private void AddStatusInfo(BamAlignment origBamAlignment, List <PreIndel> selectedIndels, List <PreIndel> existingIndels,
RealignmentResult realignResult, BamAlignment bamAlignment, bool hasExistingUnsanctionedIndels,
AlignmentSummary originalAlignmentSummary)
{
_statusCounter.AddStatusCount("INDEL STATUS\tAccepted\t" + realignResult.Indels);
_statusCounter.AddStatusCount($"Successfully realigned (ps: {selectedIndels != null})");
_statusCounter.AppendStatusStringTag("RX",
$"Successfully realigned after {realignResult.Attempts} attempts, indel is {string.Join("|", realignResult.AcceptedIndels)}",
bamAlignment);
if (existingIndels != null && existingIndels.Any())
{
_statusCounter.AppendStatusStringTag("RX",
$"Orig indels:{string.Join("|", existingIndels)}__New indels:{realignResult.Indels}",
bamAlignment);
_statusCounter.AddStatusCount(
$"Replaced existing indels (nonsanctioned: {hasExistingUnsanctionedIndels})");
}
bamAlignment.ReplaceOrAddStringTag("OC", $"{origBamAlignment.CigarData}");
bamAlignment.ReplaceOrAddStringTag("OS",
$"{originalAlignmentSummary.NumMatches}M-{originalAlignmentSummary.NumNonNSoftclips}S-{originalAlignmentSummary.NumMismatches}X-{originalAlignmentSummary.NumMismatchesIncludeSoftclip}x-{originalAlignmentSummary.NumInsertedBases}i-{originalAlignmentSummary.NumIndels}Z-{originalAlignmentSummary.SumOfMismatchingQualities}Q");
bamAlignment.ReplaceOrAddStringTag("RS",
$"{realignResult.NumMatches}M-{realignResult.NumNonNSoftclips}S-{realignResult.NumMismatches}X-{realignResult.NumMismatchesIncludeSoftclip}x-{realignResult.NumInsertedBases}i-{realignResult.NumIndels}Z-{realignResult.SumOfMismatchingQualities}Q");
}
private static void AddMdTagCountsTags(BamAlignment bamAlignment, PairResult pairResult)
{
if (pairResult.md1.IsSet)
{
bamAlignment.ReplaceOrAddStringTag("XM",
$"A: {pairResult.md1.A},{pairResult.md2.A}; T: {pairResult.md1.T},{pairResult.md2.T}; C: {pairResult.md1.C},{pairResult.md2.C}; G: {pairResult.md1.G},{pairResult.md2.G}; subA: {pairResult.md1.SubA},{pairResult.md2.SubA}; subT: {pairResult.md1.SubT},{pairResult.md2.SubT}; subC: {pairResult.md1.SubC},{pairResult.md2.SubC}; subG: {pairResult.md1.SubG},{pairResult.md2.SubG}; subN: {pairResult.md1.SubN},{pairResult.md2.SubN}; maxRun: {pairResult.md1.RunLength},{pairResult.md2.RunLength}; numRuns: {pairResult.md1.NumInRuns},{pairResult.md2.NumInRuns}");
}
else
{
bamAlignment.ReplaceOrAddStringTag("XM", $"Not set");
}
}
public void AddCombinedStatusStringTags()
{
var counter = new ReadStatusCounter();
var handler = new DebugSummaryStatusHandler(counter);
var pair = TestHelpers.GetPair("10M", "10M");
pair.Read1.ReplaceOrAddStringTag("HI", "read1_hi");
pair.Read2.ReplaceOrAddStringTag("HI", "read2_hi");
var outAlignment = new BamAlignment(pair.Read1);
outAlignment.ReplaceOrAddStringTag("HI", "nothing");
// Should not update
handler.AddCombinedStatusStringTags("HI", pair.Read1, pair.Read2, outAlignment);
Assert.Equal("nothing", outAlignment.GetStringTag("HI"));
}
public void AddCombinedStatusStringTags(string tagName, BamAlignment alignment1, BamAlignment alignment2, BamAlignment outAlignment)
{
outAlignment.ReplaceOrAddStringTag(tagName,
alignment1.GetStringTag(tagName) + "," + alignment2.GetStringTag(tagName));
}
public void UpdateStatusStringTag(string tagName, string tagValue, BamAlignment alignment)
{
alignment.ReplaceOrAddStringTag(tagName, tagValue);
}
public void AppendStatusStringTag(string tagName, string tagValue, BamAlignment alignment)
{
// TODO if there is not already a tag, don't add the comma, it's confusing
alignment.ReplaceOrAddStringTag(tagName, alignment.GetStringTag(tagName) + "," + tagValue);
}