// String in = "/home/lmose/dev/abra/leftalign.sam";
// String out = "/home/lmose/dev/abra/la.out.sam";
// String ref = "/home/lmose/reference/chr1/chr1.fa";
SAMFileReader reader = new SAMFileReader(new File(in));
SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(
reader.getFileHeader(), false, new File(out));
CompareToReference2 c2r = new CompareToReference2();
c2r.init(ref);
IndelShifter indelShifter = new IndelShifter();
for (SAMRecord read : reader) {
SAMRecord shiftedRead = indelShifter.shiftIndelsLeft(read, c2r);
writer.addAlignment(shiftedRead);
}
writer.close();
reader.close();
}