/** * Prints meta-data statistics from BAM index (.bai) file * Statistics include count of aligned and unaligned reads for each reference sequence * and a count of all records with no start coordinate */ static public BAMIndexMetaData[] getIndexStats(final BAMFileReader bam) { AbstractBAMFileIndex index = (AbstractBAMFileIndex) bam.getIndex(); // read through all the bins of every reference. int nRefs = index.getNumberOfReferences(); BAMIndexMetaData[] result = new BAMIndexMetaData[nRefs == 0 ? 1 : nRefs]; for (int i = 0; i < nRefs; i++) { result[i] = index.getMetaData(i); } if (result[0] == null) { result[0] = new BAMIndexMetaData(); } final Long noCoordCount = index.getNoCoordinateCount(); if (noCoordCount != null) // null in old index files without metadata result[0].setNoCoordinateRecordCount(noCoordCount); return result; } }
/** * Prints meta-data statistics from BAM index (.bai) file * Statistics include count of aligned and unaligned reads for each reference sequence * and a count of all records with no start coordinate */ static public BAMIndexMetaData[] getIndexStats(final BAMFileReader bam){ AbstractBAMFileIndex index = (AbstractBAMFileIndex) bam.getIndex(); // read through all the bins of every reference. int nRefs = index.getNumberOfReferences(); BAMIndexMetaData[] result = new BAMIndexMetaData[nRefs == 0 ? 1 : nRefs]; for (int i = 0; i < nRefs; i++) { result[i] = index.getMetaData(i); } if (result[0] == null){ result[0] = new BAMIndexMetaData(); } final Long noCoordCount = index.getNoCoordinateCount(); if (noCoordCount != null) // null in old index files without metadata result[0].setNoCoordinateRecordCount(noCoordCount); return result; } }
/** * Prints meta-data statistics from BAM index (.bai or .csi) file * Statistics include count of aligned and unaligned reads for each reference sequence * and a count of all records with no start coordinate */ static public BAMIndexMetaData[] getIndexStats(final BAMFileReader bam) { AbstractBAMFileIndex index = (AbstractBAMFileIndex) bam.getIndex(); // read through all the bins of every reference. int nRefs = index.getNumberOfReferences(); BAMIndexMetaData[] result = new BAMIndexMetaData[nRefs == 0 ? 1 : nRefs]; for (int i = 0; i < nRefs; i++) { result[i] = index.getMetaData(i); } if (result[0] == null) { result[0] = new BAMIndexMetaData(); } final Long noCoordCount = index.getNoCoordinateCount(); if (noCoordCount != null) // null in old index files without metadata result[0].setNoCoordinateRecordCount(noCoordCount); return result; } }