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replacing uses of deprecated class SAMFileReader #1235

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replacing uses of deprecated class SAMFileReader #1235

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7 changes: 4 additions & 3 deletions adam-cli/src/main/scala/org/bdgenomics/adam/cli/DictionaryCommand.scala
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Expand Up @@ -17,10 +17,11 @@
*/
package org.bdgenomics.adam.cli

import java.io.{ FileOutputStream, File }
import java.io.{ File, FileOutputStream }

import htsjdk.variant.utils.SAMSequenceDictionaryExtractor
import org.apache.commons.io.IOUtils
import org.bdgenomics.adam.models.SequenceDictionary
import htsjdk.samtools.SAMFileReader

trait DictionaryCommand {
private def getDictionaryFile(name: String): Option[File] = {
Expand All @@ -33,7 +34,7 @@ trait DictionaryCommand {
Some(file)
}

private def getDictionary(file: File) = Some(SequenceDictionary(SAMFileReader.getSequenceDictionary(file)))
private def getDictionary(file: File) = Some(SequenceDictionary(SAMSequenceDictionaryExtractor.extractDictionary(file)))

def loadSequenceDictionary(file: File): Option[SequenceDictionary] = {
if (file != null) {
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6 changes: 4 additions & 2 deletions adam-core/src/main/scala/org/bdgenomics/adam/models/RecordGroupDictionary.scala
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Expand Up @@ -17,9 +17,11 @@
*/
package org.bdgenomics.adam.models

import htsjdk.samtools.{ SAMFileHeader, SAMFileReader, SAMReadGroupRecord }
import java.util.Date

import htsjdk.samtools.{ SAMFileHeader, SAMReadGroupRecord, SamReader }
import org.bdgenomics.formats.avro.{ RecordGroupMetadata, Sample }

import scala.collection.JavaConversions._

object RecordGroupDictionary {
Expand All @@ -42,7 +44,7 @@ object RecordGroupDictionary {
* @param samReader SAM file header with attached read groups.
* @return Returns a new record group dictionary with the read groups attached to the file header.
*/
def fromSAMReader(samReader: SAMFileReader): RecordGroupDictionary = {
def fromSAMReader(samReader: SamReader): RecordGroupDictionary = {
fromSAMHeader(samReader.getFileHeader)
}

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14 changes: 4 additions & 10 deletions adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AnySAMOutFormatter.scala
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Expand Up @@ -17,19 +17,13 @@
*/
package org.bdgenomics.adam.rdd.read

import htsjdk.samtools.{
SAMFileReader,
SAMRecord,
SAMRecordIterator
}
import java.io.InputStream

import htsjdk.samtools._
import org.bdgenomics.adam.converters.SAMRecordConverter
import org.bdgenomics.adam.models.{
RecordGroupDictionary,
SequenceDictionary
}
import org.bdgenomics.adam.rdd.OutFormatter
import org.bdgenomics.formats.avro.AlignmentRecord

import scala.annotation.tailrec
import scala.collection.mutable.ListBuffer

Expand All @@ -47,7 +41,7 @@ class AnySAMOutFormatter extends OutFormatter[AlignmentRecord] {
val converter = new SAMRecordConverter

// make reader
val reader = new SAMFileReader(is)
val reader = SamReaderFactory.makeDefault().open(SamInputResource.of(is))

// make iterator from said reader
val iter = reader.iterator()
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7 changes: 5 additions & 2 deletions adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala
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Expand Up @@ -20,16 +20,19 @@ package org.bdgenomics.adam.converters
import htsjdk.samtools.SAMFileReader
import htsjdk.variant.variantcontext.{ Allele, GenotypeBuilder, GenotypeType, VariantContextBuilder }
import java.io.File
import org.bdgenomics.adam.models.{ VariantContext => ADAMVariantContext, SequenceDictionary }

import htsjdk.variant.utils.SAMSequenceDictionaryExtractor
import org.bdgenomics.adam.models.{ SequenceDictionary, VariantContext => ADAMVariantContext }
import org.bdgenomics.adam.util.{ ADAMFunSuite, PhredUtils }
import org.bdgenomics.formats.avro._
import org.scalatest.FunSuite

import scala.collection.JavaConversions._

class VariantContextConverterSuite extends ADAMFunSuite {
val dictionary = {
val path = testFile("dict_with_accession.dict")
SequenceDictionary(SAMFileReader.getSequenceDictionary(new File(path)))
SequenceDictionary(SAMSequenceDictionaryExtractor.extractDictionary(new File(path)))
}

def gatkSNVBuilder: VariantContextBuilder = new VariantContextBuilder()
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11 changes: 7 additions & 4 deletions adam-core/src/test/scala/org/bdgenomics/adam/models/SequenceDictionarySuite.scala
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Expand Up @@ -17,10 +17,13 @@
*/
package org.bdgenomics.adam.models

import htsjdk.samtools.{ SAMFileReader, SAMSequenceRecord, SAMSequenceDictionary }
import htsjdk.samtools.{ SAMFileReader, SAMSequenceDictionary, SAMSequenceRecord }
import htsjdk.variant.vcf.VCFFileReader
import java.io.File

import htsjdk.variant.utils.SAMSequenceDictionaryExtractor
import org.bdgenomics.adam.util.ADAMFunSuite

import scala.collection.JavaConversions._

class SequenceDictionarySuite extends ADAMFunSuite {
Expand All @@ -41,7 +44,7 @@ class SequenceDictionarySuite extends ADAMFunSuite {

test("Convert from SAM sequence dictionary file (with extra fields)") {
val path = testFile("dict_with_accession.dict")
val ssd = SAMFileReader.getSequenceDictionary(new File(path))
val ssd = SAMSequenceDictionaryExtractor.extractDictionary(new File(path))

val chr1 = ssd.getSequence("1") // Validate that extra fields are parsed
assert(chr1 != null)
Expand All @@ -55,7 +58,7 @@ class SequenceDictionarySuite extends ADAMFunSuite {

test("merge into existing dictionary") {
val path = testFile("dict_with_accession.dict")
val ssd = SAMFileReader.getSequenceDictionary(new File(path))
val ssd = SAMSequenceDictionaryExtractor.extractDictionary(new File(path))

val asd = SequenceDictionary(ssd)
assert(asd.containsRefName("1"))
Expand All @@ -68,7 +71,7 @@ class SequenceDictionarySuite extends ADAMFunSuite {

test("Convert from SAM sequence dictionary and back") {
val path = testFile("dict_with_accession.dict")
val ssd = SAMFileReader.getSequenceDictionary(new File(path))
val ssd = SAMSequenceDictionaryExtractor.extractDictionary(new File(path))
val asd = SequenceDictionary(ssd)
ssd.assertSameDictionary(SequenceDictionary.toSAMSequenceDictionary(asd))
}
Expand Down