/// <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) { long 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); } } }
/// <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 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 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) { long 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); } } }