{
foreach (Contig.AssembledSequence aseq in consumedContig.Sequences)
{
Contig.AssembledSequence newASeq = new Contig.AssembledSequence();
// lower-indexed item might be reversed or complemented.
// Construct new sequence based on setting in globalBest
// reverse of reverse, or comp of comp, equals no-op. So use xor
newASeq.IsReversed = aseq.IsReversed ^ globalBest.Reversed;
newASeq.IsComplemented = aseq.IsComplemented ^ globalBest.Complemented;
// position in the new contig is adjusted by alignment of the merged items.
// this depends on whether the contig is reverse-aligned.
if (globalBest.Reversed)
{
int rightOffset = consumedContig.Length - (aseq.Sequence.Count + aseq.Position);
newASeq.Position = globalBest.FirstOffset + rightOffset;
}
else
{
newASeq.Position = globalBest.FirstOffset + aseq.Position;
}
newASeq.Sequence = SequenceWithoutTerminalGaps(aseq.Sequence);
newContig.Sequences.Add(newASeq);
if (Trace.Want(Trace.AssemblyDetails))
{
ApplicationLog.WriteLine(
"\tseq (rev = {0} comp = {1} pos = {2}) {3}",
newASeq.IsReversed,
newASeq.IsComplemented,
newASeq.Position,
newASeq.Sequence);
}
}
}