- issueEOF
Write an end-of-file marker to the OutputStream. The specific EOF marker is
chosen based on the CRAM
- writeHeader
Write a CRAM File header and a SAM Header to an output stream.
- readCramHeader
Read CRAM header from the given InputStream.
- writeCramHeader
Writes CRAM header into the specified OutputStream.
- checkEOF
Check if the SeekableStream is properly terminated with a end-of-file marker.
- readFormatDefinition
- readSAMFileHeader
- replaceCramHeader
Attempt to replace the SAM file header in the CRAM file. This will succeed only
if there is sufficie
- toByteArray
- writeContainerForSamFileHeader
- checkHeaderAndEOF
Check if the file: 1) contains proper CRAM header. 2) given the version info
from the header check t