public void IntervalJumping_Ends()
{
var smallBam = Path.Combine(UnitTestPaths.TestDataDirectory, "Ins-L3-var12_S12.bam");
var intervals = new Dictionary <string, List <Region> >();
var chrIntervals = new List <Region>
{
new Region(28608100, 28608100), // interval in the middle of coverage
new Region(29608700, 29608800) // interval out in the boonies where there's no data
};
intervals.Add("chr13", chrIntervals);
var extractor = new BamFileAlignmentExtractor(smallBam, bamIntervals: intervals);
var read = new Read();
var numReadsLessThan = 0;
var numReadsGreaterThan = 0;
// verify we are always moving forward and not backwards (not re-reading alignments)
while (extractor.GetNextAlignment(read))
{
if (read.EndPosition + 1 < 28608100) // bam reader is off by one, see note in BamFileExtractor.Jump
{
numReadsLessThan++;
}
else if (read.Position > 28608100)
{
numReadsGreaterThan++;
}
}
Assert.Equal(1, numReadsLessThan); // this should be just the first read (before we figure out we're not in range)
Assert.Equal(0, numReadsGreaterThan);
}
private void ReadFileTest(string bamfile, int expectedReads, bool bamHasXc)
{
var extractor = new BamFileAlignmentExtractor(bamfile);
var read = new Read();
var lastPosition = -1;
var numReads = 0;
bool hasAnyStitchedCigars = false;
while (extractor.GetNextAlignment(read))
{
Assert.True(read.Position >= lastPosition); // make sure reads are read in order
Assert.False(string.IsNullOrEmpty(read.Name));
Assert.False(string.IsNullOrEmpty(read.Chromosome));
if (!bamHasXc)
{
Assert.Equal(null, read.StitchedCigar);
}
if (read.StitchedCigar != null && read.StitchedCigar.Count > 0)
{
hasAnyStitchedCigars = true;
}
lastPosition = read.Position;
numReads++;
}
if (bamHasXc)
{
Assert.True(hasAnyStitchedCigars);
}
Assert.Equal(expectedReads, numReads);
extractor.Dispose();
// make sure can't read after dispose
Assert.Throws <IOException>(() => extractor.GetNextAlignment(read));
}
public void UnalignedReads()
{
var extractor = new BamFileAlignmentExtractor(Path.Combine(TestPaths.LocalTestDataDirectory, "unaligned.bam"));
var read = new Read();
var count = 0;
while (extractor.GetNextAlignment(read))
{
count++;
}
Assert.Equal(138826, count);
Assert.Equal(null, read.Chromosome); // last reads are unaligned
}
public void ReadFileAsStitched()
{
var smallBam = Path.Combine(TestPaths.LocalTestDataDirectory, "small.bam");
//we claim its not stitched
var extractor = new BamFileAlignmentExtractor(smallBam, false);
var read = new Read();
extractor.GetNextAlignment(read);
Assert.False(extractor.SourceIsStitched);
//we claim its stitched
extractor = new BamFileAlignmentExtractor(smallBam, true);
read = new Read();
extractor.GetNextAlignment(read);
Assert.True(extractor.SourceIsStitched);
}
public void IntervalJumping_Boundaries()
{
var smallBam = Path.Combine(UnitTestPaths.TestDataDirectory, "Ins-L3-var12_S12.bam");
var intervals = new Dictionary <string, List <Region> >();
var chrIntervals = new List <Region>
{
new Region(115169880, 115169880) // feeding in an interval that's past reference max shouldnt cause it to blow up
};
intervals.Add("chr13", chrIntervals);
var extractor = new BamFileAlignmentExtractor(smallBam, bamIntervals: intervals);
var read = new Read();
while (extractor.GetNextAlignment(read))
{
}
}
public void IntervalJumping_Middle()
{
var smallBam = Path.Combine(UnitTestPaths.TestDataDirectory, "Ins-L3-var12_S12.bam");
var intervals = new Dictionary <string, List <Region> >();
var chrIntervals = new List <Region>
{
new Region(28607838, 28607838),
new Region(28608631, 28608631)
};
intervals.Add("chr13", chrIntervals);
var extractor = new BamFileAlignmentExtractor(smallBam, bamIntervals: intervals);
var read = new Read();
// verify we skip over the middle
while (extractor.GetNextAlignment(read))
{
Assert.True(read.Position < 28607840 || read.BamAlignment.GetEndPosition() >= 28608631);
}
}
public void IntervalJumping_SmallIntervals()
{
var smallBam = Path.Combine(UnitTestPaths.TestDataDirectory, "Ins-L3-var12_S12.bam");
var intervals = new Dictionary <string, List <Region> >();
var chrIntervals = new List <Region>
{
new Region(28607838, 28607838),
new Region(28607908, 28607908),
new Region(28608631, 28608631)
};
intervals.Add("chr13", chrIntervals);
var extractor = new BamFileAlignmentExtractor(smallBam, bamIntervals: intervals);
var read = new Read();
var lastPosition = 0;
// verify we are always moving forward and not backwards (not re-reading alignments)
while (extractor.GetNextAlignment(read))
{
Assert.True(read.Position >= lastPosition);
lastPosition = read.Position;
}
}
