CSI index support for BAM files #1040

valeriuo · 2017-11-22T16:35:57Z

Description

Adds the ability to read and use CSI indexes for BAM files (no write support, yet). BAI indexes still have priority. Thus, if both .bai and .csi files are present alongside a BAM file, the BAI index will be used.
Includes Bugfix for BAM index bins #1024.

Checklist

Code compiles correctly
New tests covering changes and new functionality
All tests passing
Extended the README / documentation, if necessary
Is not backward compatible (breaks binary or source compatibility)

codecov-io · 2017-11-22T16:48:38Z

Codecov Report

Merging #1040 into master will increase coverage by 0.603%.
The diff coverage is 72.089%.

@@               Coverage Diff               @@
##              master     #1040       +/-   ##
===============================================
+ Coverage     68.336%   68.939%   +0.603%     
- Complexity      8001      8208      +207     
===============================================
  Files            541       546        +5     
  Lines          32681     32971      +290     
  Branches        5536      5558       +22     
===============================================
+ Hits           22333     22730      +397     
+ Misses          8122      7987      -135     
- Partials        2226      2254       +28

Impacted Files	Coverage Δ	Complexity Δ
src/main/java/htsjdk/samtools/BamFileIoUtils.java	`0% <0%> (ø)`	`0 <0> (ø)`	⬇️
...rc/main/java/htsjdk/samtools/BAMIndexMetaData.java	`73.832% <0%> (+19.546%)`	`22 <0> (+5)`	⬆️
...ain/java/htsjdk/samtools/SAMFileWriterFactory.java	`64.189% <100%> (+2.027%)`	`48 <0> (-2)`	⬇️
src/main/java/htsjdk/samtools/SamReader.java	`82.558% <100%> (+1.308%)`	`0 <0> (ø)`	⬇️
src/main/java/htsjdk/samtools/BinWithOffset.java	`100% <100%> (ø)`	`2 <2> (?)`
src/main/java/htsjdk/samtools/BAMFileWriter.java	`65.625% <100%> (ø)`	`16 <0> (ø)`	⬇️
src/main/java/htsjdk/samtools/CRAMFileReader.java	`74.5% <100%> (ø)`	`53 <0> (ø)`	⬇️
...rc/main/java/htsjdk/samtools/BAMFileConstants.java	`80% <100%> (+13.333%)`	`1 <0> (ø)`	⬇️
...n/java/htsjdk/samtools/IndexFileBufferFactory.java	`33.333% <33.333%> (ø)`	`1 <1> (?)`
src/main/java/htsjdk/samtools/SamIndexes.java	`73.077% <42.857%> (-6.923%)`	`13 <0> (+1)`
... and 157 more

lbergelson · 2017-12-13T22:02:40Z

@valeriuo I'm sorry we haven't gotten to this yet. I've been very busy and this is obviously a complicated PR. It's a really valuable PR though, lots of people want CSI support, so we will definitely get around to reviewing it when someone has bandwidth.

valeriuo · 2017-12-19T14:39:45Z

@lbergelson I realize there is a lot of code in here. Some of it is duplicated from AbstractBAMFileIndex class, which I couldn't extend, although that might have seemed like the natural approach.
We could arrange a call, if you need me to present the solution and talk about potential improvements.

yfarjoun · 2018-06-06T19:55:55Z

@lbergelson could this be prioritized, there's a picard PR waiting on it. broadinstitute/picard#998

lbergelson · 2018-06-06T20:17:51Z

@yfarjoun Yes, I was planning on prioritizing this as the next thing after going through a bunch of small stuff that has been in flight for a while.

lbergelson · 2018-06-13T20:30:49Z

@valeriuo I've begun to take a look at this. Sorry for the extremely long delay. Are you still around and interested in helping get this in?

valeriuo · 2018-06-14T08:46:02Z

@lbergelson, definitely.

lbergelson

@valeriuo I'm still looking through this, I just wanted to post what I'd gotten through so you can see what I'm thinking. Almost all of my comments are structural / code style things rather than anything broken about the implementation. It looks pretty good to me, but I'm not super familiar with the indexes, so I may have to come back to you with questions in a bit.

I'm increasingly annoyed by the BAMIndex class hierarchy. It seems like we should be able to implement this as a subclass of AbstractBamIndex, and the fact that it isn't obvious how to do that is problematic. I think we'll need to consider moving some things around.

I haven't taken a serious look at the tests yet, but I suspect I'm going to want to add additional test cases. It looks like you have good unit test coverage, and BamIndexValidator might be checking everything I want, but as a heads up I might want more tests that open bam readers on various combinations of indexes, particularly ones accessible only through nio.Path APIs.

lbergelson · 2018-06-12T15:51:17Z

src/main/java/htsjdk/samtools/AbstractBAMFileIndex.java

-     * @param endPos 1-based end of target region, inclusive.
-     * @return bit set for each bin that may contain SAMRecords in the target region.
-     */
-    protected BitSet regionToBins(final int startPos, final int endPos) {


Instead of deleting this, please deprecate it and have it call through to the preferred one.

lbergelson · 2018-06-12T15:52:35Z

src/main/java/htsjdk/samtools/BAMCSIFileIndex.java

+import java.nio.channels.FileChannel;
+import java.util.*;
+
+public class BAMCSIFileIndex implements BrowseableBAMIndex {


I would rename this to CSIIndex. Although I guess that's a bit like ATMMachine...

lbergelson · 2018-06-13T15:35:10Z

src/main/java/htsjdk/samtools/BAMCSIFileIndex.java

+    @Override
+    public int getLevelForBin(Bin bin) {
+        if(bin == null || bin.getBinNumber() > getMaxBins()) {
+            throw new SAMException("Tried to get level for invalid bin.");


include the invalid value in the error message.

lbergelson · 2018-06-13T15:37:38Z

src/main/java/htsjdk/samtools/BAMCSIFileIndex.java

+    @Override
+    public int getFirstLocusInBin(Bin bin) {
+        if(bin == null || bin.getBinNumber() > getMaxBins()) {
+            throw new SAMException("Tried to get first locus for invalid bin.");


lbergelson · 2018-06-13T18:18:46Z

src/main/java/htsjdk/samtools/BAMCSIFileIndex.java

+    @Override
+    public void close() {}
+
+    private void verifyBAMMagicNumber(final String sourceName) {


this should be renamed to verifyCSIMagicNumer

lbergelson · 2018-06-13T19:35:01Z

src/main/java/htsjdk/samtools/BAMCSIFileIndex.java

+     * Constructors
+     */
+
+    private BAMCSIFileIndex(final SeekableStream stream, final SAMSequenceDictionary dictionary)


I think the constructors should be refactored. I would unify them by a private constructor
private BAMCSIFileIndex(IndexFileBuffer buffer, String Source, SAMSequenceDictionary dictionary) and then have the other constructers call though to that. In the end we want r 3 public constructors.

One that takes SeekableStream as the input, one for Path, and one for File.

Just to clarify, Path would be memory mapped and File would be randomly accessed. Is this what you had in mind?

lbergelson · 2018-06-13T19:45:30Z

src/main/java/htsjdk/samtools/BAMIndexMetaData.java

+     * 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[] getCSIIndexStats(final BAMFileReader bam) {


this needs a test

The index hierarchy is such a mess. I think we should consider restructuring it to some degree to make this method unnecessary.

lbergelson · 2018-06-15T21:37:54Z

src/main/java/htsjdk/samtools/BAMCSIFileIndex.java

+                metaDataSeen = true;
+                continue; // don't create a Bin
+            } else {
+                skipBytes(16 * nChunks);


lets extract a named constant here

lbergelson · 2018-06-15T21:49:43Z

src/main/java/htsjdk/samtools/BAMCSIFileIndex.java

+        return mIndexBuffer.position();
+    }
+
+    private abstract static class IndexFileBuffer {


I don't think we should not duplicate this code. Lets pull out this and the implementers as package protected classes instead. While we're at it we can make this an interface and have it extend Closeable.

lbergelson · 2018-06-15T21:51:10Z

src/main/java/htsjdk/samtools/BAMIndex.java

@@ -34,6 +34,7 @@
 public interface BAMIndex extends Closeable {

    public static final String BAMIndexSuffix = ".bai";
+    public static final String BAMIndexSuffix2 = ".csi";


It bothers me that these don't follow constant naming convetion. I would rename this to CSI_INDEX_SUFFIX , deprecate the existing BAMIndexSuffix and add a new BAM_INDEX_SUFFIX

BAI_INDEX_SUFFIX would probably be more appropriate.

You're right, that's better.

…elNumber is too big. 2. Fixes a bug: the level size for the last level was miscalculated. It should be 32768 (2^15). 3. Removes the unused method regionToBins, whose code was already implemented in the class GenomicIndexUtil.

Change `BAMIndexSuffix2` to `CSI_INDEX_SUFFIX`. Deprecate `BAMIndexSuffix` and use `BAI_INDEX_SUFFIX` instead. Make setters of `CSIIndex` private.

…vate interface `IndexFileBuffer` and classes `IndexFileBuffer`, `MemoryMappedFileBuffer` and `RandomAccessFileBuffer`. Refactor the code to use the new classes.

… `AbstractBAMFileIndex`. Fix a few index arithmetic bugs.

valeriuo · 2018-06-21T14:22:52Z

@lbergelson I've addressed all the topics mentioned in your review. I didn't add any unit tests, but I wanted to push the latest code version, because I am going on a short holiday until next week and I thought you could have another look over it in the meantime.

I've managed to refactor the BAM index class hierarchy by opening slightly the AbstractBAMFileIndex class, without exposing anything to the public interface or braking its contract, in order to allow CSIIndex to extend it, thus removing some duplicate code.

I've tested the CSI index functionality by running Picard BamIndexStats command against some indexes generated with samtools. The results were OK, but the inconvenient is that samtools generates compressed CSI files, by default, and I had to decompress them manually so that Picard could read them. For that matter, BAI files are uncompressed. I don't know if Picard can read compressed index files, but we'll have to address this limitation somehow, as I can see some usability issue.

Also, I've rebased the PR onto master.

lbergelson · 2018-06-21T14:43:21Z

@valeriuo Oh, that's awesome! I will take a look. That's interesting about the compression. It doesn't seem to mention it anywhere in the spec. I assume they're just gzip? Or are they bgzip? We should be able to add detection of the compression and automatically decompress. There was just recently some code added to make that sort of detection easier as well.

jkbonfield · 2018-06-25T08:31:42Z

Htslib writes CSI using bgzf (but I doubt it matters whether it is this or pure gzip as we have no random access capability to our indices anyway). You are correct in that it is not documented. I note that Tabix does document this, as bgzf, so I assume this is just an omission in the CSI documentation.

Note that what CSI does to BAI - allowing for longer chromosomes - needs to be applied to tabix TBI also. There is no point having long chromosome support in BAM if we then cannot analyse it and handle bgzipped VCF. Bcftools does this via an intermediate CSI/TBI hybrid, which is sadly also undocumented! It uses a tabix header as the meta-data for a CSI file, which means it doesn't have to have every #contig line present in the index and reference numbering is based on presence in the file rather than presence in the VCF header. I believe this is an attempt to handle the case where the VCF header does not exist (#contig lines are optional), but I can't really be sure. Maybe it's simply an accident of sharing code paths!

Note, I've just added CSI and BAI support for bgzipped SAM in Htslib, mainly for completeness but also as a safe workaround for when BAM just doesn't cut it (eg a chromosome more than 2Gb long). Does htsjdk support this? I haven't got TBI support for it, but arguably it's not helpful anyway given it also has the same size limit.

jrobinso · 2018-11-01T19:35:28Z

Ping, @lbergelson et al I wonder what the status of CSI support is? Just asking so I know how to respond to IGV tickets, not requesting anything.

valeriuo · 2018-11-02T09:11:28Z

I don't have anything else to add to the PR, at this point. I did some basic tests with Picard and they looked OK.

lbergelson · 2018-11-02T15:25:14Z

It's been stalled forever waiting on me. I need to do a review but I never find the time.

jrobinso · 2018-11-02T15:27:55Z

@lbergelson I understand believe me. If I can help let me know, again no pressure I just need to respond to a ticket on my side.

lbergelson · 2018-11-02T17:55:22Z

I would like to get this into the next release, but I've been saying that to myself for every release...

lbergelson

@valeriuo I started doing what should hopefully be the final review pass on this. It's looking really good. It's great that you figured out how to merge it with the existing index class hierarchy. I still haven't looked over quite everything yet, I just wanted to checkpoint what I've done so far though. Thank you for your overtaxed patience.

lbergelson · 2018-11-06T18:05:10Z

src/main/java/htsjdk/samtools/BAMFileConstants.java

@@ -39,7 +39,18 @@

    static final byte[] BAM_MAGIC = "BAM\1".getBytes();
    /**
-     * BAM index file magic number.
+     * BAM index file magic numbers.


Suggested change

* BAM index file magic numbers.

* BAM index file magic numbers.

* @deprecated prefer {@link BAI_INDEX_MAGIC}

lbergelson · 2018-11-06T18:14:27Z

src/main/java/htsjdk/samtools/AbstractBAMFileIndex.java

@@ -366,27 +366,15 @@ protected int getMaxAddressibleGenomicLocation() {
    }

    /**
+     * @deprecated Use {@link GenomicIndexUtil#regionToBins(int, int)} instead.
+     *
     * Get candidate bins for the specified region
     * @param startPos 1-based start of target region, inclusive.
     * @param endPos 1-based end of target region, inclusive.
     * @return bit set for each bin that may contain SAMRecords in the target region.
     */
    protected BitSet regionToBins(final int startPos, final int endPos) {


Suggested change

protected BitSet regionToBins(final int startPos, final int endPos) {

@Deprecated

protected BitSet regionToBins(final int startPos, final int endPos) {

Don't forget the actual deprecation tag.

lbergelson · 2018-11-06T18:17:14Z

src/main/java/htsjdk/samtools/AbstractBAMFileIndex.java


-        verifyBAMMagicNumber(stream.getSource());
+    int [] sequenceIndexes;


Suggested change

int [] sequenceIndexes;

int[] sequenceIndexes;

lbergelson · 2018-11-06T18:33:40Z

src/main/java/htsjdk/samtools/AbstractBAMFileIndex.java


-        verifyBAMMagicNumber(file.getName());
+    private AbstractBAMFileIndex(final IndexFileBuffer indexFileBuffer, final String source, final SAMSequenceDictionary dictionary) {


Note to self: revisit this comment before commiting
There's something funny about the constructor heirachy. It feels like verifyBAMMagicNumber should probably be made abstract and called always.

lbergelson · 2018-11-06T18:35:35Z

src/main/java/htsjdk/samtools/AbstractBAMFileIndex.java

-        else
-            return GenomicIndexUtil.LEVEL_STARTS[levelNumber+1]-GenomicIndexUtil.LEVEL_STARTS[levelNumber];
+        if (levelNumber >= getNumIndexLevels()) {
+            throw new SAMException("Level number is too big (" + levelNumber + ").");


Since this is duplicated it might be worth extracting a method assertLevelIsValid method.

lbergelson · 2018-11-06T23:17:34Z

src/main/java/htsjdk/samtools/CompressedIndexFileBuffer.java

+
+    @Override
+    public int position() {
+        return (int)mCompressedStream.getPosition();


This should probably check for > maxInt and throw in that case. Unlikely with an index file... but you never know...

Good call on this. BGZF compressed streams use virtual offsets, which are 64 bit by construction and usually exceed Integer.MAX_VALUE. I will change position return type and seek argument type to long.

lbergelson · 2018-11-06T23:26:23Z

src/main/java/htsjdk/samtools/CompressedIndexFileBuffer.java

+    @Override
+    public void readBytes(final byte[] bytes) {
+        try {
+            mCompressedStream.read(bytes);


I think there's a subtle bug here. mCompressedStream.read(bytes) makes no guarantee that it will read as many bytes as you ask for. You have to check the return value of read and continue reading until you either have read as many bytes as you require, or it returns -1 in which case you should probably throw.

You need something like readFully or readBytes from BinaryCodec here I think.

lbergelson · 2018-11-06T23:26:40Z

src/main/java/htsjdk/samtools/CompressedIndexFileBuffer.java

+import java.io.IOException;
+
+
+class CompressedIndexFileBuffer implements IndexFileBuffer {


needs class level javadoc

lbergelson · 2018-11-06T23:26:59Z

src/main/java/htsjdk/samtools/CompressedIndexFileBuffer.java

+
+class CompressedIndexFileBuffer implements IndexFileBuffer {
+
+    private BlockCompressedInputStream mCompressedStream;


make this final

lbergelson · 2018-11-06T23:28:51Z

src/main/java/htsjdk/samtools/IndexFileBuffer.java

+
+import java.io.Closeable;
+
+interface IndexFileBuffer extends Closeable {


This should probably get some javadoc.

lbergelson

Another round of comments. Sorry there are so many. It's a lot of complex code.

lbergelson · 2018-11-07T19:07:29Z

src/main/java/htsjdk/samtools/BAMIndexMetaData.java

-            BAMIndexMetaData[] data = getIndexStats(bam);
+
+            BAMIndexMetaData[] data = null;
+            if (bam.getIndexType().equals(SamIndexes.BAI) || bam.getIndexType().equals(SamIndexes.CSI)) {


Is this check necessary or is it effectively handled by the null -> throw check below?

lbergelson · 2018-11-07T19:23:19Z

src/main/java/htsjdk/samtools/BamIndexValidator.java

@@ -43,49 +43,73 @@ public static int exhaustivelyTestIndex(final SamReader reader) { // throws Exce
        // look at all chunk offsets in a linear index to make sure they are valid

        if (reader.indexing().hasBrowseableIndex()) {
+            if (SamIndexes.BAI.fileNameSuffix.endsWith(reader.type().indexExtension())) {


This whole file could be simplified a lot by extracting methods and rearranging things. If you don't want to do that as part of this pr we can file an issue and add this as is.

lbergelson · 2018-11-07T19:29:32Z

src/main/java/htsjdk/samtools/CSIIndex.java

+     * @param levelNumber Level for which to compute the size.
+     * @return
+     */
+


extra new line

Suggested change

lbergelson · 2018-11-07T19:29:44Z

src/main/java/htsjdk/samtools/CSIIndex.java

+     * Extends the functionality of {@link AbstractBAMFileIndex#getFirstBinInLevel(int)} ,
+     * which cannot be overridden due to its static nature.
+     */
+


same

Suggested change

lbergelson · 2018-11-07T20:12:35Z

src/main/java/htsjdk/samtools/CSIIndex.java

+     * which cannot be overridden due to its static nature.
+     */
+
+    public int getFirstBinOnLevel (final int levelNumber) {


I think it might make sense to just pull this implementation up to the base class. You would have to pull up getBinDepth as well. I guess there might be some performance concerns but I doubt this is any slower than the nested ifs and array lookups that it uses.

If you think that's not a good solution, this needs to be renamed to something more clearly different. Maybe getFirstBinInLevelForCSI

lbergelson · 2018-11-07T22:56:30Z

src/main/java/htsjdk/samtools/CSIIndex.java

+            seek(BAMFileConstants.CSI_MINSHIFT_OFFSET);
+        }
+        setMinShift(readInteger()); // min_shift
+        setBinDepth(readInteger() + 1); // depth - HTSlib doesn't count the first level (bin 0)


Thank you for this comment.

lbergelson · 2018-11-07T23:00:46Z

src/main/java/htsjdk/samtools/CSIIndex.java

+            } else if (indexBin == getMaxBins() + 1) {
+                // meta data - build the bin so that the count of bins is correct;
+                // but don't attach meta chunks to the bin, or normal queries will be off
+                for (int ci = 0; ci < nChunks; ci++) {


Lets pull out a readChunks in the superclass and use it in all 4 places this block of code is repeated.

lbergelson · 2018-11-07T23:12:18Z

src/main/java/htsjdk/samtools/IndexStreamBuffer.java

+
+    /** Continually reads from the provided {@link SeekableStream} into the buffer until the specified number of bytes are read, or
+     * until the stream is exhausted, throwing a {@link RuntimeIOException}. */
+    private static void readFully(final SeekableStream in, final byte[] buffer, final int offset, final int length) {


It might make sense to use BinaryCodec instead of reimplementing readFully.

lbergelson · 2018-11-07T23:16:48Z

src/main/java/htsjdk/samtools/CompressedIndexFileBuffer.java

+    @Override
+    public void readBytes(final byte[] bytes) {
+        try {
+            mCompressedStream.read(bytes);


You need something like readFully or readBytes from BinaryCodec here I think.

lbergelson · 2018-11-07T23:18:38Z

src/main/java/htsjdk/samtools/CompressedIndexFileBuffer.java

+
+    @Override
+    public int readInteger() {
+        final byte[] intbuff = new byte[4];


Allocating a new byte[] for each integer read is going to be super inefficient. It would make sense to reuse the buffer. This method suffers from the same problem with read not guaranteeing a definite number of bytes.

lbergelson

We need a test that actually opens a bam reader and exercises the various query methods with a file that only has a CSI index.

Fixed `CSIIndex.getStartOfLastLinearBin` method. Fixed read methods in `CompressedIndexFileBuffer` class. Changed `seek` and `position` methods to work with `long` offsets. Simplified the constructor hierarchy in `AbstractBAMFileIndex`. Added more unit tests in `BAMFileReaderTest`. Added javadoc and annotations.

valeriuo · 2018-11-28T16:54:28Z

I've addressed most of the change requests and also added a new test class BAMFileReaderTest, that makes use of the query methods in the BAMFileReader for comparing the results of BAI and CSI indexes.
The test harness currently fails due to some connection issues with the Broad ftp server.

lbergelson

@valeriuo I think this is good to go. Thank you for your extreme patience and perseverance. 👍

valeriuo mentioned this pull request Nov 22, 2017

Adds support for reading CSI indexes. broadinstitute/picard#998

Merged

5 tasks

yfarjoun mentioned this pull request Jan 15, 2018

Trouble loading bam file in IGV #1047

Closed

WimSpee mentioned this pull request Mar 12, 2018

Status of CSI support in HTS-JDK and downstream tools. #1099

Closed

yfarjoun assigned lbergelson Jun 6, 2018

lbergelson mentioned this pull request Jun 13, 2018

{tabix,csi}: specs are incomplete samtools/hts-specs#70

Open

jmarshall mentioned this pull request Jun 14, 2018

Bcftools index with BAI. samtools/bcftools#812

Closed

lbergelson reviewed Jun 15, 2018

View reviewed changes

valeriuo added 13 commits June 21, 2018 10:22

CSI index - some bin methods and associated unit tests

4dee079

Adds read support for BAM CSI indexes.

ed5aac6

Support of CSI index statistics.

c04ccce

Adds support for CSI index validator.

796aa23

Adds unit tests to most public methods for CSI indexes.

f5f35e5

Fixes unit test.

217c230

Address code review comments.

757987d

Minor fixes.

9ab2a59

Change BAMCSIFileIndex to CSIIndex.

71a6407

Change `BAMIndexSuffix2` to `CSI_INDEX_SUFFIX`. Deprecate `BAMIndexSuffix` and use `BAI_INDEX_SUFFIX` instead. Make setters of `CSIIndex` private.

Deduplicate the IndexFileBuffer hierarchy into separate, pakage-pri…

3cd30a6

…vate interface `IndexFileBuffer` and classes `IndexFileBuffer`, `MemoryMappedFileBuffer` and `RandomAccessFileBuffer`. Refactor the code to use the new classes.

Refactor the constuctors of CSIIndex.

e061a32

Refactor the BAM index class hierarchy, so that CSIIndex can extend…

0e9a1d3

… `AbstractBAMFileIndex`. Fix a few index arithmetic bugs.

valeriuo force-pushed the feature/vo2_csi2 branch from b16a421 to 0e9a1d3 Compare June 21, 2018 14:01

valeriuo added 2 commits July 6, 2018 16:33

Add support for BGZF compressed CSI index files.

e9c75ee

Add more unit tests to CSI index.

205e738

lbergelson requested changes Nov 6, 2018

View reviewed changes

lbergelson requested changes Nov 7, 2018

View reviewed changes

lbergelson approved these changes Jan 14, 2019

View reviewed changes

lbergelson merged commit 16a4e37 into samtools:master Jan 16, 2019

FredericBGA mentioned this pull request Apr 2, 2020

Support for long reference sequences #900

Open

	* BAM index file magic numbers.
	* BAM index file magic numbers.
	* @deprecated prefer {@link BAI_INDEX_MAGIC}

	protected BitSet regionToBins(final int startPos, final int endPos) {
	@Deprecated
	protected BitSet regionToBins(final int startPos, final int endPos) {


		verifyBAMMagicNumber(stream.getSource());
		int [] sequenceIndexes;


		verifyBAMMagicNumber(file.getName());
		private AbstractBAMFileIndex(final IndexFileBuffer indexFileBuffer, final String source, final SAMSequenceDictionary dictionary) {

		import java.io.IOException;


		class CompressedIndexFileBuffer implements IndexFileBuffer {


		class CompressedIndexFileBuffer implements IndexFileBuffer {

		private BlockCompressedInputStream mCompressedStream;


		import java.io.Closeable;

		interface IndexFileBuffer extends Closeable {

CSI index support for BAM files #1040

CSI index support for BAM files #1040

Conversation

valeriuo commented Nov 22, 2017

Description

Checklist

codecov-io commented Nov 22, 2017 • edited Loading

Codecov Report

lbergelson commented Dec 13, 2017

valeriuo commented Dec 19, 2017

yfarjoun commented Jun 6, 2018

lbergelson commented Jun 6, 2018

lbergelson commented Jun 13, 2018

valeriuo commented Jun 14, 2018

lbergelson left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

valeriuo Jun 19, 2018 • edited Loading

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

valeriuo commented Jun 21, 2018 • edited Loading

lbergelson commented Jun 21, 2018

jkbonfield commented Jun 25, 2018

jrobinso commented Nov 1, 2018

valeriuo commented Nov 2, 2018

lbergelson commented Nov 2, 2018

jrobinso commented Nov 2, 2018

lbergelson commented Nov 2, 2018

lbergelson left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

lbergelson left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

lbergelson left a comment

Choose a reason for hiding this comment

valeriuo commented Nov 28, 2018 • edited Loading

lbergelson left a comment

Choose a reason for hiding this comment

codecov-io commented Nov 22, 2017 •

edited

Loading

valeriuo Jun 19, 2018 •

edited

Loading

valeriuo commented Jun 21, 2018 •

edited

Loading

valeriuo commented Nov 28, 2018 •

edited

Loading