public static List <string> GetChromosomes(string filename)
{
var headers = new BAMWindowReader(filename).ReadHeaders();
return((from h in headers
where h.StartsWith("@SQ")
select h.StringAfter("SN:").StringBefore("\t")).ToList());
}
public void Test()
{
var bamfile = "../../../data/small.bam";
Assert.IsTrue(SAMUtils.IsSortedByCoordinate(bamfile));
var reader = new BAMWindowReader(bamfile);
var lines = reader.ReadHeaders();
Assert.IsTrue(lines.First().StartsWith("@HD"));
Assert.IsTrue(lines.Last().StartsWith("@PG"));
var sam = reader.ReadSAMAlignedSequence();
Assert.IsNotNull(sam);
Assert.AreEqual("HWI-ST829:174:C1A0GACXX:5:1108:12447:66009", sam.QName);
Assert.AreEqual("HWI-ST829:174:C1A0GACXX:5:1108:12447:66009 256 chr1 3020293 0 101M * 0 0 GTCTACCTTTTCAGGTGTGTTAGGGTGCCCTGGACTGGGCGAAGTGGGTGTTCTGGGTTCTGATGATGGTGAGTGGTCCTGGTTTCTGTTAGTAGGATTCT CCCFFFFFHHHHDGI?ECFEHIGIJFEHIGEHHEGIIIGDHFFGFGIGHIHGJJJJH=CEFFCFFDFEECCCEDDBCCDDCCACDDDDDDCDCDDDCCDCC AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:101 YT:Z:UU NH:i:10 CC:Z:= CP:i:86775490 HI:i:0", reader.SAMToString(sam));
}
public static ISAMFile GetReader(string filename, bool skipHeaders = false)
{
ISAMFile result = null;
if (SAMUtils.IsBAMFile(filename) && !SystemUtils.IsLinux)
{
result = new BAMWindowReader(filename);
}
else
{
result = new SAMLinuxReader("samtools", filename);
}
if (skipHeaders)
{
result.ReadHeaders();
}
return result;
}
public static ISAMFile GetReader(string filename, bool skipHeaders = false, string rangeInBedFile = null)
{
ISAMFile result = null;
if (SAMUtils.IsBAMFile(filename) && !SystemUtils.IsLinux)
{
result = new BAMWindowReader(filename);
}
else
{
result = new SAMLinuxReader("samtools", filename, rangeInBedFile);
}
if (skipHeaders)
{
result.ReadHeaders();
}
return(result);
}
