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Description: use correct SamReader API
Author: Sascha Steinbiss <satta@debian.org>
--- a/uk/ac/babraham/FastQC/Sequence/BAMFile.java
+++ b/uk/ac/babraham/FastQC/Sequence/BAMFile.java
@@ -27,7 +27,9 @@
import htsjdk.samtools.CigarElement;
import htsjdk.samtools.CigarOperator;
-import htsjdk.samtools.SAMFileReader;
+import htsjdk.samtools.SamInputResource;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
import htsjdk.samtools.SAMFormatException;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.ValidationStringency;
@@ -44,7 +46,7 @@
// only way to access the file pointer.
private FileInputStream fis;
- private SAMFileReader br;
+ private SamReader br;
private String name;
private Sequence nextSequence = null;
Iterator<SAMRecord> it;
@@ -56,11 +58,12 @@
name = file.getName();
this.onlyMapped = onlyMapped;
- SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
-
fis = new FileInputStream(file);
-
- br = new SAMFileReader(fis);
+
+ SamInputResource sir = SamInputResource.of(fis);
+ SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+
+ br = srf.open(sir);
it = br.iterator();
readNext();
@@ -135,7 +138,7 @@
// through the file.
if (recordSize == 0) {
recordSize = (record.getReadLength()*2)+150;
- if (br.isBinary()) {
+ if (br.type() == SamReader.Type.BAM_TYPE || br.type() == SamReader.Type.CRAM_TYPE) {
recordSize /= 4;
}
}
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