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samtools · Aug 16, 2023 · 583e0f3 · 583e0f3
1 parent db71294
commit 583e0f3
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Showing 4 changed files with 14 additions and 13 deletions.
diff --git a/src/main/java/htsjdk/samtools/SAMUtils.java b/src/main/java/htsjdk/samtools/SAMUtils.java
@@ -25,12 +25,16 @@
 
 import htsjdk.samtools.seekablestream.SeekablePathStream;
 import htsjdk.samtools.seekablestream.SeekableStream;
-import htsjdk.samtools.util.*;
+import htsjdk.samtools.util.BinaryCodec;
+import htsjdk.samtools.util.CigarUtil;
+import htsjdk.samtools.util.CloserUtil;
+import htsjdk.samtools.util.CoordMath;
+import htsjdk.samtools.util.RuntimeEOFException;
+import htsjdk.samtools.util.StringUtil;
 import htsjdk.tribble.annotation.Strand;
 
 import java.io.File;
 import java.io.IOException;
-import java.io.InputStream;
 import java.io.UnsupportedEncodingException;
 import java.math.BigInteger;
 import java.nio.file.Path;
@@ -675,7 +679,6 @@ public static int combineMapqs(int m1, int m2) {
 
     }
 
-    // tsato: to delete
     public static long findVirtualOffsetOfFirstRecordInBam(final Path bamFile) {
         try {
             SeekableStream ss = new SeekablePathStream(bamFile);

diff --git a/src/main/java/htsjdk/samtools/SamReader.java b/src/main/java/htsjdk/samtools/SamReader.java
@@ -593,7 +593,7 @@ public SAMRecord next() {
                 final SAMRecord previous = checker.getPreviousRecord();
                 if (!checker.isSorted(result)) {
                     throw new IllegalStateException(String.format(
-                            "Record %s should come after %s when sorting with %s ordering.", // tsato: why doesn't this code get triggered when you have a bad sort order?
+                            "Record %s should come after %s when sorting with %s ordering.",
                             previous.getSAMString().trim(),
                             result.getSAMString().trim(), checker.getSortOrder()));
                 }

diff --git a/src/main/java/htsjdk/samtools/filter/FilteringSamIterator.java b/src/main/java/htsjdk/samtools/filter/FilteringSamIterator.java
@@ -60,9 +60,9 @@ public class FilteringSamIterator implements CloseableIterator<SAMRecord> {
     public FilteringSamIterator(final Iterator<SAMRecord> iterator, final SamRecordFilter filter,
                                 final boolean filterByPair) {
 
-        if (filterByPair && iterator instanceof SAMRecordIterator) { // tsato: this whole thing has code smell
-            ((SAMRecordIterator)iterator).assertSorted(SAMFileHeader.SortOrder.queryname); // tsato: wtf is this?
-        } // tsato: this does not throw an error here if the sort order is mismatched...bizarre.
+        if (filterByPair && iterator instanceof SAMRecordIterator) {
+            ((SAMRecordIterator)iterator).assertSorted(SAMFileHeader.SortOrder.queryname);
+        }
 
         this.iterator = new PeekableIterator<SAMRecord>(iterator);
         this.filter = filter;
@@ -137,7 +137,7 @@ private SAMRecord getNextRecord() {
             if (filterReadPairs && record.getReadPairedFlag() && record.getFirstOfPairFlag() &&
                 iterator.hasNext()) {
 
-                SamPairUtil.assertMate(record, iterator.peek()); // tsato: why is the code complaining?
+                SamPairUtil.assertMate(record, iterator.peek());
 
                 if (filter.filterOut(record, iterator.peek())) {
                     // skip second read
@@ -148,7 +148,7 @@ private SAMRecord getNextRecord() {
             } else if (filterReadPairs && record.getReadPairedFlag() &&
                 record.getSecondOfPairFlag()) {
                 // assume that we did a pass(first, second) and it passed the filter
-                return record; // tsato: doesn't the first of pair always appear first if queryname sorted?
+                return record;
             } else if (!filter.filterOut(record)) {
                 return record;
             }

diff --git a/src/main/java/htsjdk/samtools/util/BlockCompressedInputStream.java b/src/main/java/htsjdk/samtools/util/BlockCompressedInputStream.java
@@ -704,13 +704,11 @@ static void readFully(SeekableByteChannel channel, ByteBuffer dst) throws IOExce
         }
     }
 
+    @Deprecated
     public static void assertNonDefectiveFile(final File file) throws IOException {
-        if (checkTermination(file) == FileTermination.DEFECTIVE) {
-            throw new SAMException(file.getAbsolutePath() + " does not have a valid GZIP block at the end of the file.");
-        }
+        assertNonDefectivePath(file.toPath());
     }
 
-    // tsato: can I consolidate with above?
     public static void assertNonDefectivePath(final Path file) throws IOException {
         if (checkTermination(file) == FileTermination.DEFECTIVE) {
             throw new SAMException(file.toUri() + " does not have a valid GZIP block at the end of the file.");