private int WritePositionBlocks(Stream jsonStream, Stream jasixStream,
BinaryWriter writer)
{
var blockCount = 0;
using (var reader = new BgzBlockReader(jsonStream, true))
using (var jasixIndex = new JasixIndex(jasixStream))
{
var positionSectionBegin = jasixIndex.GetSectionBegin(JasixCommons.PositionsSectionTag);
if (positionSectionBegin == -1)
{
return(0); //no positions found. and therefore, cannot have genes either.
}
var positionSectionEnd = jasixIndex.GetSectionEnd(JasixCommons.PositionsSectionTag);
var geneSectionBegin = jasixIndex.GetSectionBegin(JasixCommons.GenesSectionTag);
var isFirstBlock = true;
for (int count = reader.ReadCompressedBlock(BgzBlock); count > 0; count = reader.ReadCompressedBlock(BgzBlock))
{
if (isFirstBlock)
{
if (_isFirstHeaderBlock)
{
writer.Write(BgzBlock, 0, count);
_isFirstHeaderBlock = false;
}
isFirstBlock = false;
continue;
}
//we need the following check because there is one block between the positions and the genes block that we want to skip
// the block that contains: ],"genes":[...
// the 16 bit left shift is due to the representation of the position in bgzip file
if (reader.Position >= positionSectionEnd >> 16)
{
//we have read the last position block
blockCount++;
writer.Write(BgzBlock, 0, count);
if (geneSectionBegin != -1)
{
jsonStream.Position = geneSectionBegin >> 16;
}
return(blockCount);
}
blockCount++;
writer.Write(BgzBlock, 0, count);
}
}
return(blockCount);
}
private static int WritePositionBlocks(Stream jsonStream, Stream jasixStream,
BinaryWriter writer)
{
var blockCount = 0;
using (var reader = new BgzBlockReader(jsonStream, true))
using (var jasixIndex = new JasixIndex(jasixStream))
{
int count;
var isFirstBlock = true;
var positionSectionBegin = jasixIndex.GetSectionBegin(JasixCommons.PositionsSectionTag);
var geneSectionBegin = jasixIndex.GetSectionBegin(JasixCommons.GenesSectionTag);
var geneSectionEnd = jasixIndex.GetSectionEnd(JasixCommons.GenesSectionTag);
do
{
count = reader.ReadCompressedBlock(BgzBlock);
if (isFirstBlock)
{
if (_isFirstHeaderBlock)
{
writer.Write(BgzBlock, 0, count);
_isFirstHeaderBlock = false;
}
isFirstBlock = false;
}
else
{
if (count <= 0)
{
continue;
}
// the 16 bit left shift is due to the format of bgzip file
if (reader.Position << 16 > geneSectionBegin && reader.Position << 16 <= geneSectionEnd)
{
//setting back the stream to the gene section begin
jsonStream.Position = geneSectionBegin >> 16;
return(blockCount);
}
if (reader.Position << 16 <= positionSectionBegin ||
reader.Position << 16 >= geneSectionBegin)
{
continue;
}
blockCount++;
writer.Write(BgzBlock, 0, count);
}
} while (count > 0);
}
return(blockCount);
}
public void Begin_end_section_and_readback()
{
var index = new JasixIndex();
const string section = "section1";
index.BeginSection(section, 0);
Assert.Throws <UserErrorException>(() => index.BeginSection(section, 1));
index.EndSection(section, 100);
Assert.Throws <UserErrorException>(() => index.EndSection(section, 101));
Assert.Equal(0, index.GetSectionBegin(section));
Assert.Equal(100, index.GetSectionEnd(section));
}