[med-svn] [picard-tools] 01/01: Imported Upstream version 1.105
Olivier Sallou
osallou at debian.org
Tue Dec 24 10:16:56 UTC 2013
This is an automated email from the git hooks/post-receive script.
osallou pushed a commit to branch upstream
in repository picard-tools.
commit 711211f17ef4b81039ae7d053d9a42cd63d59908
Author: Olivier Sallou <olivier.sallou at debian.org>
Date: Tue Dec 24 11:14:22 2013 +0100
Imported Upstream version 1.105
---
Picard-public.ipr | 4 +
build.xml | 6 +-
src/c/inteldeflater/IntelDeflater.c | 247 +++++++++
.../net/sf/picard/cmdline/CommandLineProgram.java | 6 +-
src/java/net/sf/picard/fastq/BasicFastqWriter.java | 19 +-
.../sf/picard/fastq/Casava18ReadNameEncoder.java | 46 ++
src/java/net/sf/picard/fastq/FastqReader.java | 33 +-
.../net/sf/picard/fastq/FastqWriterFactory.java | 6 +-
.../sf/picard/fastq/IlluminaReadNameEncoder.java | 28 +
src/java/net/sf/picard/fastq/ReadNameEncoder.java | 17 +
.../picard/illumina/ClusterDataToSamConverter.java | 10 +-
.../picard/illumina/ExtractIlluminaBarcodes.java | 246 +++++----
.../picard/illumina/IlluminaBasecallsToFastq.java | 86 +++-
.../parser/readers/TileMetricsOutReader.java | 9 +-
src/java/net/sf/picard/io/IoUtil.java | 12 +-
.../net/sf/picard/metrics/MultiLevelCollector.java | 36 +-
src/java/net/sf/picard/sam/FastqToSam.java | 14 +-
src/java/net/sf/picard/sam/SamToFastq.java | 9 +-
src/java/net/sf/picard/sam/ValidateSamFile.java | 5 +-
src/java/net/sf/picard/util/IlluminaUtil.java | 9 -
src/java/net/sf/picard/util/IntervalUtil.java | 21 +-
src/java/net/sf/picard/util/MathUtil.java | 110 +++-
src/java/net/sf/picard/vcf/MakeSitesOnlyVcf.java | 2 +-
src/java/net/sf/samtools/Defaults.java | 9 +
.../net/sf/samtools/SAMSequenceDictionary.java | 28 +
src/java/net/sf/samtools/SAMSequenceRecord.java | 10 +
src/java/net/sf/samtools/SAMUtils.java | 2 +-
.../seekablestream/ISeekableStreamFactory.java | 33 ++
.../samtools/seekablestream/SeekableFTPStream.java | 2 +-
.../seekablestream/SeekableStreamFactory.java | 56 +-
.../samtools/util/BlockCompressedOutputStream.java | 8 +-
src/java/net/sf/samtools/util/CollectionUtil.java | 8 +
src/java/net/sf/samtools/util/IOUtil.java | 2 +-
src/java/net/sf/samtools/util/Lazy.java | 35 ++
src/java/net/sf/samtools/util/StringUtil.java | 5 +
src/java/net/sf/samtools/util/ftp/FTPUtils.java | 20 +-
.../net/sf/samtools/util/zip/DeflaterFactory.java | 78 +++
.../net/sf/samtools/util/zip/IntelDeflater.java | 567 +++++++++++++++++++++
src/java/net/sf/samtools/util/zip/ZStreamRef.java | 48 ++
.../org/broad/tribble/AbstractFeatureReader.java | 47 +-
src/java/org/broad/tribble/TabixFeatureReader.java | 5 +
src/java/org/broad/tribble/Tribble.java | 5 +-
.../broad/tribble/TribbleIndexedFeatureReader.java | 10 +-
.../org/broad/tribble/readers/TabixReader.java | 23 +-
src/java/org/broad/tribble/util/ParsingUtils.java | 29 ++
.../variant/variantcontext/VariantContext.java | 47 ++
.../variantcontext/VariantContextComparator.java | 23 +-
.../variantcontext/VariantContextUtils.java | 61 ++-
.../variant/variantcontext/writer/BCF2Writer.java | 27 +-
.../writer/IndexingVariantContextWriter.java | 82 ++-
.../writer/IntGenotypeFieldAccessors.java | 2 +-
.../variant/variantcontext/writer/VCFWriter.java | 499 +++---------------
.../writer/VariantContextWriterFactory.java | 21 +-
.../variant/vcf/AbstractVCFCodec.java | 26 +-
.../variant/vcf/VCFContigHeaderLine.java | 2 +-
.../org/broadinstitute/variant/vcf/VCFEncoder.java | 381 ++++++++++++++
.../org/broadinstitute/variant/vcf/VCFHeader.java | 4 +-
.../broadinstitute/variant/vcf/VCFRecordCodec.java | 63 +++
src/scripts/build_intel_deflater.sh | 64 +++
.../net/sf/picard/analysis/rnaSeqCoverage.R | 43 +-
src/scripts/release_picard.sh | 3 +-
.../illumina/IlluminaBasecallsToFastqTest.java | 16 +-
src/tests/java/net/sf/picard/io/IoUtilTest.java | 12 +
.../java/net/sf/picard/sam/FastqToSamTest.java | 77 +--
.../java/net/sf/picard/sam/SamToFastqTest.java | 3 +-
.../java/net/sf/picard/util/MathUtilTest.java | 45 ++
.../java/net/sf/picard/vcf/SplitVcfsTest.java | 16 +-
.../variantcontext/VariantJEXLContextUnitTest.java | 2 +-
.../variantcontext/writer/VCFWriterUnitTest.java | 54 +-
.../broadinstitute/variant/vcf/VCFEncoderTest.java | 45 ++
.../IlluminaBasecallsToFastqTest/AACTTGAC.1.fastq | 26 +-
.../AACTTGAC.barcode_1.fastq | 26 +-
.../AACTTGACTTGAGCCT.1.fastq | 26 +-
.../AACTTGACTTGAGCCT.barcode_1.fastq | 26 +-
.../AACTTGACTTGAGCCT.barcode_2.fastq | 26 +-
.../IlluminaBasecallsToFastqTest/AAGGATGT.1.fastq | 26 +-
.../AAGGATGT.barcode_1.fastq | 26 +-
.../AAGGATGTTTCGCTGA.1.fastq | 26 +-
.../AAGGATGTTTCGCTGA.barcode_1.fastq | 26 +-
.../AAGGATGTTTCGCTGA.barcode_2.fastq | 26 +-
.../IlluminaBasecallsToFastqTest/ACCAACTG.1.fastq | 18 +-
.../ACCAACTG.barcode_1.fastq | 18 +-
.../ACCAACTGTGTCGGAT.1.fastq | 18 +-
.../ACCAACTGTGTCGGAT.barcode_1.fastq | 18 +-
.../ACCAACTGTGTCGGAT.barcode_2.fastq | 18 +-
.../IlluminaBasecallsToFastqTest/AGCAATTC.1.fastq | 16 +-
.../AGCAATTC.barcode_1.fastq | 16 +-
.../AGCAATTCTGCTCGAC.1.fastq | 16 +-
.../AGCAATTCTGCTCGAC.barcode_1.fastq | 16 +-
.../AGCAATTCTGCTCGAC.barcode_2.fastq | 16 +-
.../IlluminaBasecallsToFastqTest/AGTTGCTT.1.fastq | 16 +-
.../AGTTGCTT.barcode_1.fastq | 16 +-
.../AGTTGCTTTCTGGCGA.1.fastq | 16 +-
.../AGTTGCTTTCTGGCGA.barcode_1.fastq | 16 +-
.../AGTTGCTTTCTGGCGA.barcode_2.fastq | 16 +-
.../IlluminaBasecallsToFastqTest/ATTATGTT.1.fastq | 6 +-
.../ATTATGTT.barcode_1.fastq | 6 +-
.../ATTATGTTTCGGAATG.1.fastq | 6 +-
.../ATTATGTTTCGGAATG.barcode_1.fastq | 6 +-
.../ATTATGTTTCGGAATG.barcode_2.fastq | 6 +-
.../IlluminaBasecallsToFastqTest/CACATCCT.1.fastq | 18 +-
.../CACATCCT.barcode_1.fastq | 18 +-
.../CACATCCTTACTTAGC.1.fastq | 18 +-
.../CACATCCTTACTTAGC.barcode_1.fastq | 18 +-
.../CACATCCTTACTTAGC.barcode_2.fastq | 18 +-
.../IlluminaBasecallsToFastqTest/CAGGAGCC.1.fastq | 18 +-
.../CAGGAGCC.barcode_1.fastq | 18 +-
.../CAGGAGCCGTATAACA.1.fastq | 18 +-
.../CAGGAGCCGTATAACA.barcode_1.fastq | 18 +-
.../CAGGAGCCGTATAACA.barcode_2.fastq | 18 +-
.../IlluminaBasecallsToFastqTest/CATAGCGA.1.fastq | 24 +-
.../CATAGCGA.barcode_1.fastq | 24 +-
.../CATAGCGAGGTCCAGA.1.fastq | 24 +-
.../CATAGCGAGGTCCAGA.barcode_1.fastq | 24 +-
.../CATAGCGAGGTCCAGA.barcode_2.fastq | 24 +-
.../IlluminaBasecallsToFastqTest/CATGCTTA.1.fastq | 10 +-
.../CATGCTTA.barcode_1.fastq | 10 +-
.../CATGCTTAGCACATCT.1.fastq | 10 +-
.../CATGCTTAGCACATCT.barcode_1.fastq | 10 +-
.../CATGCTTAGCACATCT.barcode_2.fastq | 10 +-
.../IlluminaBasecallsToFastqTest/CCAGTTAG.1.fastq | 22 +-
.../CCAGTTAG.barcode_1.fastq | 22 +-
.../CCAGTTAGGCACACGA.1.fastq | 22 +-
.../CCAGTTAGGCACACGA.barcode_1.fastq | 22 +-
.../CCAGTTAGGCACACGA.barcode_2.fastq | 22 +-
.../IlluminaBasecallsToFastqTest/CCTACCAT.1.fastq | 4 +-
.../CCTACCAT.barcode_1.fastq | 4 +-
.../CCTACCATCTACCAGG.1.fastq | 4 +-
.../CCTACCATCTACCAGG.barcode_1.fastq | 4 +-
.../CCTACCATCTACCAGG.barcode_2.fastq | 4 +-
.../IlluminaBasecallsToFastqTest/CTACCAGG.1.fastq | 12 +-
.../CTACCAGG.barcode_1.fastq | 12 +-
.../CTACCAGGCCTACCAT.1.fastq | 12 +-
.../CTACCAGGCCTACCAT.barcode_1.fastq | 12 +-
.../CTACCAGGCCTACCAT.barcode_2.fastq | 12 +-
.../IlluminaBasecallsToFastqTest/GCACACGA.1.fastq | 18 +-
.../GCACACGA.barcode_1.fastq | 18 +-
.../GCACACGACCAGTTAG.1.fastq | 18 +-
.../GCACACGACCAGTTAG.barcode_1.fastq | 18 +-
.../GCACACGACCAGTTAG.barcode_2.fastq | 18 +-
.../IlluminaBasecallsToFastqTest/GCACATCT.1.fastq | 6 +-
.../GCACATCT.barcode_1.fastq | 6 +-
.../GCACATCTCATGCTTA.1.fastq | 6 +-
.../GCACATCTCATGCTTA.barcode_1.fastq | 6 +-
.../GCACATCTCATGCTTA.barcode_2.fastq | 6 +-
.../IlluminaBasecallsToFastqTest/GGTCCAGA.1.fastq | 14 +-
.../GGTCCAGA.barcode_1.fastq | 14 +-
.../GGTCCAGACATAGCGA.1.fastq | 14 +-
.../GGTCCAGACATAGCGA.barcode_1.fastq | 14 +-
.../GGTCCAGACATAGCGA.barcode_2.fastq | 14 +-
.../IlluminaBasecallsToFastqTest/GTATAACA.1.fastq | 20 +-
.../GTATAACA.barcode_1.fastq | 20 +-
.../GTATAACACAGGAGCC.1.fastq | 20 +-
.../GTATAACACAGGAGCC.barcode_1.fastq | 20 +-
.../GTATAACACAGGAGCC.barcode_2.fastq | 20 +-
.../IlluminaBasecallsToFastqTest/N.1.fastq | 446 ++++++++--------
.../IlluminaBasecallsToFastqTest/N.barcode_1.fastq | 446 ++++++++--------
.../IlluminaBasecallsToFastqTest/NN.1.fastq | 446 ++++++++--------
.../NN.barcode_1.fastq | 446 ++++++++--------
.../NN.barcode_2.fastq | 446 ++++++++--------
.../IlluminaBasecallsToFastqTest/TACTTAGC.1.fastq | 16 +-
.../TACTTAGC.barcode_1.fastq | 16 +-
.../TACTTAGCCACATCCT.1.fastq | 16 +-
.../TACTTAGCCACATCCT.barcode_1.fastq | 16 +-
.../TACTTAGCCACATCCT.barcode_2.fastq | 16 +-
.../IlluminaBasecallsToFastqTest/TCGGAATG.1.fastq | 14 +-
.../TCGGAATG.barcode_1.fastq | 14 +-
.../TCGGAATGATTATGTT.1.fastq | 14 +-
.../TCGGAATGATTATGTT.barcode_1.fastq | 14 +-
.../TCGGAATGATTATGTT.barcode_2.fastq | 14 +-
.../IlluminaBasecallsToFastqTest/TCTGGCGA.1.fastq | 10 +-
.../TCTGGCGA.barcode_1.fastq | 10 +-
.../TCTGGCGAAGTTGCTT.1.fastq | 10 +-
.../TCTGGCGAAGTTGCTT.barcode_1.fastq | 10 +-
.../TCTGGCGAAGTTGCTT.barcode_2.fastq | 10 +-
.../IlluminaBasecallsToFastqTest/TGCTCGAC.1.fastq | 10 +-
.../TGCTCGAC.barcode_1.fastq | 10 +-
.../TGCTCGACAGCAATTC.1.fastq | 10 +-
.../TGCTCGACAGCAATTC.barcode_1.fastq | 10 +-
.../TGCTCGACAGCAATTC.barcode_2.fastq | 10 +-
.../IlluminaBasecallsToFastqTest/TGTCGGAT.1.fastq | 8 +-
.../TGTCGGAT.barcode_1.fastq | 8 +-
.../TGTCGGATACCAACTG.1.fastq | 8 +-
.../TGTCGGATACCAACTG.barcode_1.fastq | 8 +-
.../TGTCGGATACCAACTG.barcode_2.fastq | 8 +-
.../IlluminaBasecallsToFastqTest/TTCGCTGA.1.fastq | 10 +-
.../TTCGCTGA.barcode_1.fastq | 10 +-
.../TTCGCTGAAAGGATGT.1.fastq | 10 +-
.../TTCGCTGAAAGGATGT.barcode_1.fastq | 10 +-
.../TTCGCTGAAAGGATGT.barcode_2.fastq | 10 +-
.../IlluminaBasecallsToFastqTest/TTGAGCCT.1.fastq | 12 +-
.../TTGAGCCT.barcode_1.fastq | 12 +-
.../TTGAGCCTAACTTGAC.1.fastq | 12 +-
.../TTGAGCCTAACTTGAC.barcode_1.fastq | 12 +-
.../TTGAGCCTAACTTGAC.barcode_2.fastq | 12 +-
.../nonBarcoded.1.fastq | 120 ++---
.../nonBarcoded.2.fastq | 120 ++---
testdata/net/sf/picard/io/5newline5.txt | 2 +
testdata/net/sf/picard/io/empty.txt | 0
.../illumina-sanger_full_range_as_sanger-62.fastq | 4 +
.../sf/picard/sam/fastq2bam/ok-paired/pair1.txt | 2 +-
.../sam/fastq2bam/ok-paired/s_1_1_sequence.txt | 40 ++
.../sam/fastq2bam/ok-paired/s_1_2_sequence.txt | 41 ++
.../sam/fastq2bam/ok-paired/s_1_sequence.txt | 40 ++
.../{ok-paired => permissive-format}/pair1.txt | 5 +
.../sam/fastq2bam/permissive-format/pair2.txt | 28 +
.../fastq2bam/permissive-format/s_1_1_sequence.txt | 51 ++
.../fastq2bam/permissive-format/s_1_2_sequence.txt | 41 ++
.../fastq2bam/permissive-format/s_1_sequence.txt | 62 +++
209 files changed, 5219 insertions(+), 2966 deletions(-)
diff --git a/Picard-public.ipr b/Picard-public.ipr
index ab72fb3..1cc83ca 100644
--- a/Picard-public.ipr
+++ b/Picard-public.ipr
@@ -273,8 +273,12 @@
<words>
<w>bgzipped</w>
<w>codecs</w>
+ <w>demultiplex</w>
+ <w>demultiplexed</w>
+ <w>eamss</w>
<w>endian</w>
<w>gzipped</w>
+ <w>illumina's</w>
<w>indexable</w>
<w>inferer</w>
<w>inferrer</w>
diff --git a/build.xml b/build.xml
index e5c07bc..a58ab94 100755
--- a/build.xml
+++ b/build.xml
@@ -43,7 +43,7 @@
<!-- Get SVN revision, if available, otherwise leave it blank. -->
<exec executable="svnversion" outputproperty="repository.revision" failifexecutionfails="false"/>
<property name="repository.revision" value=""/>
- <property name="sam-version" value="1.101"/>
+ <property name="sam-version" value="1.105"/>
<property name="picard-version" value="${sam-version}"/>
<property name="tribble-version" value="${sam-version}"/>
<property name="variant-version" value="${sam-version}"/>
@@ -348,6 +348,8 @@
<zip zipfile="${dist}/picard-tools-${picard-version}.zip">
<zipfileset dir="${dist}" includes="*.jar" prefix="picard-tools-${picard-version}"/>
<zipfileset dir="${lib}" includes="snappy*.jar"/>
+ <!-- distribute libJniDeflater.so in same directory as jarfiles-->
+ <zipfileset dir="${lib}/jni" includes="*" prefix="picard-tools-${picard-version}"/>
</zip>
</target>
@@ -372,6 +374,8 @@
<fileset dir="${command_tmp}" includes="org/xerial/snappy/native/Linux/**/*"/>
<fileset dir="${command_tmp}" includes="org/xerial/snappy/VERSION"/>
<fileset dir="${command_tmp}" includes="META-INF/maven/org.xerial.snappy/snappy-java/pom.properties"/>
+ <!-- Force inclusion of IntelDeflater, which is dynamically linked. -->
+ <fileset dir="${command_tmp}" includes="net/sf/samtools/util/zip/*"/>
<filesets/>
<manifest>
<attribute name="Implementation-Title" value="@{title}"/>
diff --git a/src/c/inteldeflater/IntelDeflater.c b/src/c/inteldeflater/IntelDeflater.c
new file mode 100644
index 0000000..39a3a57
--- /dev/null
+++ b/src/c/inteldeflater/IntelDeflater.c
@@ -0,0 +1,247 @@
+/*
+ * Copyright (c) 1997, 2010, Oracle and/or its affiliates. All rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * This code is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU General Public License version 2 only, as
+ * published by the Free Software Foundation. Oracle designates this
+ * particular file as subject to the "Classpath" exception as provided
+ * by Oracle in the LICENSE file that accompanied this code.
+ *
+ * This code is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
+ * version 2 for more details (a copy is included in the LICENSE file that
+ * accompanied this code).
+ *
+ * You should have received a copy of the GNU General Public License version
+ * 2 along with this work; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
+ * or visit www.oracle.com if you need additional information or have any
+ * questions.
+ */
+
+/*
+ * Native method support for net.sf.samtools.util.zip.IntelDeflater.
+ * This is copied from OpenJDK native support for java.util.zip.Deflater, with only package and class name changed.
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include "jlong.h"
+#include "jni.h"
+#include "jni_util.h"
+#include "zlib.h"
+
+#include "net_sf_samtools_util_zip_IntelDeflater.h"
+
+#define DEF_MEM_LEVEL 8
+
+static jfieldID levelID;
+static jfieldID strategyID;
+static jfieldID setParamsID;
+static jfieldID finishID;
+static jfieldID finishedID;
+static jfieldID bufID, offID, lenID;
+
+JNIEXPORT void JNICALL
+Java_net_sf_samtools_util_zip_IntelDeflater_initIDs(JNIEnv *env, jclass cls)
+{
+ levelID = (*env)->GetFieldID(env, cls, "level", "I");
+ strategyID = (*env)->GetFieldID(env, cls, "strategy", "I");
+ setParamsID = (*env)->GetFieldID(env, cls, "setParams", "Z");
+ finishID = (*env)->GetFieldID(env, cls, "finish", "Z");
+ finishedID = (*env)->GetFieldID(env, cls, "finished", "Z");
+ bufID = (*env)->GetFieldID(env, cls, "buf", "[B");
+ offID = (*env)->GetFieldID(env, cls, "off", "I");
+ lenID = (*env)->GetFieldID(env, cls, "len", "I");
+}
+
+JNIEXPORT jlong JNICALL
+Java_net_sf_samtools_util_zip_IntelDeflater_init(JNIEnv *env, jclass cls, jint level,
+ jint strategy, jboolean nowrap)
+{
+ z_stream *strm = calloc(1, sizeof(z_stream));
+
+ if (strm == 0) {
+ JNU_ThrowOutOfMemoryError(env, 0);
+ return jlong_zero;
+ } else {
+ char *msg;
+ switch (deflateInit2(strm, level, Z_DEFLATED,
+ nowrap ? -MAX_WBITS : MAX_WBITS,
+ DEF_MEM_LEVEL, strategy)) {
+ case Z_OK:
+ return ptr_to_jlong(strm);
+ case Z_MEM_ERROR:
+ free(strm);
+ JNU_ThrowOutOfMemoryError(env, 0);
+ return jlong_zero;
+ case Z_STREAM_ERROR:
+ free(strm);
+ JNU_ThrowIllegalArgumentException(env, 0);
+ return jlong_zero;
+ default:
+ msg = strm->msg;
+ free(strm);
+ JNU_ThrowInternalError(env, msg);
+ return jlong_zero;
+ }
+ }
+}
+
+JNIEXPORT void JNICALL
+Java_net_sf_samtools_util_zip_IntelDeflater_setDictionary(JNIEnv *env, jclass cls, jlong addr,
+ jarray b, jint off, jint len)
+{
+ Bytef *buf = (*env)->GetPrimitiveArrayCritical(env, b, 0);
+ int res;
+ if (buf == 0) {/* out of memory */
+ return;
+ }
+ res = deflateSetDictionary((z_stream *)jlong_to_ptr(addr), buf + off, len);
+ (*env)->ReleasePrimitiveArrayCritical(env, b, buf, 0);
+ switch (res) {
+ case Z_OK:
+ break;
+ case Z_STREAM_ERROR:
+ JNU_ThrowIllegalArgumentException(env, 0);
+ break;
+ default:
+ JNU_ThrowInternalError(env, ((z_stream *)jlong_to_ptr(addr))->msg);
+ break;
+ }
+}
+
+JNIEXPORT jint JNICALL
+Java_net_sf_samtools_util_zip_IntelDeflater_deflateBytes(JNIEnv *env, jobject this, jlong addr,
+ jarray b, jint off, jint len, jint flush)
+{
+ z_stream *strm = jlong_to_ptr(addr);
+
+ jarray this_buf = (*env)->GetObjectField(env, this, bufID);
+ jint this_off = (*env)->GetIntField(env, this, offID);
+ jint this_len = (*env)->GetIntField(env, this, lenID);
+ jbyte *in_buf;
+ jbyte *out_buf;
+ int res;
+ if ((*env)->GetBooleanField(env, this, setParamsID)) {
+ int level = (*env)->GetIntField(env, this, levelID);
+ int strategy = (*env)->GetIntField(env, this, strategyID);
+ in_buf = (*env)->GetPrimitiveArrayCritical(env, this_buf, 0);
+ if (in_buf == NULL) {
+ // Throw OOME only when length is not zero
+ if (this_len != 0)
+ JNU_ThrowOutOfMemoryError(env, 0);
+ return 0;
+ }
+ out_buf = (*env)->GetPrimitiveArrayCritical(env, b, 0);
+ if (out_buf == NULL) {
+ (*env)->ReleasePrimitiveArrayCritical(env, this_buf, in_buf, 0);
+ if (len != 0)
+ JNU_ThrowOutOfMemoryError(env, 0);
+ return 0;
+ }
+
+ strm->next_in = (Bytef *) (in_buf + this_off);
+ strm->next_out = (Bytef *) (out_buf + off);
+ strm->avail_in = this_len;
+ strm->avail_out = len;
+ res = deflateParams(strm, level, strategy);
+ (*env)->ReleasePrimitiveArrayCritical(env, b, out_buf, 0);
+ (*env)->ReleasePrimitiveArrayCritical(env, this_buf, in_buf, 0);
+
+ switch (res) {
+ case Z_OK:
+ (*env)->SetBooleanField(env, this, setParamsID, JNI_FALSE);
+ this_off += this_len - strm->avail_in;
+ (*env)->SetIntField(env, this, offID, this_off);
+ (*env)->SetIntField(env, this, lenID, strm->avail_in);
+ return len - strm->avail_out;
+ case Z_BUF_ERROR:
+ (*env)->SetBooleanField(env, this, setParamsID, JNI_FALSE);
+ return 0;
+ default:
+ JNU_ThrowInternalError(env, strm->msg);
+ return 0;
+ }
+ } else {
+ jboolean finish = (*env)->GetBooleanField(env, this, finishID);
+ in_buf = (*env)->GetPrimitiveArrayCritical(env, this_buf, 0);
+ if (in_buf == NULL) {
+ if (this_len != 0)
+ JNU_ThrowOutOfMemoryError(env, 0);
+ return 0;
+ }
+ out_buf = (*env)->GetPrimitiveArrayCritical(env, b, 0);
+ if (out_buf == NULL) {
+ (*env)->ReleasePrimitiveArrayCritical(env, this_buf, in_buf, 0);
+ if (len != 0)
+ JNU_ThrowOutOfMemoryError(env, 0);
+
+ return 0;
+ }
+
+ strm->next_in = (Bytef *) (in_buf + this_off);
+ strm->next_out = (Bytef *) (out_buf + off);
+ strm->avail_in = this_len;
+ strm->avail_out = len;
+ res = deflate(strm, finish ? Z_FINISH : flush);
+ (*env)->ReleasePrimitiveArrayCritical(env, b, out_buf, 0);
+ (*env)->ReleasePrimitiveArrayCritical(env, this_buf, in_buf, 0);
+
+ switch (res) {
+ case Z_STREAM_END:
+ (*env)->SetBooleanField(env, this, finishedID, JNI_TRUE);
+ /* fall through */
+ case Z_OK:
+ this_off += this_len - strm->avail_in;
+ (*env)->SetIntField(env, this, offID, this_off);
+ (*env)->SetIntField(env, this, lenID, strm->avail_in);
+ return len - strm->avail_out;
+ case Z_BUF_ERROR:
+ return 0;
+ default:
+ JNU_ThrowInternalError(env, strm->msg);
+ return 0;
+ }
+ }
+}
+
+JNIEXPORT jint JNICALL
+Java_net_sf_samtools_util_zip_IntelDeflater_getAdler(JNIEnv *env, jclass cls, jlong addr)
+{
+ return ((z_stream *)jlong_to_ptr(addr))->adler;
+}
+
+JNIEXPORT jlong JNICALL
+Java_net_sf_samtools_util_zip_IntelDeflater_getBytesRead(JNIEnv *env, jclass cls, jlong addr)
+{
+ return ((z_stream *)jlong_to_ptr(addr))->total_in;
+}
+
+JNIEXPORT jlong JNICALL
+Java_net_sf_samtools_util_zip_IntelDeflater_getBytesWritten(JNIEnv *env, jclass cls, jlong addr)
+{
+ return ((z_stream *)jlong_to_ptr(addr))->total_out;
+}
+
+JNIEXPORT void JNICALL
+Java_net_sf_samtools_util_zip_IntelDeflater_reset(JNIEnv *env, jclass cls, jlong addr)
+{
+ if (deflateReset((z_stream *)jlong_to_ptr(addr)) != Z_OK) {
+ JNU_ThrowInternalError(env, 0);
+ }
+}
+
+JNIEXPORT void JNICALL
+Java_net_sf_samtools_util_zip_IntelDeflater_end(JNIEnv *env, jclass cls, jlong addr)
+{
+ if (deflateEnd((z_stream *)jlong_to_ptr(addr)) == Z_STREAM_ERROR) {
+ JNU_ThrowInternalError(env, 0);
+ } else {
+ free((z_stream *)jlong_to_ptr(addr));
+ }
+}
diff --git a/src/java/net/sf/picard/cmdline/CommandLineProgram.java b/src/java/net/sf/picard/cmdline/CommandLineProgram.java
index bad3046..ac65a59 100644
--- a/src/java/net/sf/picard/cmdline/CommandLineProgram.java
+++ b/src/java/net/sf/picard/cmdline/CommandLineProgram.java
@@ -40,6 +40,7 @@ import net.sf.samtools.SAMFileWriterImpl;
import net.sf.samtools.util.BlockCompressedOutputStream;
import net.sf.samtools.util.BlockCompressedStreamConstants;
import net.sf.samtools.util.IOUtil;
+import net.sf.samtools.util.zip.DeflaterFactory;
/**
* Abstract class to facilitate writing command-line programs.
@@ -89,7 +90,7 @@ public abstract class CommandLineProgram {
@Option(doc = "Whether to create a BAM index when writing a coordinate-sorted BAM file.", common=true)
public Boolean CREATE_INDEX = Defaults.CREATE_INDEX;
- @Option(doc="Whether to create an MD5 digest for any BAM files created. ", common=true)
+ @Option(doc="Whether to create an MD5 digest for any BAM or FASTQ files created. ", common=true)
public boolean CREATE_MD5_FILE = Defaults.CREATE_MD5;
private final String standardUsagePreamble = CommandLineParser.getStandardUsagePreamble(getClass());
@@ -167,7 +168,8 @@ public abstract class CommandLineProgram {
" on " + System.getProperty("os.name") + " " + System.getProperty("os.version") +
" " + System.getProperty("os.arch") + "; " + System.getProperty("java.vm.name") +
" " + System.getProperty("java.runtime.version") +
- "; Picard version: " + commandLineParser.getVersion());
+ "; Picard version: " + commandLineParser.getVersion() +
+ " " + (DeflaterFactory.usingIntelDeflater()? "IntelDeflater": "JdkDeflater"));
}
catch (Exception e) { /* Unpossible! */ }
}
diff --git a/src/java/net/sf/picard/fastq/BasicFastqWriter.java b/src/java/net/sf/picard/fastq/BasicFastqWriter.java
index 3633af0..07ee661 100644
--- a/src/java/net/sf/picard/fastq/BasicFastqWriter.java
+++ b/src/java/net/sf/picard/fastq/BasicFastqWriter.java
@@ -27,6 +27,7 @@ import net.sf.picard.PicardException;
import net.sf.picard.io.IoUtil;
import java.io.File;
+import java.io.OutputStream;
import java.io.PrintStream;
/**
@@ -38,15 +39,19 @@ public class BasicFastqWriter implements FastqWriter {
private final PrintStream writer;
public BasicFastqWriter(final File file) {
- this(file, new PrintStream(IoUtil.openFileForWriting(file)));
+ this(file, false);
}
- private BasicFastqWriter(File file, PrintStream writer) {
+ public BasicFastqWriter(final File file, final boolean createMd5) {
+ this(file, new PrintStream(maybeMd5Wrap(file, createMd5)));
+ }
+
+ private BasicFastqWriter(final File file, final PrintStream writer) {
this.path = (file != null? file.getAbsolutePath(): "");
this.writer = writer;
}
- public BasicFastqWriter(PrintStream writer) {
+ public BasicFastqWriter(final PrintStream writer) {
this(null, writer);
}
@@ -69,4 +74,12 @@ public class BasicFastqWriter implements FastqWriter {
public void close() {
writer.close();
}
+
+ private static OutputStream maybeMd5Wrap(final File file, final boolean createMd5) {
+ if (createMd5) {
+ return IoUtil.openFileForMd5CalculatingWriting(file);
+ } else {
+ return IoUtil.openFileForWriting(file);
+ }
+ }
}
diff --git a/src/java/net/sf/picard/fastq/Casava18ReadNameEncoder.java b/src/java/net/sf/picard/fastq/Casava18ReadNameEncoder.java
new file mode 100644
index 0000000..90c1ade
--- /dev/null
+++ b/src/java/net/sf/picard/fastq/Casava18ReadNameEncoder.java
@@ -0,0 +1,46 @@
+package net.sf.picard.fastq;
+
+import net.sf.picard.illumina.parser.ClusterData;
+import net.sf.samtools.util.StringUtil;
+
+/**
+ * A read name encoder conforming to the standard described by Illumina Casava 1.8.
+ *
+ * @see <a href="http://biowulf.nih.gov/apps/CASAVA1_8_Changes.pdf">Casava 1.8 update</a>
+ * @author mccowan
+ */
+public class Casava18ReadNameEncoder implements ReadNameEncoder {
+ final static int CONTROL_FIELD_VALUE = 0;
+ final String runId, instrumentName, flowcellId;
+
+ static enum PassesFilterLabel {
+ Y, N;
+ static PassesFilterLabel get(final boolean passesFilter) {
+ return passesFilter ? Y : N;
+ }
+ }
+
+ public Casava18ReadNameEncoder(final String instrumentName, final String runId, final String flowcellId) {
+ this.runId = runId;
+ this.instrumentName = instrumentName;
+ this.flowcellId = flowcellId;
+ }
+
+ @Override
+ public String generateReadName(final ClusterData cluster, final Integer pairNumber) {
+ return String.format(
+ "%s:%s:%s:%d:%d:%d:%d %s:%s:%d:%s",
+ instrumentName,
+ runId,
+ flowcellId,
+ cluster.getLane(),
+ cluster.getTile(),
+ cluster.getX(),
+ cluster.getY(),
+ StringUtil.asEmptyIfNull(pairNumber),
+ PassesFilterLabel.get(cluster.isPf()),
+ CONTROL_FIELD_VALUE,
+ StringUtil.asEmptyIfNull(cluster.getMatchedBarcode())
+ );
+ }
+}
diff --git a/src/java/net/sf/picard/fastq/FastqReader.java b/src/java/net/sf/picard/fastq/FastqReader.java
index 654d02b..76a27ba 100755
--- a/src/java/net/sf/picard/fastq/FastqReader.java
+++ b/src/java/net/sf/picard/fastq/FastqReader.java
@@ -41,9 +41,16 @@ public class FastqReader implements Iterator<FastqRecord>, Iterable<FastqRecord>
final private File fastqFile;
final private BufferedReader reader;
private FastqRecord nextRecord;
- private int line=1;
+ private int line=1;
+
+ final private boolean skipBlankLines;
public FastqReader(final File file) {
+ this(file,false);
+ }
+
+ public FastqReader(final File file, final boolean skipBlankLines) {
+ this.skipBlankLines=skipBlankLines;
try {
fastqFile = file;
reader = IoUtil.openFileForBufferedReading(fastqFile);
@@ -54,21 +61,22 @@ public class FastqReader implements Iterator<FastqRecord>, Iterable<FastqRecord>
}
}
- public FastqReader(BufferedReader reader) {
+ public FastqReader(final BufferedReader reader) {
this(null, reader);
}
- public FastqReader(final File file, BufferedReader reader) {
+ public FastqReader(final File file, final BufferedReader reader) {
fastqFile = file;
this.reader = reader;
nextRecord = readNextRecord();
+ skipBlankLines = false;
}
private FastqRecord readNextRecord() {
try {
// Read sequence header
- final String seqHeader = reader.readLine();
+ final String seqHeader = readLineConditionallySkippingBlanks();
if (seqHeader == null) return null ;
if (StringUtil.isBlank(seqHeader)) {
throw new PicardException(error("Missing sequence header"));
@@ -78,18 +86,18 @@ public class FastqReader implements Iterator<FastqRecord>, Iterable<FastqRecord>
}
// Read sequence line
- final String seqLine = reader.readLine();
+ final String seqLine = readLineConditionallySkippingBlanks();
checkLine(seqLine,"sequence line");
// Read quality header
- final String qualHeader = reader.readLine();
+ final String qualHeader = readLineConditionallySkippingBlanks();
checkLine(qualHeader,"quality header");
if (!qualHeader.startsWith(FastqConstants.QUALITY_HEADER)) {
throw new PicardException(error("Quality header must start with "+ FastqConstants.QUALITY_HEADER+": "+qualHeader));
}
// Read quality line
- final String qualLine = reader.readLine();
+ final String qualLine = readLineConditionallySkippingBlanks();
checkLine(qualLine,"quality line");
// Check sequence and quality lines are same length
@@ -160,4 +168,15 @@ public class FastqReader implements Iterator<FastqRecord>, Iterable<FastqRecord>
if (fastqFile == null) return "";
else return fastqFile.getAbsolutePath();
}
+
+ private String readLineConditionallySkippingBlanks() throws IOException {
+ String line;
+ do {
+ line = reader.readLine();
+ if (line == null) return line;
+ } while(skipBlankLines && StringUtil.isBlank(line));
+ return line;
+ }
+
+
}
diff --git a/src/java/net/sf/picard/fastq/FastqWriterFactory.java b/src/java/net/sf/picard/fastq/FastqWriterFactory.java
index 92372ce..5045a6f 100644
--- a/src/java/net/sf/picard/fastq/FastqWriterFactory.java
+++ b/src/java/net/sf/picard/fastq/FastqWriterFactory.java
@@ -11,12 +11,16 @@ import java.io.File;
*/
public class FastqWriterFactory {
boolean useAsyncIo = Defaults.USE_ASYNC_IO;
+ boolean createMd5 = Defaults.CREATE_MD5;
/** Sets whether or not to use async io (i.e. a dedicated thread per writer. */
public void setUseAsyncIo(final boolean useAsyncIo) { this.useAsyncIo = useAsyncIo; }
+ /** If true, compute MD5 and write appropriately-named file when file is closed. */
+ public void setCreateMd5(final boolean createMd5) { this.createMd5 = createMd5; }
+
public FastqWriter newWriter(final File out) {
- final FastqWriter writer = new BasicFastqWriter(out);
+ final FastqWriter writer = new BasicFastqWriter(out, createMd5);
if (useAsyncIo) {
return new AsyncFastqWriter(writer, AsyncFastqWriter.DEFAULT_QUEUE_SIZE);
}
diff --git a/src/java/net/sf/picard/fastq/IlluminaReadNameEncoder.java b/src/java/net/sf/picard/fastq/IlluminaReadNameEncoder.java
new file mode 100644
index 0000000..a00dc55
--- /dev/null
+++ b/src/java/net/sf/picard/fastq/IlluminaReadNameEncoder.java
@@ -0,0 +1,28 @@
+package net.sf.picard.fastq;
+
+import net.sf.picard.illumina.parser.ClusterData;
+
+/**
+ * A read name encoder following the encoding initially produced by picard fastq writers.
+ *
+ * @see <a href="http://en.wikipedia.org/wiki/FASTQ_format#Illumina_sequence_identifiers">Illumina sequence identifiers</a> almost describes the format used here, except instead of an instrumnet name, we write the run barcode
+ * @author mccowan
+ */
+public class IlluminaReadNameEncoder implements ReadNameEncoder {
+ final String runBarcode;
+ public IlluminaReadNameEncoder(final String runBarcode) {
+ this.runBarcode = runBarcode;
+ }
+
+ @Override
+ public String generateReadName(final ClusterData cluster, final Integer pairNumber) {
+ return runBarcode + ":" + cluster.getLane() + ":" + cluster.getTile() + ":" + cluster.getX() + ":" + cluster.getY() + generatePairNumberSuffix(pairNumber);
+ }
+
+ private static String generatePairNumberSuffix(final Integer pairNumber) {
+ if (pairNumber == null)
+ return "";
+ else
+ return "/" + pairNumber;
+ }
+}
diff --git a/src/java/net/sf/picard/fastq/ReadNameEncoder.java b/src/java/net/sf/picard/fastq/ReadNameEncoder.java
new file mode 100644
index 0000000..2ede364
--- /dev/null
+++ b/src/java/net/sf/picard/fastq/ReadNameEncoder.java
@@ -0,0 +1,17 @@
+package net.sf.picard.fastq;
+
+import net.sf.picard.illumina.parser.ClusterData;
+
+/**
+ * @author mccowan
+ */
+public interface ReadNameEncoder {
+ /**
+ * Generates a read name string for the provided cluster.
+ *
+ * @param cluster The cluster whose reads are having its name generated
+ * @param pairNumber 1 if this is the first of the pair, 2 if it is the second, or null if this not a paired read.
+ * @return The read name
+ */
+ String generateReadName(ClusterData cluster, Integer pairNumber);
+}
diff --git a/src/java/net/sf/picard/illumina/ClusterDataToSamConverter.java b/src/java/net/sf/picard/illumina/ClusterDataToSamConverter.java
index 3588863..8b2a9a6 100644
--- a/src/java/net/sf/picard/illumina/ClusterDataToSamConverter.java
+++ b/src/java/net/sf/picard/illumina/ClusterDataToSamConverter.java
@@ -23,6 +23,8 @@
*/
package net.sf.picard.illumina;
+import net.sf.picard.fastq.IlluminaReadNameEncoder;
+import net.sf.picard.fastq.ReadNameEncoder;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.picard.filter.SolexaNoiseFilter;
import net.sf.picard.illumina.parser.ClusterData;
@@ -56,7 +58,8 @@ public class ClusterDataToSamConverter implements
private final int [] barcodeIndices;
private final AdapterPair[] adaptersToCheck;
private final int outputRecordsPerCluster;
-
+ private final ReadNameEncoder readNameEncoder;
+
/**
* Constructor
*
@@ -72,6 +75,8 @@ public class ClusterDataToSamConverter implements
final List<IlluminaUtil.IlluminaAdapterPair> adapters) {
this.runBarcode = runBarcode;
this.readGroupId = readGroupId;
+
+ this.readNameEncoder = new IlluminaReadNameEncoder(runBarcode);
this.isPairedEnd = readStructure.templates.length() == 2;
this.isBarcoded = !readStructure.barcodes.isEmpty();
@@ -127,8 +132,7 @@ public class ClusterDataToSamConverter implements
public IlluminaBasecallsToSam.SAMRecordsForCluster convertClusterToOutputRecord(final ClusterData cluster) {
final IlluminaBasecallsToSam.SAMRecordsForCluster ret = new IlluminaBasecallsToSam.SAMRecordsForCluster(outputRecordsPerCluster);
-
- final String readName = IlluminaUtil.makeReadName(runBarcode, cluster.getLane(), cluster.getTile(), cluster.getX(), cluster.getY());
+ final String readName = readNameEncoder.generateReadName(cluster, null); // Use null here to prevent /1 or /2 suffixes on read name.
// Get and transform the unmatched barcode, if any, to store with the reads
String unmatchedBarcode = null;
diff --git a/src/java/net/sf/picard/illumina/ExtractIlluminaBarcodes.java b/src/java/net/sf/picard/illumina/ExtractIlluminaBarcodes.java
index 60b7dfc..23d7042 100644
--- a/src/java/net/sf/picard/illumina/ExtractIlluminaBarcodes.java
+++ b/src/java/net/sf/picard/illumina/ExtractIlluminaBarcodes.java
@@ -23,25 +23,25 @@
*/
package net.sf.picard.illumina;
-import net.sf.picard.illumina.parser.*;
-import net.sf.picard.illumina.parser.readers.BclQualityEvaluationStrategy;
-import net.sf.picard.util.IlluminaUtil;
-import net.sf.picard.util.Log;
-import net.sf.picard.util.TabbedTextFileWithHeaderParser;
import net.sf.picard.cmdline.CommandLineProgram;
import net.sf.picard.cmdline.Option;
import net.sf.picard.cmdline.StandardOptionDefinitions;
import net.sf.picard.cmdline.Usage;
+import net.sf.picard.illumina.parser.*;
+import net.sf.picard.illumina.parser.readers.BclQualityEvaluationStrategy;
import net.sf.picard.io.IoUtil;
import net.sf.picard.metrics.MetricBase;
import net.sf.picard.metrics.MetricsFile;
+import net.sf.picard.util.IlluminaUtil;
+import net.sf.picard.util.Log;
+import net.sf.picard.util.TabbedTextFileWithHeaderParser;
import net.sf.samtools.util.SequenceUtil;
import net.sf.samtools.util.StringUtil;
import java.io.BufferedWriter;
import java.io.File;
-import java.util.*;
import java.text.NumberFormat;
+import java.util.*;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.TimeUnit;
@@ -54,8 +54,8 @@ import java.util.concurrent.TimeUnit;
* - read subsequence at barcode position
* - Y or N indicating if there was a barcode match
* - matched barcode sequence (empty if read did not match one of the barcodes). If there is no match
- * but we're close to the threshold of calling it a match we output the barcode that would have been
- * matched but in lower case
+ * but we're close to the threshold of calling it a match we output the barcode that would have been
+ * matched but in lower case
*
* @author jburke at broadinstitute.org
*/
@@ -64,56 +64,56 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
// The following attributes define the command-line arguments
@Usage
public String USAGE =
- getStandardUsagePreamble() + "Determine the barcode for each read in an Illumina lane.\n" +
- "For each tile, a file is written to the basecalls directory of the form s_<lane>_<tile>_barcode.txt. " +
- "An output file contains a line for each read in the tile, aligned with the regular basecall output. \n" +
- "The output file contains the following tab-separated columns: \n" +
- " * read subsequence at barcode position\n" +
- " * Y or N indicating if there was a barcode match\n" +
- " * matched barcode sequence\n" +
- "Note that the order of specification of barcodes can cause arbitrary differences in output for poorly matching barcodes.\n\n";
-
- @Option(doc="The Illumina basecalls directory. ", shortName="B")
+ getStandardUsagePreamble() + "Determine the barcode for each read in an Illumina lane.\n" +
+ "For each tile, a file is written to the basecalls directory of the form s_<lane>_<tile>_barcode.txt. " +
+ "An output file contains a line for each read in the tile, aligned with the regular basecall output. \n" +
+ "The output file contains the following tab-separated columns: \n" +
+ " * read subsequence at barcode position\n" +
+ " * Y or N indicating if there was a barcode match\n" +
+ " * matched barcode sequence\n" +
+ "Note that the order of specification of barcodes can cause arbitrary differences in output for poorly matching barcodes.\n\n";
+
+ @Option(doc = "The Illumina basecalls directory. ", shortName = "B")
public File BASECALLS_DIR;
- @Option(doc="Where to write _barcode.txt files. By default, these are written to BASECALLS_DIR.", optional = true)
+ @Option(doc = "Where to write _barcode.txt files. By default, these are written to BASECALLS_DIR.", optional = true)
public File OUTPUT_DIR;
- @Option(doc="Lane number. ", shortName= StandardOptionDefinitions.LANE_SHORT_NAME)
+ @Option(doc = "Lane number. ", shortName = StandardOptionDefinitions.LANE_SHORT_NAME)
public Integer LANE;
- @Option(doc= ReadStructure.PARAMETER_DOC, shortName="RS")
+ @Option(doc = ReadStructure.PARAMETER_DOC, shortName = "RS")
public String READ_STRUCTURE;
- @Option(doc="Barcode sequence. These must be unique, and all the same length. This cannot be used with reads that " +
+ @Option(doc = "Barcode sequence. These must be unique, and all the same length. This cannot be used with reads that " +
"have more than one barcode; use BARCODE_FILE in that case. ", mutex = {"BARCODE_FILE"})
public List<String> BARCODE = new ArrayList<String>();
- @Option(doc="Tab-delimited file of barcode sequences, barcode name and, optionally, library name. " +
+ @Option(doc = "Tab-delimited file of barcode sequences, barcode name and, optionally, library name. " +
"Barcodes must be unique and all the same length. Column headers must be 'barcode_sequence_1', " +
"'barcode_sequence_2' (optional), 'barcode_name', and 'library_name'.", mutex = {"BARCODE"})
public File BARCODE_FILE;
- @Option(doc="Per-barcode and per-lane metrics written to this file.", shortName = StandardOptionDefinitions.METRICS_FILE_SHORT_NAME)
+ @Option(doc = "Per-barcode and per-lane metrics written to this file.", shortName = StandardOptionDefinitions.METRICS_FILE_SHORT_NAME)
public File METRICS_FILE;
- @Option(doc="Maximum mismatches for a barcode to be considered a match.")
+ @Option(doc = "Maximum mismatches for a barcode to be considered a match.")
public int MAX_MISMATCHES = 1;
- @Option(doc="Minimum difference between number of mismatches in the best and second best barcodes for a barcode to be considered a match.")
+ @Option(doc = "Minimum difference between number of mismatches in the best and second best barcodes for a barcode to be considered a match.")
public int MIN_MISMATCH_DELTA = 1;
- @Option(doc="Maximum allowable number of no-calls in a barcode read before it is considered unmatchable.")
+ @Option(doc = "Maximum allowable number of no-calls in a barcode read before it is considered unmatchable.")
public int MAX_NO_CALLS = 2;
-
- @Option(shortName="Q", doc="Minimum base quality. Any barcode bases falling below this quality will be considered a mismatch even in the bases match.")
+
+ @Option(shortName = "Q", doc = "Minimum base quality. Any barcode bases falling below this quality will be considered a mismatch even in the bases match.")
public int MINIMUM_BASE_QUALITY = 0;
- @Option(doc="The minimum quality (after transforming 0s to 1s) expected from reads. If qualities are lower than this value, an error is thrown." +
+ @Option(doc = "The minimum quality (after transforming 0s to 1s) expected from reads. If qualities are lower than this value, an error is thrown." +
"The default of 2 is what the Illumina's spec describes as the minimum, but in practice the value has been observed lower.")
public int MINIMUM_QUALITY = BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY;
-
- @Option(shortName="GZIP", doc="Compress output s_l_t_barcode.txt files using gzip and append a .gz extension to the filenames.")
+
+ @Option(shortName = "GZIP", doc = "Compress output s_l_t_barcode.txt files using gzip and append a .gz extension to the file names.")
public boolean COMPRESS_OUTPUTS = false;
@Option(doc = "Run this many PerTileBarcodeExtractors in parallel. If NUM_PROCESSORS = 0, number of cores is automatically set to " +
@@ -121,18 +121,14 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
"the number available on the machine less NUM_PROCESSORS.")
public int NUM_PROCESSORS = 1;
- private final Log log = Log.getInstance(ExtractIlluminaBarcodes.class);
+ private static final Log LOG = Log.getInstance(ExtractIlluminaBarcodes.class);
/** The read structure of the actual Illumina Run, i.e. the readStructure of the input data */
private ReadStructure readStructure;
- /** The read structure of the output cluster data, this may be different from the input readStructure if there are SKIPs in the input readStructure */
- private ReadStructure outputReadStructure;
-
private IlluminaDataProviderFactory factory;
- private final Map<String,BarcodeMetric> barcodeToMetrics = new LinkedHashMap<String,BarcodeMetric>();
- private BarcodeMetric noMatchMetric = null;
+ private final Map<String, BarcodeMetric> barcodeToMetrics = new LinkedHashMap<String, BarcodeMetric>();
private final NumberFormat tileNumberFormatter = NumberFormat.getNumberInstance();
private BclQualityEvaluationStrategy bclQualityEvaluationStrategy;
@@ -143,7 +139,7 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
}
@Override
- protected int doWork() {
+ protected int doWork() {
IoUtil.assertFileIsWritable(METRICS_FILE);
if (OUTPUT_DIR == null) {
@@ -159,26 +155,35 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
noMatchBarcode[index++] = StringUtil.repeatCharNTimes('N', d.length);
}
}
- noMatchMetric = new BarcodeMetric(null, null, IlluminaUtil.barcodeSeqsToString(noMatchBarcode), noMatchBarcode);
+
+ final BarcodeMetric noMatchMetric = new BarcodeMetric(null, null, IlluminaUtil.barcodeSeqsToString(noMatchBarcode), noMatchBarcode);
final int numProcessors;
if (NUM_PROCESSORS == 0) {
numProcessors = Runtime.getRuntime().availableProcessors();
- }
- else if (NUM_PROCESSORS < 0) {
+ } else if (NUM_PROCESSORS < 0) {
numProcessors = Runtime.getRuntime().availableProcessors() + NUM_PROCESSORS;
- }
- else {
+ } else {
numProcessors = NUM_PROCESSORS;
}
- log.info("Processing with " + numProcessors + " PerTileBarcodeExtractor(s).");
+ LOG.info("Processing with " + numProcessors + " PerTileBarcodeExtractor(s).");
final ExecutorService pool = Executors.newFixedThreadPool(numProcessors);
final List<PerTileBarcodeExtractor> extractors = new ArrayList<PerTileBarcodeExtractor>(factory.getAvailableTiles().size());
for (final int tile : factory.getAvailableTiles()) {
- final PerTileBarcodeExtractor extractor = new PerTileBarcodeExtractor(tile, getBarcodeFile(tile));
+ final PerTileBarcodeExtractor extractor = new PerTileBarcodeExtractor(
+ tile,
+ getBarcodeFile(tile),
+ barcodeToMetrics,
+ noMatchMetric,
+ factory,
+ MINIMUM_BASE_QUALITY,
+ MAX_NO_CALLS,
+ MAX_MISMATCHES,
+ MIN_MISMATCH_DELTA
+ );
pool.submit(extractor);
extractors.add(extractor);
}
@@ -189,24 +194,23 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
pool.shutdownNow(); // Cancel any still-executing tasks
// Wait a while for tasks to respond to being cancelled
if (!pool.awaitTermination(60, TimeUnit.SECONDS))
- log.error("Pool did not terminate");
+ LOG.error("Pool did not terminate");
return 1;
}
- }
- catch (InterruptedException ie) {
+ } catch (InterruptedException ie) {
// (Re-)Cancel if current thread also interrupted
pool.shutdownNow();
return 2;
}
- log.info("Processed " + extractors.size() + " tiles.");
+ LOG.info("Processed " + extractors.size() + " tiles.");
for (final PerTileBarcodeExtractor extractor : extractors) {
for (final String key : barcodeToMetrics.keySet()) {
barcodeToMetrics.get(key).merge(extractor.getMetrics().get(key));
}
noMatchMetric.merge(extractor.getNoMatchMetric());
if (extractor.getException() != null) {
- log.error("Abandoning metrics calculation because one or more PerTileBarcodeExtractors failed.");
+ LOG.error("Abandoning metrics calculation because one or more PerTileBarcodeExtractors failed.");
return 4;
}
}
@@ -223,54 +227,54 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
}
if (totalReads > 0) {
- noMatchMetric.PCT_MATCHES = noMatchMetric.READS/(double)totalReads;
+ noMatchMetric.PCT_MATCHES = noMatchMetric.READS / (double) totalReads;
double bestPctOfAllBarcodeMatches = 0;
for (final BarcodeMetric barcodeMetric : barcodeToMetrics.values()) {
- barcodeMetric.PCT_MATCHES = barcodeMetric.READS/(double)totalReads;
+ barcodeMetric.PCT_MATCHES = barcodeMetric.READS / (double) totalReads;
if (barcodeMetric.PCT_MATCHES > bestPctOfAllBarcodeMatches) {
bestPctOfAllBarcodeMatches = barcodeMetric.PCT_MATCHES;
}
}
if (bestPctOfAllBarcodeMatches > 0) {
noMatchMetric.RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT =
- noMatchMetric.PCT_MATCHES/bestPctOfAllBarcodeMatches;
+ noMatchMetric.PCT_MATCHES / bestPctOfAllBarcodeMatches;
for (final BarcodeMetric barcodeMetric : barcodeToMetrics.values()) {
barcodeMetric.RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT =
- barcodeMetric.PCT_MATCHES/bestPctOfAllBarcodeMatches;
+ barcodeMetric.PCT_MATCHES / bestPctOfAllBarcodeMatches;
}
}
}
if (totalPfReads > 0) {
- noMatchMetric.PF_PCT_MATCHES = noMatchMetric.PF_READS/(double)totalPfReads;
+ noMatchMetric.PF_PCT_MATCHES = noMatchMetric.PF_READS / (double) totalPfReads;
double bestPctOfAllBarcodeMatches = 0;
for (final BarcodeMetric barcodeMetric : barcodeToMetrics.values()) {
- barcodeMetric.PF_PCT_MATCHES = barcodeMetric.PF_READS/(double)totalPfReads;
+ barcodeMetric.PF_PCT_MATCHES = barcodeMetric.PF_READS / (double) totalPfReads;
if (barcodeMetric.PF_PCT_MATCHES > bestPctOfAllBarcodeMatches) {
bestPctOfAllBarcodeMatches = barcodeMetric.PF_PCT_MATCHES;
}
}
if (bestPctOfAllBarcodeMatches > 0) {
noMatchMetric.PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT =
- noMatchMetric.PF_PCT_MATCHES/bestPctOfAllBarcodeMatches;
+ noMatchMetric.PF_PCT_MATCHES / bestPctOfAllBarcodeMatches;
for (final BarcodeMetric barcodeMetric : barcodeToMetrics.values()) {
barcodeMetric.PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT =
- barcodeMetric.PF_PCT_MATCHES/bestPctOfAllBarcodeMatches;
+ barcodeMetric.PF_PCT_MATCHES / bestPctOfAllBarcodeMatches;
}
}
}
// Warn about minimum qualities and assert that we've achieved the minimum.
for (Map.Entry<Byte, Integer> entry : bclQualityEvaluationStrategy.getPoorQualityFrequencies().entrySet()) {
- log.warn(String.format("Observed low quality of %s %s times.", entry.getKey(), entry.getValue()));
+ LOG.warn(String.format("Observed low quality of %s %s times.", entry.getKey(), entry.getValue()));
}
bclQualityEvaluationStrategy.assertMinimumQualities();
-
+
// Calculate the normalized matches
if (totalPfReadsAssigned > 0) {
final double mean = (double) totalPfReadsAssigned / (double) barcodeToMetrics.values().size();
for (final BarcodeMetric m : barcodeToMetrics.values()) {
- m.PF_NORMALIZED_MATCHES = m.PF_READS / mean;
+ m.PF_NORMALIZED_MATCHES = m.PF_READS / mean;
}
}
@@ -283,12 +287,10 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
return 0;
}
- /**
- * Create a barcode filename corresponding to the given tile qseq file.
- */
+ /** Create a barcode filename corresponding to the given tile qseq file. */
private File getBarcodeFile(final int tile) {
return new File(OUTPUT_DIR,
- "s_" + LANE + "_" + tileNumberFormatter.format(tile) + "_barcode.txt" + (COMPRESS_OUTPUTS ? ".gz" : ""));
+ "s_" + LANE + "_" + tileNumberFormatter.format(tile) + "_barcode.txt" + (COMPRESS_OUTPUTS ? ".gz" : ""));
}
/**
@@ -302,18 +304,17 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
final ArrayList<String> messages = new ArrayList<String>();
this.bclQualityEvaluationStrategy = new BclQualityEvaluationStrategy(MINIMUM_QUALITY);
-
+
/**
* In extract illumina barcodes we NEVER want to look at the template reads, therefore replace them with skips because
* IlluminaDataProvider and its factory will not open these nor produce ClusterData with the template reads in them, thus reducing
* the file IO and value copying done by the data provider
*/
readStructure = new ReadStructure(READ_STRUCTURE.replaceAll("T", "S"));
- final IlluminaDataType[] datatypes = (MINIMUM_BASE_QUALITY > 0) ?
- new IlluminaDataType[] {IlluminaDataType.BaseCalls, IlluminaDataType.PF, IlluminaDataType.QualityScores}:
- new IlluminaDataType[] {IlluminaDataType.BaseCalls, IlluminaDataType.PF};
+ final IlluminaDataType[] datatypes = (MINIMUM_BASE_QUALITY > 0) ?
+ new IlluminaDataType[]{IlluminaDataType.BaseCalls, IlluminaDataType.PF, IlluminaDataType.QualityScores} :
+ new IlluminaDataType[]{IlluminaDataType.BaseCalls, IlluminaDataType.PF};
factory = new IlluminaDataProviderFactory(BASECALLS_DIR, LANE, readStructure, bclQualityEvaluationStrategy, datatypes);
- outputReadStructure = factory.getOutputReadStructure();
if (BARCODE_FILE != null) {
parseBarcodeFile(messages);
@@ -366,7 +367,7 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
for (final ReadDescriptor rd : readStructure.descriptors) {
if (rd.type != ReadType.Barcode) continue;
final String header = barcodeNum == 1 ? sequenceColumn : "barcode_sequence_" + String.valueOf(barcodeNum);
- bcStrings[barcodeNum-1] = row.getField(header);
+ bcStrings[barcodeNum - 1] = row.getField(header);
barcodeNum++;
}
final String bcStr = IlluminaUtil.barcodeSeqsToString(bcStrings);
@@ -374,8 +375,8 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
messages.add("Barcode " + bcStr + " specified more than once in " + BARCODE_FILE);
}
barcodes.add(bcStr);
- final String barcodeName = (hasBarcodeName? row.getField(BARCODE_NAME_COLUMN): "");
- final String libraryName = (hasLibraryName? row.getField(LIBRARY_NAME_COLUMN): "");
+ final String barcodeName = (hasBarcodeName ? row.getField(BARCODE_NAME_COLUMN) : "");
+ final String libraryName = (hasLibraryName ? row.getField(LIBRARY_NAME_COLUMN) : "");
final BarcodeMetric metric = new BarcodeMetric(barcodeName, libraryName, bcStr, bcStrings);
barcodeToMetrics.put(StringUtil.join("", bcStrings), metric);
}
@@ -425,9 +426,8 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
* The rate of PF reads matching this barcode to PF reads matching the most prevelant barcode. For the
* most prevelant barcode this will be 1, for all others it will be less than 1 (except for the possible
* exception of when there are more orphan reads than for any other barcode, in which case the value
- * may be arbitrarily large). One over the lowest number in this column gives you the fold-difference
+ * may be arbitrarily large). One over the lowest number in this column gives you the fold-difference
* in representation of PF reads between barcodes.
- *
*/
public double PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT = 0d;
@@ -452,16 +452,12 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
}
}
- /**
- * This ctor is necessary for when reading metrics from file
- */
+ /** This ctor is necessary for when reading metrics from file */
public BarcodeMetric() {
barcodeBytes = null;
}
- /**
- * Creates a copy of metric initialized with only non-accumulated and non-calculated values set
- */
+ /** Creates a copy of metric initialized with only non-accumulated and non-calculated values set */
public static BarcodeMetric copy(final BarcodeMetric metric) {
final BarcodeMetric result = new BarcodeMetric();
result.BARCODE = metric.BARCODE;
@@ -473,7 +469,8 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
/**
- * Adds the non-calculated
+ * Adds the non-calculated
+ *
* @param metric
*/
public void merge(final BarcodeMetric metric) {
@@ -487,16 +484,17 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
}
- /**
- * Extracts barcodes and accumulates metrics for an entire tile.
- */
- private class PerTileBarcodeExtractor implements Runnable {
+ /** Extracts barcodes and accumulates metrics for an entire tile. */
+ private static class PerTileBarcodeExtractor implements Runnable {
private final int tile;
private final File barcodeFile;
- private final Map<String,BarcodeMetric> metrics;
+ private final Map<String, BarcodeMetric> metrics;
private final BarcodeMetric noMatch;
private Exception exception = null;
- private final boolean usingQualityScores= MINIMUM_BASE_QUALITY > 0;
+ private final boolean usingQualityScores;
+ private final IlluminaDataProvider provider;
+ private final ReadStructure outputReadStructure;
+ private final int maxNoCalls, maxMismatches, minMismatchDelta, minimumBaseQuality;
/** Utility class to hang onto data about the best match for a given barcode */
class BarcodeMatch {
@@ -508,40 +506,63 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
/**
* Constructor
- * @param tile The number of the tile being processed; used for logging only.
- * @param barcodeFile The file to write the barcodes to
+ *
+ * @param tile The number of the tile being processed; used for logging only.
+ * @param barcodeFile The file to write the barcodes to
+ * @param noMatchMetric A "template" metric that is cloned and the clone is stored internally for accumulating data
+ * @param barcodeToMetrics A "template" metric map whose metrics are cloned, and the clones are stored internally for accumulating data
*/
- public PerTileBarcodeExtractor(final int tile, final File barcodeFile) {
+ public PerTileBarcodeExtractor(
+ final int tile,
+ final File barcodeFile,
+ final Map<String, BarcodeMetric> barcodeToMetrics,
+ final BarcodeMetric noMatchMetric,
+ final IlluminaDataProviderFactory factory,
+ final int minimumBaseQuality,
+ final int maxNoCalls,
+ final int maxMismatches,
+ final int minMismatchDelta
+ ) {
this.tile = tile;
this.barcodeFile = barcodeFile;
- this.metrics = new LinkedHashMap<String,BarcodeMetric>(barcodeToMetrics.size());
+ this.usingQualityScores = minimumBaseQuality > 0;
+ this.maxNoCalls = maxNoCalls;
+ this.maxMismatches = maxMismatches;
+ this.minMismatchDelta = minMismatchDelta;
+ this.minimumBaseQuality = minimumBaseQuality;
+ this.metrics = new LinkedHashMap<String, BarcodeMetric>(barcodeToMetrics.size());
for (final String key : barcodeToMetrics.keySet()) {
this.metrics.put(key, BarcodeMetric.copy(barcodeToMetrics.get(key)));
}
this.noMatch = BarcodeMetric.copy(noMatchMetric);
+ this.provider = factory.makeDataProvider(Arrays.asList(tile));
+ this.outputReadStructure = factory.getOutputReadStructure();
+
}
// These methods return the results of the extraction
- public synchronized Map<String,BarcodeMetric> getMetrics() { return this.metrics; }
+ public synchronized Map<String, BarcodeMetric> getMetrics() {
+ return this.metrics;
+ }
+
public synchronized BarcodeMetric getNoMatchMetric() { return this.noMatch; }
+
public synchronized Exception getException() { return this.exception; }
- /**
- * run method which extracts barcodes and accumulates metrics for an entire tile
- */
+ /** run method which extracts barcodes and accumulates metrics for an entire tile */
synchronized public void run() {
try {
- log.info("Extracting barcodes for tile " + tile);
+ LOG.info("Extracting barcodes for tile " + tile);
//Sometimes makeDataProvider takes a while waiting for slow file IO, for each tile the needed set of files
//is non-overlapping sets of files so make the data providers in the individual threads for PerTileBarcodeExtractors
//so they are not all waiting for each others file operations
- final IlluminaDataProvider provider = factory.makeDataProvider(Arrays.asList(tile));
+
//Most likely we have SKIPS in our read structure since we replace all template reads with skips in the input data structure
//(see customCommnandLineValidation), therefore we must use the outputReadStructure to index into the output cluster data
- final int [] barcodeIndices = outputReadStructure.barcodes.getIndices();
+ final int[] barcodeIndices = outputReadStructure.barcodes.getIndices();
final BufferedWriter writer = IoUtil.openFileForBufferedWriting(barcodeFile);
final byte barcodeSubsequences[][] = new byte[barcodeIndices.length][];
final byte qualityScores[][] = usingQualityScores ? new byte[barcodeIndices.length][] : null;
@@ -553,7 +574,7 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
if (usingQualityScores) qualityScores[i] = cluster.getRead(barcodeIndices[i]).getQualities();
}
final boolean passingFilter = cluster.isPf();
- final BarcodeMatch match = findBestBarcodeAndUpdateMetrics(barcodeSubsequences, qualityScores, passingFilter, metrics, noMatchMetric);
+ final BarcodeMatch match = findBestBarcodeAndUpdateMetrics(barcodeSubsequences, qualityScores, passingFilter, metrics, noMatch);
final String yOrN = (match.matched ? "Y" : "N");
@@ -565,17 +586,17 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
writer.newLine();
}
writer.close();
- }
- catch (Exception e) {
- log.error(e, "Error processing tile ", this.tile);
+ } catch (Exception e) {
+ LOG.error(e, "Error processing tile ", this.tile);
this.exception = e;
}
}
/**
* Find the best barcode match for the given read sequence, and accumulate metrics
+ *
* @param readSubsequences portion of read containing barcode
- * @param passingFilter PF flag for the current read
+ * @param passingFilter PF flag for the current read
* @return perfect barcode string, if there was a match within tolerance, or null if not.
*/
private BarcodeMatch findBestBarcodeAndUpdateMetrics(final byte[][] readSubsequences,
@@ -612,9 +633,9 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
}
final boolean matched = bestBarcodeMetric != null &&
- numNoCalls <= MAX_NO_CALLS &&
- numMismatchesInBestBarcode <= MAX_MISMATCHES &&
- numMismatchesInSecondBestBarcode - numMismatchesInBestBarcode >= MIN_MISMATCH_DELTA;
+ numNoCalls <= maxNoCalls &&
+ numMismatchesInBestBarcode <= maxMismatches &&
+ numMismatchesInSecondBestBarcode - numMismatchesInBestBarcode >= minMismatchDelta;
final BarcodeMatch match = new BarcodeMatch();
@@ -624,8 +645,7 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
match.mismatches = numMismatchesInBestBarcode;
match.mismatchesToSecondBest = numMismatchesInSecondBestBarcode;
match.barcode = bestBarcodeMetric.BARCODE.toLowerCase().replaceAll(IlluminaUtil.BARCODE_DELIMITER, "");
- }
- else {
+ } else {
match.mismatches = totalBarcodeReadBases;
match.barcode = "";
}
@@ -649,8 +669,7 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
match.matched = true;
match.barcode = bestBarcodeMetric.BARCODE.replaceAll(IlluminaUtil.BARCODE_DELIMITER, "");
- }
- else {
+ } else {
++noMatchBarcodeMetric.READS;
if (passingFilter) {
++noMatchBarcodeMetric.PF_READS;
@@ -662,6 +681,7 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
/**
* Compare barcode sequence to bases from read
+ *
* @return how many bases did not match
*/
private int countMismatches(final byte[][] barcodeBytes, final byte[][] readSubsequence, final byte[][] qualities) {
@@ -672,7 +692,7 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
for (int i = 0; i < basesToCheck; ++i) {
if (!SequenceUtil.isNoCall(readSubsequence[j][i])) {
if (!SequenceUtil.basesEqual(barcodeBytes[j][i], readSubsequence[j][i])) ++numMismatches;
- else if (qualities != null && qualities[j][i] < MINIMUM_BASE_QUALITY) ++numMismatches;
+ else if (qualities != null && qualities[j][i] < minimumBaseQuality) ++numMismatches;
}
}
}
diff --git a/src/java/net/sf/picard/illumina/IlluminaBasecallsToFastq.java b/src/java/net/sf/picard/illumina/IlluminaBasecallsToFastq.java
index 3a5bdfa..9b316e6 100644
--- a/src/java/net/sf/picard/illumina/IlluminaBasecallsToFastq.java
+++ b/src/java/net/sf/picard/illumina/IlluminaBasecallsToFastq.java
@@ -68,9 +68,15 @@ public class IlluminaBasecallsToFastq extends CommandLineProgram {
mutex = {"MULTIPLEX_PARAMS"})
public File OUTPUT_PREFIX;
- @Option(doc = "The barcode of the run. Prefixed to read names.")
+ @Option(doc = "The barcode of the run. Prefixed to read names.", optional = false)
public String RUN_BARCODE;
+ @Option(doc = "The name of the machine on which the run was sequenced; required if emitting Casava1.8-style read name headers", optional = true)
+ public String MACHINE_NAME;
+
+ @Option(doc = "The barcode of the flowcell that was sequenced; required if emitting Casava1.8-style read name headers", optional = true)
+ public String FLOWCELL_BARCODE;
+
@Option(doc = ReadStructure.PARAMETER_DOC, shortName = "RS")
public String READ_STRUCTURE;
@@ -117,13 +123,21 @@ public class IlluminaBasecallsToFastq extends CommandLineProgram {
"The default of 2 is what the Illumina's spec describes as the minimum, but in practice the value has been observed lower.")
public int MINIMUM_QUALITY = BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY;
+ @Option(doc="The read name header formatting to emit. Casava1.8 formatting has additional information beyond Illumina, including: " +
+ "the passing-filter flag value for the read, the flowcell name, and the sequencer name.", optional = false)
+ public ReadNameFormat READ_NAME_FORMAT = ReadNameFormat.CASAVA_1_8;
+ /** Simple switch to control the read name format to emit. */
+ public enum ReadNameFormat {
+ CASAVA_1_8, ILLUMINA
+ }
+
private final Map<String, FastqRecordsWriter> barcodeFastqWriterMap = new HashMap<String, FastqRecordsWriter>();
private ReadStructure readStructure;
IlluminaBasecallsConverter<FastqRecordsForCluster> basecallsConverter;
private static final Log log = Log.getInstance(IlluminaBasecallsToFastq.class);
private final FastqWriterFactory fastqWriterFactory = new FastqWriterFactory();
-
+ private ReadNameEncoder readNameEncoder;
private static final Comparator<FastqRecordsForCluster> queryNameComparator = new Comparator<FastqRecordsForCluster>() {
@Override
public int compare(final FastqRecordsForCluster r1, final FastqRecordsForCluster r2) {
@@ -131,7 +145,6 @@ public class IlluminaBasecallsToFastq extends CommandLineProgram {
r2.templateRecords[0].getReadHeader());
}
};
- private BclQualityEvaluationStrategy bclQualityEvaluationStrategy;
@Override
@@ -143,11 +156,39 @@ public class IlluminaBasecallsToFastq extends CommandLineProgram {
return 0;
}
+ @Override
+ protected String[] customCommandLineValidation() {
+ final LinkedList<String> errors = new LinkedList<String>();
+ if (READ_NAME_FORMAT == ReadNameFormat.CASAVA_1_8 && MACHINE_NAME == null) {
+ errors.add("MACHINE_NAME is required when using Casava1.8-style read name headers.");
+ }
+
+ if (READ_NAME_FORMAT == ReadNameFormat.CASAVA_1_8 && FLOWCELL_BARCODE == null) {
+ errors.add("FLOWCELL_BARCODE is required when using Casava1.8-style read name headers.");
+ }
+
+ if (errors.isEmpty()) {
+ return null;
+ } else {
+ return errors.toArray(new String[errors.size()]);
+ }
+ }
+
/**
* Prepares loggers, initiates garbage collection thread, parses arguments and initialized variables appropriately/
*/
private void initialize() {
- bclQualityEvaluationStrategy = new BclQualityEvaluationStrategy(MINIMUM_QUALITY);
+ fastqWriterFactory.setCreateMd5(CREATE_MD5_FILE);
+ switch (READ_NAME_FORMAT) {
+ case CASAVA_1_8:
+ readNameEncoder = new Casava18ReadNameEncoder(MACHINE_NAME, RUN_BARCODE, FLOWCELL_BARCODE);
+ break;
+ case ILLUMINA:
+ readNameEncoder = new IlluminaReadNameEncoder(RUN_BARCODE);
+ break;
+ }
+
+ final BclQualityEvaluationStrategy bclQualityEvaluationStrategy = new BclQualityEvaluationStrategy(MINIMUM_QUALITY);
readStructure = new ReadStructure(READ_STRUCTURE);
if (MULTIPLEX_PARAMS != null) {
IoUtil.assertFileIsReadable(MULTIPLEX_PARAMS);
@@ -160,7 +201,7 @@ public class IlluminaBasecallsToFastq extends CommandLineProgram {
populateWritersFromMultiplexParams();
demultiplex = true;
}
- int readsPerCluster = readStructure.templates.length() + readStructure.barcodes.length();
+ final int readsPerCluster = readStructure.templates.length() + readStructure.barcodes.length();
basecallsConverter = new IlluminaBasecallsConverter<FastqRecordsForCluster>(BASECALLS_DIR, LANE, readStructure,
barcodeFastqWriterMap, demultiplex, MAX_READS_IN_RAM_PER_TILE/readsPerCluster, TMP_DIR, NUM_PROCESSORS,
FORCE_GC, FIRST_TILE, TILE_LIMIT, queryNameComparator,
@@ -170,7 +211,9 @@ public class IlluminaBasecallsToFastq extends CommandLineProgram {
log.info("READ STRUCTURE IS " + readStructure.toString());
- basecallsConverter.setConverter(new ClusterToFastqRecordsForClusterConverter());
+ basecallsConverter.setConverter(
+ new ClusterToFastqRecordsForClusterConverter(
+ basecallsConverter.getFactory().getOutputReadStructure()));
}
@@ -320,33 +363,32 @@ public class IlluminaBasecallsToFastq extends CommandLineProgram {
private final int [] templateIndices;
private final int [] barcodeIndices;
- ClusterToFastqRecordsForClusterConverter() {
- this.templateIndices = readStructure.templates.getIndices();
- this.barcodeIndices = readStructure.barcodes.getIndices();
+ ClusterToFastqRecordsForClusterConverter(final ReadStructure outputReadStructure) {
+ this.templateIndices = outputReadStructure.templates.getIndices();
+ this.barcodeIndices = outputReadStructure.barcodes.getIndices();
}
@Override
public FastqRecordsForCluster convertClusterToOutputRecord(final ClusterData cluster) {
- final FastqRecordsForCluster ret =
- new FastqRecordsForCluster(readStructure.templates.length(), readStructure.barcodes.length());
- final String readName = IlluminaUtil.makeReadName(RUN_BARCODE, cluster.getLane(), cluster.getTile(),
- cluster.getX(), cluster.getY());
+ final FastqRecordsForCluster ret = new FastqRecordsForCluster(readStructure.templates.length(), readStructure.barcodes.length());
final boolean appendReadNumberSuffix = ret.templateRecords.length > 1;
- makeFastqRecords(ret.templateRecords, templateIndices, readName, cluster, appendReadNumberSuffix);
- makeFastqRecords(ret.barcodeRecords, barcodeIndices, readName, cluster, false);
+ makeFastqRecords(ret.templateRecords, templateIndices, cluster, appendReadNumberSuffix);
+ makeFastqRecords(ret.barcodeRecords, barcodeIndices, cluster, false);
return ret;
}
- private void makeFastqRecords(final FastqRecord[] recs, final int[] indices, final String readName,
+ private void makeFastqRecords(final FastqRecord[] recs, final int[] indices,
final ClusterData cluster, final boolean appendReadNumberSuffix) {
- for (int i = 0; i < indices.length; ++i) {
+ for (short i = 0; i < indices.length; ++i) {
final ReadData readData = cluster.getRead(indices[i]);
final String readBases = StringUtil.bytesToString(readData.getBases()).replace('.', 'N');
- final String readNameForEnd;
- if (appendReadNumberSuffix) readNameForEnd = readName + "/" + (i+1);
- else readNameForEnd = readName;
- recs[i] = new FastqRecord(readNameForEnd, readBases, null,
- SAMUtils.phredToFastq(readData.getQualities()));
+ final String readName = readNameEncoder.generateReadName(cluster, appendReadNumberSuffix ? i + 1 : null);
+ recs[i] = new FastqRecord(
+ readName,
+ readBases,
+ null,
+ SAMUtils.phredToFastq(readData.getQualities())
+ );
}
}
}
diff --git a/src/java/net/sf/picard/illumina/parser/readers/TileMetricsOutReader.java b/src/java/net/sf/picard/illumina/parser/readers/TileMetricsOutReader.java
index df75391..4f3f329 100644
--- a/src/java/net/sf/picard/illumina/parser/readers/TileMetricsOutReader.java
+++ b/src/java/net/sf/picard/illumina/parser/readers/TileMetricsOutReader.java
@@ -72,7 +72,7 @@ public class TileMetricsOutReader implements Iterator<TileMetricsOutReader.Illum
/**
* IlluminaTileMetrics corresponds to a single record in a TileMetricsOut file
*/
- public class IlluminaTileMetrics {
+ public static class IlluminaTileMetrics {
private final int laneNumber;
private final int tileNumber;
private final int metricCode;
@@ -85,6 +85,13 @@ public class TileMetricsOutReader implements Iterator<TileMetricsOutReader.Illum
metricValue = bb.getFloat();
}
+ public IlluminaTileMetrics(int laneNumber, int tileNumber, int metricCode, float metricValue) {
+ this.laneNumber = laneNumber;
+ this.tileNumber = tileNumber;
+ this.metricCode = metricCode;
+ this.metricValue = metricValue;
+ }
+
public int getLaneNumber() {
return laneNumber;
}
diff --git a/src/java/net/sf/picard/io/IoUtil.java b/src/java/net/sf/picard/io/IoUtil.java
index 647d826..89fd1c7 100644
--- a/src/java/net/sf/picard/io/IoUtil.java
+++ b/src/java/net/sf/picard/io/IoUtil.java
@@ -26,9 +26,7 @@ package net.sf.picard.io;
import net.sf.picard.PicardException;
import net.sf.picard.util.IterableOnceIterator;
import net.sf.samtools.Defaults;
-import net.sf.samtools.util.CloserUtil;
-import net.sf.samtools.util.CollectionUtil;
-import net.sf.samtools.util.RuntimeIOException;
+import net.sf.samtools.util.*;
import java.io.*;
import java.nio.charset.Charset;
@@ -36,6 +34,7 @@ import java.util.*;
import java.util.regex.Pattern;
import java.util.zip.GZIPInputStream;
import java.util.zip.GZIPOutputStream;
+
import org.apache.tools.bzip2.CBZip2InputStream;
import org.apache.tools.bzip2.CBZip2OutputStream;
@@ -354,6 +353,10 @@ public class IoUtil extends net.sf.samtools.util.IOUtil {
}
}
+ public static OutputStream openFileForMd5CalculatingWriting(final File file) {
+ return new Md5CalculatingOutputStream(IoUtil.openFileForWriting(file), new File(file.getAbsolutePath() + ".md5"));
+ }
+
/**
* Utility method to copy the contents of input to output. The caller is responsible for
* opening and closing both streams.
@@ -610,7 +613,8 @@ public class IoUtil extends net.sf.samtools.util.IOUtil {
/** Reads all of the stream into a String, decoding with the provided {@link Charset} then closes the stream quietly. */
public static String slurp(final InputStream is, final Charset charSet) {
- return CollectionUtil.getSoleElement(tokenSlurp(is, charSet, "\\A"));
+ final List<String> tokenOrEmpty = tokenSlurp(is, charSet, "\\A");
+ return tokenOrEmpty.isEmpty() ? StringUtil.EMPTY_STRING : CollectionUtil.getSoleElement(tokenOrEmpty);
}
/** Tokenizes the provided input stream into memory using the given delimiter. */
diff --git a/src/java/net/sf/picard/metrics/MultiLevelCollector.java b/src/java/net/sf/picard/metrics/MultiLevelCollector.java
index b2aebf3..73c986f 100644
--- a/src/java/net/sf/picard/metrics/MultiLevelCollector.java
+++ b/src/java/net/sf/picard/metrics/MultiLevelCollector.java
@@ -24,6 +24,7 @@
package net.sf.picard.metrics;
+import net.sf.picard.PicardException;
import net.sf.picard.analysis.MetricAccumulationLevel;
import net.sf.picard.reference.ReferenceSequence;
import net.sf.samtools.SAMReadGroupRecord;
@@ -59,6 +60,7 @@ import java.util.*;
*/
public abstract class MultiLevelCollector<METRIC_TYPE extends MetricBase, HISTOGRAM_KEY extends Comparable, ARGTYPE> {
+ public static final String UNKNOWN = "unknown";
//The collector that will accept all records (allReads is NULL if !calculateAll)
private PerUnitMetricCollector<METRIC_TYPE, HISTOGRAM_KEY, ARGTYPE> allReadCollector;
@@ -116,6 +118,8 @@ public abstract class MultiLevelCollector<METRIC_TYPE extends MetricBase, HISTOG
//Make a PerUnitMetricCollector for this given Distributor
protected abstract PerUnitMetricCollector<METRIC_TYPE, HISTOGRAM_KEY, ARGTYPE> makeCollector(final SAMReadGroupRecord rg);
+ protected abstract PerUnitMetricCollector<METRIC_TYPE, HISTOGRAM_KEY, ARGTYPE> makeUnknownCollector();
+
public Distributor(final List<SAMReadGroupRecord> rgRecs) {
collectors = new LinkedHashMap<String, PerUnitMetricCollector<METRIC_TYPE, HISTOGRAM_KEY, ARGTYPE>>();
for(final SAMReadGroupRecord rg : rgRecs) {
@@ -136,14 +140,22 @@ public abstract class MultiLevelCollector<METRIC_TYPE extends MetricBase, HISTOG
/** Call acceptRecord(args) on the record collector identified by getKey */
public void acceptRecord(final ARGTYPE args, final SAMReadGroupRecord rg) {
- String key = "unknown";
+ String key = UNKNOWN;
if(rg != null) {
final String computedKey = getKey(rg);
if(computedKey != null) {
key = computedKey;
}
}
- collectors.get(key).acceptRecord(args);
+ PerUnitMetricCollector<METRIC_TYPE, HISTOGRAM_KEY, ARGTYPE> collector = collectors.get(key);
+ if (collector == null) {
+ if (!UNKNOWN.equals(key)) {
+ throw new PicardException("Could not find collector for " + key);
+ }
+ collector = makeUnknownCollector();
+ collectors.put(key, collector);
+ }
+ collector.acceptRecord(args);
}
/** Add all records to the MetricsFile passed in, this will happen in the order they were
@@ -181,6 +193,11 @@ public abstract class MultiLevelCollector<METRIC_TYPE extends MetricBase, HISTOG
}
@Override
+ protected PerUnitMetricCollector<METRIC_TYPE, HISTOGRAM_KEY, ARGTYPE> makeUnknownCollector() {
+ throw new UnsupportedOperationException("Should not happen");
+ }
+
+ @Override
public void finish() {
allReadCollector.finish();
}
@@ -206,6 +223,11 @@ public abstract class MultiLevelCollector<METRIC_TYPE extends MetricBase, HISTOG
protected PerUnitMetricCollector<METRIC_TYPE, HISTOGRAM_KEY, ARGTYPE> makeCollector(SAMReadGroupRecord rg) {
return makeSampleCollector(rg);
}
+
+ @Override
+ protected PerUnitMetricCollector<METRIC_TYPE, HISTOGRAM_KEY, ARGTYPE> makeUnknownCollector() {
+ return makeChildCollector(UNKNOWN, null, null);
+ }
}
//Discriminates between records based on library name, and calls acceptRecord on the appropriate PerUnitMetricCollectors
@@ -223,6 +245,11 @@ public abstract class MultiLevelCollector<METRIC_TYPE extends MetricBase, HISTOG
protected PerUnitMetricCollector<METRIC_TYPE, HISTOGRAM_KEY, ARGTYPE> makeCollector(SAMReadGroupRecord rg) {
return makeLibraryCollector(rg);
}
+
+ @Override
+ protected PerUnitMetricCollector<METRIC_TYPE, HISTOGRAM_KEY, ARGTYPE> makeUnknownCollector() {
+ return makeChildCollector(UNKNOWN, UNKNOWN, null);
+ }
}
//Discriminates between records based on read group name, and calls acceptRecord on the appropriate PerUnitMetricCollectors
@@ -240,6 +267,11 @@ public abstract class MultiLevelCollector<METRIC_TYPE extends MetricBase, HISTOG
protected PerUnitMetricCollector<METRIC_TYPE, HISTOGRAM_KEY, ARGTYPE> makeCollector(SAMReadGroupRecord rg) {
return makeReadGroupCollector(rg);
}
+
+ @Override
+ protected PerUnitMetricCollector<METRIC_TYPE, HISTOGRAM_KEY, ARGTYPE> makeUnknownCollector() {
+ return makeChildCollector(UNKNOWN, UNKNOWN, UNKNOWN);
+ }
}
/**
diff --git a/src/java/net/sf/picard/sam/FastqToSam.java b/src/java/net/sf/picard/sam/FastqToSam.java
index 21eabfd..af9d0f3 100644
--- a/src/java/net/sf/picard/sam/FastqToSam.java
+++ b/src/java/net/sf/picard/sam/FastqToSam.java
@@ -111,6 +111,10 @@ public class FastqToSam extends CommandLineProgram {
@Option(doc="If true and this is an unpaired fastq any occurance of '/1' will be removed from the end of a read name.")
public Boolean STRIP_UNPAIRED_MATE_NUMBER = false;
+
+ @Option(doc="Allow (and ignore) empty lines")
+ public Boolean ALLOW_AND_IGNORE_EMPTY_LINES = false;
+
private static final SolexaQualityConverter solexaQualityConverter = SolexaQualityConverter.getSingleton();
/** Stock main method. */
@@ -122,11 +126,11 @@ public class FastqToSam extends CommandLineProgram {
protected int doWork() {
if (QUALITY_FORMAT == null) {
final QualityEncodingDetector detector = new QualityEncodingDetector();
- final FastqReader reader = new FastqReader(FASTQ);
+ final FastqReader reader = new FastqReader(FASTQ,ALLOW_AND_IGNORE_EMPTY_LINES);
if (FASTQ2 == null) {
detector.add(QualityEncodingDetector.DEFAULT_MAX_RECORDS_TO_ITERATE, reader);
} else {
- final FastqReader reader2 = new FastqReader(FASTQ2);
+ final FastqReader reader2 = new FastqReader(FASTQ2,ALLOW_AND_IGNORE_EMPTY_LINES);
detector.add(QualityEncodingDetector.DEFAULT_MAX_RECORDS_TO_ITERATE, reader, reader2);
reader2.close();
}
@@ -147,7 +151,7 @@ public class FastqToSam extends CommandLineProgram {
IoUtil.assertFileIsReadable(FASTQ);
IoUtil.assertFileIsWritable(OUTPUT);
- final FastqReader freader = new FastqReader(FASTQ);
+ final FastqReader freader = new FastqReader(FASTQ,ALLOW_AND_IGNORE_EMPTY_LINES);
final SAMFileHeader header = createFileHeader();
final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, false, OUTPUT);
@@ -171,8 +175,8 @@ public class FastqToSam extends CommandLineProgram {
IoUtil.assertFileIsReadable(FASTQ2);
IoUtil.assertFileIsWritable(OUTPUT);
- final FastqReader freader1 = new FastqReader(FASTQ);
- final FastqReader freader2 = new FastqReader(FASTQ2);
+ final FastqReader freader1 = new FastqReader(FASTQ,ALLOW_AND_IGNORE_EMPTY_LINES);
+ final FastqReader freader2 = new FastqReader(FASTQ2,ALLOW_AND_IGNORE_EMPTY_LINES);
final SAMFileHeader header = createFileHeader() ;
final SAMFileWriter writer = (new SAMFileWriterFactory()).makeSAMOrBAMWriter(header, false, OUTPUT);
diff --git a/src/java/net/sf/picard/sam/SamToFastq.java b/src/java/net/sf/picard/sam/SamToFastq.java
index 7e62978..e56d98d 100755
--- a/src/java/net/sf/picard/sam/SamToFastq.java
+++ b/src/java/net/sf/picard/sam/SamToFastq.java
@@ -34,10 +34,7 @@ import net.sf.picard.fastq.FastqWriterFactory;
import net.sf.picard.io.IoUtil;
import net.sf.picard.util.Log;
import net.sf.picard.util.ProgressLogger;
-import net.sf.samtools.SAMFileReader;
-import net.sf.samtools.SAMReadGroupRecord;
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMUtils;
+import net.sf.samtools.*;
import net.sf.samtools.util.SequenceUtil;
import net.sf.samtools.util.StringUtil;
@@ -126,6 +123,7 @@ public class SamToFastq extends CommandLineProgram {
final SAMFileReader reader = new SAMFileReader(IoUtil.openFileForReading(INPUT));
final Map<String,SAMRecord> firstSeenMates = new HashMap<String,SAMRecord>();
final FastqWriterFactory factory = new FastqWriterFactory();
+ factory.setCreateMd5(CREATE_MD5_FILE);
final Map<SAMReadGroupRecord, List<FastqWriter>> writers = getWriters(reader.getFileHeader().getReadGroups(), factory);
final ProgressLogger progress = new ProgressLogger(log);
@@ -187,7 +185,8 @@ public class SamToFastq extends CommandLineProgram {
}
if (firstSeenMates.size() > 0) {
- throw new PicardException("Found " + firstSeenMates.size() + " unpaired mates");
+ SAMUtils.processValidationError(new SAMValidationError(SAMValidationError.Type.MATE_NOT_FOUND,
+ "Found " + firstSeenMates.size() + " unpaired mates", null), VALIDATION_STRINGENCY);
}
return 0;
diff --git a/src/java/net/sf/picard/sam/ValidateSamFile.java b/src/java/net/sf/picard/sam/ValidateSamFile.java
index dd4242d..1f11fb5 100644
--- a/src/java/net/sf/picard/sam/ValidateSamFile.java
+++ b/src/java/net/sf/picard/sam/ValidateSamFile.java
@@ -152,7 +152,10 @@ public class ValidateSamFile extends CommandLineProgram {
if (VALIDATE_INDEX){
validator.setValidateIndex(VALIDATE_INDEX);
}
- validator.validateBamFileTermination(INPUT);
+ if (IoUtil.isRegularPath(INPUT)) {
+ // Do not check termination if reading from a stream
+ validator.validateBamFileTermination(INPUT);
+ }
result = false;
diff --git a/src/java/net/sf/picard/util/IlluminaUtil.java b/src/java/net/sf/picard/util/IlluminaUtil.java
index 6736457..4a901ab 100644
--- a/src/java/net/sf/picard/util/IlluminaUtil.java
+++ b/src/java/net/sf/picard/util/IlluminaUtil.java
@@ -40,15 +40,6 @@ public class IlluminaUtil {
public static final String BARCODE_DELIMITER = "-";
/**
- * Standard Broad algorithm for creating a read name
- * @return read name in standard Broad format, without end suffix.
- */
- public static String makeReadName(final String runBarcode, final int lane, final int tile, final int xCoordinate,
- final int yCoordinate) {
- return runBarcode + ":" + lane + ":" + tile + ":" + xCoordinate + ":" + yCoordinate;
- }
-
- /**
* Parse the tile # from the read name.
* If we find that there are other elements needed from the read name, it might be a good idea to put
* makeReadName() and various get..() methods into a new class.
diff --git a/src/java/net/sf/picard/util/IntervalUtil.java b/src/java/net/sf/picard/util/IntervalUtil.java
index 6608368..dd2b63c 100644
--- a/src/java/net/sf/picard/util/IntervalUtil.java
+++ b/src/java/net/sf/picard/util/IntervalUtil.java
@@ -25,6 +25,7 @@ package net.sf.picard.util;
import net.sf.picard.PicardException;
import net.sf.samtools.SAMSequenceDictionary;
+import net.sf.samtools.SAMSequenceRecord;
import java.util.Iterator;
@@ -33,23 +34,37 @@ import java.util.Iterator;
*/
public class IntervalUtil {
+ /** Return true if the sequence/position lie in the provided interval. */
+ public static boolean contains(final Interval interval, final String sequenceName, final long position) {
+ return interval.getSequence().equals(sequenceName) && (position >= interval.getStart() && position <= interval.getEnd());
+ }
+
+ /** Return true if the sequence/position lie in the provided interval list. */
+ public static boolean contains(final IntervalList intervalList, final String sequenceName, final long position) {
+ for (final Interval interval : intervalList.getUniqueIntervals()) {
+ if (contains(interval, sequenceName, position))
+ return true;
+ }
+ return false;
+ }
+
/**
* Throws RuntimeException if the given intervals are not locus ordered and non-overlapping
* @param intervals
* @param sequenceDictionary used to determine order of sequences
*/
- public static void assertOrderedNonOverlapping(Iterator<Interval> intervals, SAMSequenceDictionary sequenceDictionary) {
+ public static void assertOrderedNonOverlapping(final Iterator<Interval> intervals, final SAMSequenceDictionary sequenceDictionary) {
if (!intervals.hasNext()) {
return;
}
Interval prevInterval = intervals.next();
int prevSequenceIndex = sequenceDictionary.getSequenceIndex(prevInterval.getSequence());
while (intervals.hasNext()) {
- Interval interval = intervals.next();
+ final Interval interval = intervals.next();
if (prevInterval.intersects(interval)) {
throw new PicardException("Intervals should not overlap: " + prevInterval + "; " + interval);
}
- int thisSequenceIndex = sequenceDictionary.getSequenceIndex(interval.getSequence());
+ final int thisSequenceIndex = sequenceDictionary.getSequenceIndex(interval.getSequence());
if (prevSequenceIndex > thisSequenceIndex ||
(prevSequenceIndex == thisSequenceIndex && prevInterval.compareTo(interval) >= 0)) {
throw new PicardException("Intervals not in order: " + prevInterval + "; " + interval);
diff --git a/src/java/net/sf/picard/util/MathUtil.java b/src/java/net/sf/picard/util/MathUtil.java
index 192e350..039e18c 100644
--- a/src/java/net/sf/picard/util/MathUtil.java
+++ b/src/java/net/sf/picard/util/MathUtil.java
@@ -40,11 +40,11 @@ public class MathUtil {
/** Calculated the mean of an array of doubles. */
public static double mean(final double[] in, final int start, final int stop) {
double total = 0;
- for (int i=start; i<stop; ++i) {
+ for (int i = start; i < stop; ++i) {
total += in[i];
}
- return total / (stop-start);
+ return total / (stop - start);
}
/** Calculated the standard deviation of an array of doubles. */
@@ -55,26 +55,26 @@ public class MathUtil {
/** Calculated the standard deviation of an array of doubles. */
public static double stddev(final double[] in, final int start, final int stop, final double mean) {
double total = 0;
- for (int i=start; i<stop; ++i) {
+ for (int i = start; i < stop; ++i) {
total += (in[i] * in[i]);
}
- return Math.sqrt((total / (stop-start)) - (mean*mean));
+ return Math.sqrt((total / (stop - start)) - (mean * mean));
}
public static int compare(final int v1, final int v2) {
- return (v1 < v2? -1: (v1 == v2? 0: 1));
+ return (v1 < v2 ? -1 : (v1 == v2 ? 0 : 1));
}
/**
* Obtains percentage of two Longs
- * @param numerator dividend
+ * @param numerator dividend
* @param denominator divisor
* @return numerator/(double)denominator if both are non-null and denominator != 0, else returns null.
*/
public static Double percentageOrNull(final Long numerator, final Long denominator) {
if (numerator != null && denominator != null && denominator != 0) {
- return numerator.doubleValue()/denominator.doubleValue();
+ return numerator.doubleValue() / denominator.doubleValue();
} else {
return null;
}
@@ -86,13 +86,13 @@ public class MathUtil {
public static double round(final double num, final int precision) {
BigDecimal bd = new BigDecimal(num);
bd = bd.setScale(precision, BigDecimal.ROUND_HALF_UP);
- return bd.doubleValue();
+ return bd.doubleValue();
}
/** Returns the largest value stored in the array. */
public static double max(final double[] nums) {
double max = nums[0];
- for (int i=1; i<nums.length; ++i) {
+ for (int i = 1; i < nums.length; ++i) {
if (nums[i] > max) max = nums[i];
}
@@ -102,17 +102,35 @@ public class MathUtil {
/** Returns the smallest value stored in the array. */
public static double min(final double[] nums) {
double min = nums[0];
- for (int i=1; i<nums.length; ++i) {
+ for (int i = 1; i < nums.length; ++i) {
if (nums[i] < min) min = nums[i];
}
return min;
}
+ /** Mimic's R's seq() function to produce a sequence of equally spaced numbers. */
+ public static double[] seq(final double from, final double to, final double by) {
+ if (from < to && by <= 0) return new double[0];
+ if (from > to && by >= 0) return new double[0];
+ final int values = 1 + (int) Math.floor((to - from) / by);
+ final double[] results = new double[values];
+
+ BigDecimal value = new BigDecimal(from);
+ BigDecimal increment = new BigDecimal(by);
+
+ for (int i=0; i<values; ++i) {
+ results[i] = value.doubleValue();
+ value = value.add(increment);
+ }
+
+ return results;
+ }
+
/** "Promotes" an int[] into a double array with the same values (or as close as precision allows). */
public static double[] promote(final int[] is) {
final double[] ds = new double[is.length];
- for (int i=0; i<is.length; ++i) ds[i] = is[i];
+ for (int i = 0; i < is.length; ++i) ds[i] = is[i];
return ds;
}
@@ -131,17 +149,17 @@ public class MathUtil {
final double[] tmp = new double[likelihoods.length];
double total = 0;
- for (int i=0; i<likelihoods.length; ++i) {
- tmp[i] = pow(10,likelihoods[i]+bump);
+ for (int i = 0; i < likelihoods.length; ++i) {
+ tmp[i] = pow(10, likelihoods[i] + bump);
total += tmp[i];
}
final double maxP = MAX_PROB_BELOW_ONE;
- final double minP = (1-MAX_PROB_BELOW_ONE) / (tmp.length-1);
+ final double minP = (1 - MAX_PROB_BELOW_ONE) / (tmp.length - 1);
- for (int i=0; i<likelihoods.length; ++i) {
+ for (int i = 0; i < likelihoods.length; ++i) {
tmp[i] /= total;
- if (tmp[i] > maxP) tmp[i] = maxP;
+ if (tmp[i] > maxP) tmp[i] = maxP;
else if (tmp[i] < minP) tmp[i] = minP;
}
@@ -154,7 +172,7 @@ public class MathUtil {
final int len = lhs.length;
final double[] result = new double[len];
- for (int i=0; i<len; ++i) result[i] = lhs[i] * rhs[i];
+ for (int i = 0; i < len; ++i) result[i] = lhs[i] * rhs[i];
return result;
}
@@ -164,4 +182,62 @@ public class MathUtil {
for (final double next : arr) result += next;
return result;
}
+
+ public static final LogMath LOG_2_MATH = new LogMath(2);
+ public static final LogMath NATURAL_LOG_MATH = new LogMath(Math.exp(1)) {
+ @Override
+ public double getLogValue(final double nonLogValue) {
+ return Math.log(nonLogValue);
+ }
+ };
+
+ public static final LogMath LOG_10_MATH = new LogMath(10) {
+ @Override
+ public double getLogValue(final double nonLogValue) {
+ return Math.log10(nonLogValue);
+ }
+ };
+
+ /**
+ * A collection of common math operations that work with log values. To use it, pass values from log space, the operation will be
+ * computed in non-log space, and a value in log space will be returned.
+ */
+ public static class LogMath {
+ private final double base;
+
+ private LogMath(final double base) {
+ this.base = base;
+ }
+
+ /** Returns the decimal representation of the provided log values. */
+ public double getNonLogValue(final double logValue) {
+ return Math.pow(base, logValue);
+ }
+
+ /** Returns the log-representation of the provided decimal value. */
+ public double getLogValue(final double nonLogValue) {
+ return Math.log(nonLogValue) / Math.log(base);
+ }
+
+ /** Computes the mean of the provided log values. */
+ public double mean(final double... logValues) {
+ return sum(logValues) - getLogValue(logValues.length);
+ }
+
+ /** Computes the sum of the provided log values. */
+ public double sum(final double... logValues) {
+ // Avoid overflow via scaling.
+ final double scalingFactor = max(logValues);
+ double simpleAdditionResult = 0;
+ for (final double v : logValues) {
+ simpleAdditionResult += getNonLogValue(v - scalingFactor);
+ }
+ return getLogValue(simpleAdditionResult) + scalingFactor;
+ }
+
+ /** Computes the sum of the provided log values. */
+ public double product(final double... logValues) {
+ return MathUtil.sum(logValues);
+ }
+ }
}
diff --git a/src/java/net/sf/picard/vcf/MakeSitesOnlyVcf.java b/src/java/net/sf/picard/vcf/MakeSitesOnlyVcf.java
index cc708ee..289f506 100644
--- a/src/java/net/sf/picard/vcf/MakeSitesOnlyVcf.java
+++ b/src/java/net/sf/picard/vcf/MakeSitesOnlyVcf.java
@@ -56,7 +56,7 @@ public class MakeSitesOnlyVcf extends CommandLineProgram {
IoUtil.assertFileIsWritable(OUTPUT);
final VCFFileReader reader = new VCFFileReader(INPUT);
- final VCFHeader header = new VCFHeader(reader.getFileHeader());
+ final VCFHeader header = new VCFHeader(reader.getFileHeader().getMetaDataInInputOrder());
final SAMSequenceDictionary sequenceDictionary =
SEQUENCE_DICTIONARY != null
? SAMFileReader.getSequenceDictionary(SEQUENCE_DICTIONARY)
diff --git a/src/java/net/sf/samtools/Defaults.java b/src/java/net/sf/samtools/Defaults.java
index 4c3a652..199e00a 100644
--- a/src/java/net/sf/samtools/Defaults.java
+++ b/src/java/net/sf/samtools/Defaults.java
@@ -22,12 +22,21 @@ public class Defaults {
/** Buffer size, in bytes, used whenever reading/writing files or streams. Default = 128k. */
public static final int BUFFER_SIZE;
+ /** Should BlockCompressedOutputStream attempt to load libIntelDeflater? */
+ public static final boolean TRY_USE_INTEL_DEFLATER;
+
+ /** Path to libIntelDeflater.so. If this is not set, the library is looked for in the directory
+ * where the executable jar lives. */
+ public static final String INTEL_DEFLATER_SHARED_LIBRARY_PATH;
+
static {
CREATE_INDEX = getBooleanProperty("create_index", false);
CREATE_MD5 = getBooleanProperty("create_md5", false);
USE_ASYNC_IO = getBooleanProperty("use_async_io", false);
COMPRESSION_LEVEL = getIntProperty("compression_level", 5);
BUFFER_SIZE = getIntProperty("buffer_size", 1024 * 128);
+ TRY_USE_INTEL_DEFLATER = getBooleanProperty("try_use_intel_deflater", true);
+ INTEL_DEFLATER_SHARED_LIBRARY_PATH = getStringProperty("intel_deflater_so_path", null);
}
/** Gets a string system property, prefixed with "samjdk." using the default if the property does not exist.*/
diff --git a/src/java/net/sf/samtools/SAMSequenceDictionary.java b/src/java/net/sf/samtools/SAMSequenceDictionary.java
index bb2bc96..49f3f61 100644
--- a/src/java/net/sf/samtools/SAMSequenceDictionary.java
+++ b/src/java/net/sf/samtools/SAMSequenceDictionary.java
@@ -50,6 +50,7 @@ public class SAMSequenceDictionary {
/**
* Replaces the existing list of SAMSequenceRecords with the given list.
+ *
* @param list This value is used directly, rather than being copied.
*/
public void setSequences(final List<SAMSequenceRecord> list) {
@@ -115,6 +116,33 @@ public class SAMSequenceDictionary {
return mSequences.isEmpty();
}
+ private static String DICT_MISMATCH_TEMPLATE = "SAM dictionaries are not the same: %s.";
+ /**
+ * Non-comprehensive {@link #equals(Object)}-assertion: instead of calling {@link SAMSequenceRecord#equals(Object)} on constituent
+ * {@link SAMSequenceRecord}s in this dictionary against its pair in the target dictionary, in order, call
+ * {@link SAMSequenceRecord#isSameSequence(SAMSequenceRecord)}.
+ *
+ * @throws AssertionError When the dictionaries are not the same, with some human-readable information as to why
+ */
+ public void assertSameDictionary(final SAMSequenceDictionary that) {
+ if (this == that) return;
+
+ final Iterator<SAMSequenceRecord> thatSequences = that.mSequences.iterator();
+ for (final SAMSequenceRecord thisSequence : mSequences) {
+ if (!thatSequences.hasNext())
+ throw new AssertionError(String.format(DICT_MISMATCH_TEMPLATE, thisSequence + " is present in only one dictionary"));
+ else {
+ final SAMSequenceRecord thatSequence = thatSequences.next();
+ if(!thatSequence.isSameSequence(thisSequence))
+ throw new AssertionError(
+ String.format(DICT_MISMATCH_TEMPLATE, thatSequence + " was found when " + thisSequence + " was expected")
+ );
+ }
+ }
+ if (thatSequences.hasNext())
+ throw new AssertionError(String.format(DICT_MISMATCH_TEMPLATE, thatSequences.next() + " is present in only one dictionary"));
+ }
+
@Override
public boolean equals(Object o) {
if (this == o) return true;
diff --git a/src/java/net/sf/samtools/SAMSequenceRecord.java b/src/java/net/sf/samtools/SAMSequenceRecord.java
index 629a70a..f49fd31 100644
--- a/src/java/net/sf/samtools/SAMSequenceRecord.java
+++ b/src/java/net/sf/samtools/SAMSequenceRecord.java
@@ -211,5 +211,15 @@ public class SAMSequenceRecord extends AbstractSAMHeaderRecord implements Clonea
}
}
+ @Override
+ public String toString() {
+ return String.format(
+ "SAMSequenceRecord(name=%s,length=%s,dict_index=%s,assembly=%s)",
+ getSequenceName(),
+ getSequenceLength(),
+ getSequenceIndex(),
+ getAssembly()
+ );
+ }
}
diff --git a/src/java/net/sf/samtools/SAMUtils.java b/src/java/net/sf/samtools/SAMUtils.java
index e9b4930..71a8203 100644
--- a/src/java/net/sf/samtools/SAMUtils.java
+++ b/src/java/net/sf/samtools/SAMUtils.java
@@ -455,7 +455,7 @@ public final class SAMUtils
}
}
- static void processValidationError(final SAMValidationError validationError,
+ public static void processValidationError(final SAMValidationError validationError,
SAMFileReader.ValidationStringency validationStringency) {
if (validationStringency == SAMFileReader.ValidationStringency.STRICT) {
throw new SAMFormatException("SAM validation error: " + validationError);
diff --git a/src/java/net/sf/samtools/seekablestream/ISeekableStreamFactory.java b/src/java/net/sf/samtools/seekablestream/ISeekableStreamFactory.java
new file mode 100644
index 0000000..901583d
--- /dev/null
+++ b/src/java/net/sf/samtools/seekablestream/ISeekableStreamFactory.java
@@ -0,0 +1,33 @@
+package net.sf.samtools.seekablestream;
+
+import java.io.IOException;
+import java.net.URL;
+
+/**
+ * Factory for creating {@link SeekableStream}s based on URLs/paths.
+ * Implementations can be set as the default with {@link SeekableStreamFactory#setInstance(ISeekableStreamFactory)}
+ * @author jacob
+ * @date 2013-Oct-24
+ */
+public interface ISeekableStreamFactory {
+
+ public SeekableStream getStreamFor(URL url) throws IOException;
+
+ public SeekableStream getStreamFor(String path) throws IOException;
+
+ /**
+ * Return a buffered {@code SeekableStream} which wraps the input {@code stream}
+ * using the default buffer size
+ * @param stream
+ * @return
+ */
+ public SeekableStream getBufferedStream(SeekableStream stream);
+
+ /**
+ * Return a buffered {@code SeekableStream} which wraps the input {@code stream}
+ * @param stream
+ * @param bufferSize
+ * @return
+ */
+ public SeekableStream getBufferedStream(SeekableStream stream, int bufferSize);
+}
diff --git a/src/java/net/sf/samtools/seekablestream/SeekableFTPStream.java b/src/java/net/sf/samtools/seekablestream/SeekableFTPStream.java
index 95b926c..253a568 100644
--- a/src/java/net/sf/samtools/seekablestream/SeekableFTPStream.java
+++ b/src/java/net/sf/samtools/seekablestream/SeekableFTPStream.java
@@ -92,7 +92,7 @@ public class SeekableFTPStream extends SeekableStream {
long startPosition = (args.length < 2) ? 0x0b66c78l : Long.parseLong(args[1]);
int len = (args.length < 3) ? 8 : Integer.parseInt(args[2]);
int skipLen = (args.length < 4) ? 0x18 : Integer.parseInt(args[3]);
- SeekableStream s = SeekableStreamFactory.getStreamFor(testURL);
+ SeekableStream s = SeekableStreamFactory.getInstance().getStreamFor(testURL);
byte[] buffer = new byte[len];
s.seek(startPosition);
s.read(buffer, 0, len);
diff --git a/src/java/net/sf/samtools/seekablestream/SeekableStreamFactory.java b/src/java/net/sf/samtools/seekablestream/SeekableStreamFactory.java
index fc44448..e69ca72 100644
--- a/src/java/net/sf/samtools/seekablestream/SeekableStreamFactory.java
+++ b/src/java/net/sf/samtools/seekablestream/SeekableStreamFactory.java
@@ -28,13 +28,29 @@ import java.io.IOException;
import java.net.URL;
/**
+ * Singleton class for getting {@link SeekableStream}s from URL/paths
+ * Applications using this library can set their own factory
* @author jrobinso
* @date Nov 30, 2009
*/
-public class SeekableStreamFactory {
+public class SeekableStreamFactory{
- public static SeekableStream getStreamFor(URL url) throws IOException{
- return getStreamFor(url.toExternalForm());
+ private static final ISeekableStreamFactory DEFAULT_FACTORY;
+ private static ISeekableStreamFactory currentFactory;
+
+ static{
+ DEFAULT_FACTORY = new DefaultSeekableStreamFactory();
+ currentFactory = DEFAULT_FACTORY;
+ }
+
+ private SeekableStreamFactory(){}
+
+ public static void setInstance(final ISeekableStreamFactory factory){
+ currentFactory = factory;
+ }
+
+ public static ISeekableStreamFactory getInstance(){
+ return currentFactory;
}
/**
@@ -46,17 +62,33 @@ public class SeekableStreamFactory {
return ! ( path.startsWith("http:") || path.startsWith("https:") || path.startsWith("ftp:") );
}
- public static SeekableStream getStreamFor(String path) throws IOException {
- // todo -- add support for SeekableBlockInputStream
+ private static class DefaultSeekableStreamFactory implements ISeekableStreamFactory {
+
+ public SeekableStream getStreamFor(final URL url) throws IOException {
+ return getStreamFor(url.toExternalForm());
+ }
+
+ public SeekableStream getStreamFor(final String path) throws IOException {
+ // todo -- add support for SeekableBlockInputStream
+
+ if (path.startsWith("http:") || path.startsWith("https:")) {
+ final URL url = new URL(path);
+ return new SeekableHTTPStream(url);
+ } else if (path.startsWith("ftp:")) {
+ return new SeekableFTPStream(new URL(path));
+ } else {
+ return new SeekableFileStream(new File(path));
+ }
+ }
- if (path.startsWith("http:") || path.startsWith("https:")) {
- final URL url = new URL(path);
- return new SeekableHTTPStream(url);
- } else if (path.startsWith("ftp:")) {
- return new SeekableFTPStream(new URL(path));
- } else {
- return new SeekableFileStream(new File(path));
+ public SeekableStream getBufferedStream(SeekableStream stream){
+ return getBufferedStream(stream, SeekableBufferedStream.DEFAULT_BUFFER_SIZE);
}
+
+ public SeekableStream getBufferedStream(SeekableStream stream, int bufferSize){
+ return new SeekableBufferedStream(stream, bufferSize);
+ }
+
}
}
diff --git a/src/java/net/sf/samtools/util/BlockCompressedOutputStream.java b/src/java/net/sf/samtools/util/BlockCompressedOutputStream.java
index 5b453e6..ac1834c 100644
--- a/src/java/net/sf/samtools/util/BlockCompressedOutputStream.java
+++ b/src/java/net/sf/samtools/util/BlockCompressedOutputStream.java
@@ -23,6 +23,8 @@
*/
package net.sf.samtools.util;
+import net.sf.samtools.util.zip.DeflaterFactory;
+
import java.io.File;
import java.io.IOException;
import java.io.OutputStream;
@@ -83,6 +85,8 @@ public class BlockCompressedOutputStream
// which would attempt to compress up to 64K bytes, and if the resulting compressed block was too large,
// try compressing fewer input bytes (aka "downshifting'). The problem with downshifting is that
// getFilePointer might return an inaccurate value.
+ // I assume (AW 29-Oct-2013) that there is no value in using hardware-assisted deflater for no-compression mode,
+ // so just use JDK standard.
private final Deflater noCompressionDeflater = new Deflater(Deflater.NO_COMPRESSION, true);
private final CRC32 crc32 = new CRC32();
private File file = null;
@@ -121,7 +125,7 @@ public class BlockCompressedOutputStream
public BlockCompressedOutputStream(final File file, final int compressionLevel) {
this.file = file;
codec = new BinaryCodec(file, true);
- deflater = new Deflater(compressionLevel, true);
+ deflater = DeflaterFactory.makeDeflater(compressionLevel, true);
}
/**
@@ -138,7 +142,7 @@ public class BlockCompressedOutputStream
if (file != null) {
codec.setOutputFileName(file.getAbsolutePath());
}
- deflater = new Deflater(compressionLevel, true);
+ deflater = DeflaterFactory.makeDeflater(compressionLevel, true);
}
/**
diff --git a/src/java/net/sf/samtools/util/CollectionUtil.java b/src/java/net/sf/samtools/util/CollectionUtil.java
index e8a4760..58bcd5f 100755
--- a/src/java/net/sf/samtools/util/CollectionUtil.java
+++ b/src/java/net/sf/samtools/util/CollectionUtil.java
@@ -31,6 +31,14 @@ import java.util.*;
*/
public class CollectionUtil {
+ /** Simple case-insensitive lexical comparator of objects using their {@link Object#toString()} value. */
+ final public static Comparator<Object> OBJECT_TOSTRING_COMPARATOR = new Comparator<Object>() {
+ @Override
+ public int compare(final Object o1, final Object o2) {
+ return o1.toString().compareToIgnoreCase(o2.toString());
+ }
+ };
+
public static <T> List<T> makeList (final T... list) {
final List<T> result = new ArrayList<T>();
Collections.addAll(result, list);
diff --git a/src/java/net/sf/samtools/util/IOUtil.java b/src/java/net/sf/samtools/util/IOUtil.java
index 9665c68..875ee48 100644
--- a/src/java/net/sf/samtools/util/IOUtil.java
+++ b/src/java/net/sf/samtools/util/IOUtil.java
@@ -96,7 +96,7 @@ public class IOUtil {
File f = null;
for (int i=0; i<tmpDirs.length; ++i) {
- if (tmpDirs[i].getUsableSpace() > minBytesFree || i == tmpDirs.length-1) {
+ if ( i == tmpDirs.length-1 || tmpDirs[i].getUsableSpace() > minBytesFree) {
f = File.createTempFile(prefix, suffix, tmpDirs[i]);
f.deleteOnExit();
break;
diff --git a/src/java/net/sf/samtools/util/Lazy.java b/src/java/net/sf/samtools/util/Lazy.java
new file mode 100644
index 0000000..0d8c3ec
--- /dev/null
+++ b/src/java/net/sf/samtools/util/Lazy.java
@@ -0,0 +1,35 @@
+package net.sf.samtools.util;
+
+/**
+ * Simple utility for building an on-demand (lazy) object-initializer.
+ *
+ * Works by accepting an initializer describing how to build the on-demand object, which is only called once and only after the first
+ * invocation of {@link #get()} (or it may not be called at all).
+ *
+ * @author mccowan
+ */
+public class Lazy<T> {
+ private final LazyInitializer<T> initializer;
+ private boolean isInitialized = false;
+ private T instance;
+
+ /** Simple cons */
+ public Lazy(final LazyInitializer<T> initializer) {
+ this.initializer = initializer;
+ }
+
+ /** Returns the instance associated with this {@link Lazy}, initializing it if necessary. */
+ public synchronized T get() {
+ if (!isInitialized) {
+ this.instance = initializer.make();
+ isInitialized = true;
+ }
+ return instance;
+ }
+
+ /** Describes how to build the instance of the lazy object. */
+ public interface LazyInitializer<T> {
+ /** Returns the desired object instance. */
+ T make();
+ }
+}
diff --git a/src/java/net/sf/samtools/util/StringUtil.java b/src/java/net/sf/samtools/util/StringUtil.java
index 22b60a7..eee2161 100644
--- a/src/java/net/sf/samtools/util/StringUtil.java
+++ b/src/java/net/sf/samtools/util/StringUtil.java
@@ -458,4 +458,9 @@ public class StringUtil {
return String.valueOf(output);
}
+ /** Returns {@link Object#toString()} of the provided value if it isn't null; "" otherwise. */
+ public static final String EMPTY_STRING = "";
+ public static String asEmptyIfNull(final Object string) {
+ return string == null ? EMPTY_STRING : string.toString();
+ }
}
diff --git a/src/java/net/sf/samtools/util/ftp/FTPUtils.java b/src/java/net/sf/samtools/util/ftp/FTPUtils.java
index 37bde32..539f13d 100644
--- a/src/java/net/sf/samtools/util/ftp/FTPUtils.java
+++ b/src/java/net/sf/samtools/util/ftp/FTPUtils.java
@@ -64,13 +64,19 @@ public class FTPUtils {
}
public static long getContentLength(URL url) throws IOException {
- // Use JDK url
- URLConnection connection = url.openConnection();
- connection.setConnectTimeout(TIMEOUT);
- //For reasons beyond my ken, on Java 7 getContentLength
- //returns -1 without attempting a connection
- //contentLength = connection.getContentLength();
- return connection.getInputStream().available();
+ FTPClient ftp = null;
+ try {
+ ftp = FTPUtils.connect(url.getHost(), url.getUserInfo(), null);
+ String sizeString = ftp.executeCommand("size " + url.getPath()).getReplyString();
+ return Integer.parseInt(sizeString);
+ } catch (Exception e) {
+ return -1 ;
+ }
+ finally {
+ if(ftp != null) {
+ ftp.disconnect();
+ }
+ }
}
diff --git a/src/java/net/sf/samtools/util/zip/DeflaterFactory.java b/src/java/net/sf/samtools/util/zip/DeflaterFactory.java
new file mode 100644
index 0000000..0c6af8c
--- /dev/null
+++ b/src/java/net/sf/samtools/util/zip/DeflaterFactory.java
@@ -0,0 +1,78 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2013 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+package net.sf.samtools.util.zip;
+
+import net.sf.samtools.Defaults;
+import net.sf.samtools.SAMException;
+
+import java.lang.reflect.Constructor;
+import java.util.zip.Deflater;
+
+/**
+ * Create zlib-based Deflater if JNI library and other require libraries are available, otherwise create standard
+ * JDK Deflater.
+ * Java 7 has its own Deflater implementation (libzip.so). This is almost as fast as a zlib-based Deflater, so in general
+ * there isn't a compelling reason to use zlib. However, Intel has created a hardware-assisted zlib implementation
+ * as part of their IPP (Integrated Performance Primitives) package that can run significantly faster on some Intel
+ * hardware. We have seen compression times reduced by 13% to 33% depending on particular hardware, and hope that
+ * newer Intel processors will be even better.
+ *
+ * Note that this class will no longer be necessary once Java 8 is required, because JDK 8 will use zlib instead
+ * of libzip implementation.
+ */
+public class DeflaterFactory {
+
+ private static Constructor<IntelDeflater> intelDeflaterConstructor;
+
+ static {
+ try {
+ if (Defaults.TRY_USE_INTEL_DEFLATER) {
+ final Class<IntelDeflater> clazz = (Class<IntelDeflater>) Class.forName("net.sf.samtools.util.zip.IntelDeflater");
+ intelDeflaterConstructor = clazz.getConstructor(Integer.TYPE, Boolean.TYPE);
+ }
+ } catch (ClassNotFoundException e) {
+ intelDeflaterConstructor = null;
+ } catch (NoSuchMethodException e) {
+ intelDeflaterConstructor = null;
+ } catch (UnsatisfiedLinkError e) {
+ intelDeflaterConstructor = null;
+ }
+ }
+
+ public static Deflater makeDeflater(final int compressionLevel, final boolean nowrap) {
+ if (intelDeflaterConstructor != null) {
+ try {
+ return intelDeflaterConstructor.newInstance(compressionLevel, nowrap);
+ } catch (Exception e) {
+ throw new SAMException("Exception constructing IntelDeflater", e);
+ }
+ } else {
+ return new Deflater(compressionLevel, nowrap);
+ }
+ }
+
+ public static boolean usingIntelDeflater() {
+ return intelDeflaterConstructor != null;
+ }
+}
diff --git a/src/java/net/sf/samtools/util/zip/IntelDeflater.java b/src/java/net/sf/samtools/util/zip/IntelDeflater.java
new file mode 100644
index 0000000..1ce5de6
--- /dev/null
+++ b/src/java/net/sf/samtools/util/zip/IntelDeflater.java
@@ -0,0 +1,567 @@
+/*
+ * Copyright (c) 1996, 2010, Oracle and/or its affiliates. All rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * This code is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU General Public License version 2 only, as
+ * published by the Free Software Foundation. Oracle designates this
+ * particular file as subject to the "Classpath" exception as provided
+ * by Oracle in the LICENSE file that accompanied this code.
+ *
+ * This code is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
+ * version 2 for more details (a copy is included in the LICENSE file that
+ * accompanied this code).
+ *
+ * You should have received a copy of the GNU General Public License version
+ * 2 along with this work; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
+ * or visit www.oracle.com if you need additional information or have any
+ * questions.
+ */
+package net.sf.samtools.util.zip;
+
+import net.sf.samtools.Defaults;
+
+import java.io.File;
+import java.net.URL;
+import java.util.zip.Deflater;
+
+/**
+ * This is a copy of java.util.zip.Deflater from OpenJDK 7, with the following changes:
+ * - package and class name changed
+ * - static block to load libIntelDeflater library
+ * - extends java.util.zip.Deflater so that IntelDeflater object can be used as regular Deflater object.
+ * Note however that all methods of Deflater are overridden.
+ *
+ * The shared library is found via one of the following mechanisms:
+ * 1. if samjdk.intel_deflater_so_path system property is set, this is assumed to be the path of libIntelDeflater.so
+ * 2. If system property is not set, directory where the jarfile that this class came from lives is tried as location
+ * of libIntelDeflater.so
+ * 3. If either of the above fails to find the library, regular LD_LIBRARY_PATH is used to find the library.
+ * 4. If that doesn't work, class fails to load and code falls back to regular Java Deflater class.
+ *
+ *
+ * The rest of this document is copied verbatim from the original OpenJDK file.
+ *
+ * This class provides support for general purpose compression using the
+ * popular ZLIB compression library. The ZLIB compression library was
+ * initially developed as part of the PNG graphics standard and is not
+ * protected by patents. It is fully described in the specifications at
+ * the <a href="package-summary.html#package_description">java.util.zip
+ * package description</a>.
+ *
+ * <p>The following code fragment demonstrates a trivial compression
+ * and decompression of a string using <tt>IntelDeflater</tt> and
+ * <tt>Inflater</tt>.
+ *
+ * <blockquote><pre>
+ * try {
+ * // Encode a String into bytes
+ * String inputString = "blahblahblah";
+ * byte[] input = inputString.getBytes("UTF-8");
+ *
+ * // Compress the bytes
+ * byte[] output = new byte[100];
+ * IntelDeflater compresser = new IntelDeflater();
+ * compresser.setInput(input);
+ * compresser.finish();
+ * int compressedDataLength = compresser.deflate(output);
+ * compresser.end();
+ *
+ * // Decompress the bytes
+ * Inflater decompresser = new Inflater();
+ * decompresser.setInput(output, 0, compressedDataLength);
+ * byte[] result = new byte[100];
+ * int resultLength = decompresser.inflate(result);
+ * decompresser.end();
+ *
+ * // Decode the bytes into a String
+ * String outputString = new String(result, 0, resultLength, "UTF-8");
+ * } catch(java.io.UnsupportedEncodingException ex) {
+ * // handle
+ * } catch (java.util.zip.DataFormatException ex) {
+ * // handle
+ * }
+ * </pre></blockquote>
+ *
+ * @see java.util.zip.Inflater
+ * @author David Connelly
+ */
+public
+class IntelDeflater extends Deflater {
+
+ private final ZStreamRef zsRef;
+ private byte[] buf = new byte[0];
+ private int off, len;
+ private int level, strategy;
+ private boolean setParams;
+ private boolean finish, finished;
+
+ /**
+ * Compression flush mode used to achieve best compression result.
+ *
+ * @see IntelDeflater#deflate(byte[], int, int, int)
+ * @since 1.7
+ */
+ public static final int NO_FLUSH = 0;
+
+ /**
+ * Compression flush mode used to flush out all pending output; may
+ * degrade compression for some compression algorithms.
+ *
+ * @see IntelDeflater#deflate(byte[], int, int, int)
+ * @since 1.7
+ */
+ public static final int SYNC_FLUSH = 2;
+
+ /**
+ * Compression flush mode used to flush out all pending output and
+ * reset the deflater. Using this mode too often can seriously degrade
+ * compression.
+ *
+ * @see IntelDeflater#deflate(byte[], int, int, int)
+ * @since 1.7
+ */
+ public static final int FULL_FLUSH = 3;
+
+ static {
+ try {
+ final File sharedLibrary;
+ if (Defaults.INTEL_DEFLATER_SHARED_LIBRARY_PATH != null) {
+ // Load via path set by -Dsamjdk.intel_deflater_so_path=<path>
+ sharedLibrary = new File(Defaults.INTEL_DEFLATER_SHARED_LIBRARY_PATH);
+ } else {
+ // Look in directory containing this class for the library
+ URL jarUrl = IntelDeflater.class.getProtectionDomain().getCodeSource().getLocation();
+ sharedLibrary = new File(new File(jarUrl.getPath()).getParentFile(), "libIntelDeflater.so");
+ }
+ System.load(sharedLibrary.getAbsolutePath());
+ } catch (Throwable e) {
+ // Possible exceptions:
+ // System.load: UnsatisfiedLinkError
+ // getProtectionDomain: SecurityException
+ // NullPointerException due to getCodeSource returning null
+
+ // Try to find via LD_LIBRARY_PATH
+ System.loadLibrary("IntelDeflater");
+ }
+ initIDs();
+ }
+
+ /**
+ * Creates a new compressor using the specified compression level.
+ * If 'nowrap' is true then the ZLIB header and checksum fields will
+ * not be used in order to support the compression format used in
+ * both GZIP and PKZIP.
+ * @param level the compression level (0-9)
+ * @param nowrap if true then use GZIP compatible compression
+ */
+ public IntelDeflater(int level, boolean nowrap) {
+ this.level = level;
+ this.strategy = DEFAULT_STRATEGY;
+ this.zsRef = new ZStreamRef(init(level, DEFAULT_STRATEGY, nowrap));
+ }
+
+ /**
+ * Creates a new compressor using the specified compression level.
+ * Compressed data will be generated in ZLIB format.
+ * @param level the compression level (0-9)
+ */
+ public IntelDeflater(int level) {
+ this(level, false);
+ }
+
+ /**
+ * Creates a new compressor with the default compression level.
+ * Compressed data will be generated in ZLIB format.
+ */
+ public IntelDeflater() {
+ this(DEFAULT_COMPRESSION, false);
+ }
+
+ /**
+ * Sets input data for compression. This should be called whenever
+ * needsInput() returns true indicating that more input data is required.
+ * @param b the input data bytes
+ * @param off the start offset of the data
+ * @param len the length of the data
+ * @see IntelDeflater#needsInput
+ */
+ @Override
+ public void setInput(byte[] b, int off, int len) {
+ if (b== null) {
+ throw new NullPointerException();
+ }
+ if (off < 0 || len < 0 || off > b.length - len) {
+ throw new ArrayIndexOutOfBoundsException();
+ }
+ synchronized (zsRef) {
+ this.buf = b;
+ this.off = off;
+ this.len = len;
+ }
+ }
+
+ /**
+ * Sets input data for compression. This should be called whenever
+ * needsInput() returns true indicating that more input data is required.
+ * @param b the input data bytes
+ * @see IntelDeflater#needsInput
+ */
+ @Override
+ public void setInput(byte[] b) {
+ setInput(b, 0, b.length);
+ }
+
+ /**
+ * Sets preset dictionary for compression. A preset dictionary is used
+ * when the history buffer can be predetermined. When the data is later
+ * uncompressed with Inflater.inflate(), Inflater.getAdler() can be called
+ * in order to get the Adler-32 value of the dictionary required for
+ * decompression.
+ * @param b the dictionary data bytes
+ * @param off the start offset of the data
+ * @param len the length of the data
+ * @see java.util.zip.Inflater#inflate
+ * @see java.util.zip.Inflater#getAdler
+ */
+ @Override
+ public void setDictionary(byte[] b, int off, int len) {
+ if (b == null) {
+ throw new NullPointerException();
+ }
+ if (off < 0 || len < 0 || off > b.length - len) {
+ throw new ArrayIndexOutOfBoundsException();
+ }
+ synchronized (zsRef) {
+ ensureOpen();
+ setDictionary(zsRef.address(), b, off, len);
+ }
+ }
+
+ /**
+ * Sets preset dictionary for compression. A preset dictionary is used
+ * when the history buffer can be predetermined. When the data is later
+ * uncompressed with Inflater.inflate(), Inflater.getAdler() can be called
+ * in order to get the Adler-32 value of the dictionary required for
+ * decompression.
+ * @param b the dictionary data bytes
+ * @see java.util.zip.Inflater#inflate
+ * @see java.util.zip.Inflater#getAdler
+ */
+ @Override
+ public void setDictionary(byte[] b) {
+ setDictionary(b, 0, b.length);
+ }
+
+ /**
+ * Sets the compression strategy to the specified value.
+ * @param strategy the new compression strategy
+ * @exception IllegalArgumentException if the compression strategy is
+ * invalid
+ */
+ @Override
+ public void setStrategy(int strategy) {
+ switch (strategy) {
+ case DEFAULT_STRATEGY:
+ case FILTERED:
+ case HUFFMAN_ONLY:
+ break;
+ default:
+ throw new IllegalArgumentException();
+ }
+ synchronized (zsRef) {
+ if (this.strategy != strategy) {
+ this.strategy = strategy;
+ setParams = true;
+ }
+ }
+ }
+
+ /**
+ * Sets the current compression level to the specified value.
+ * @param level the new compression level (0-9)
+ * @exception IllegalArgumentException if the compression level is invalid
+ */
+ @Override
+ public void setLevel(int level) {
+ if ((level < 0 || level > 9) && level != DEFAULT_COMPRESSION) {
+ throw new IllegalArgumentException("invalid compression level");
+ }
+ synchronized (zsRef) {
+ if (this.level != level) {
+ this.level = level;
+ setParams = true;
+ }
+ }
+ }
+
+ /**
+ * Returns true if the input data buffer is empty and setInput()
+ * should be called in order to provide more input.
+ * @return true if the input data buffer is empty and setInput()
+ * should be called in order to provide more input
+ */
+ @Override
+ public boolean needsInput() {
+ return len <= 0;
+ }
+
+ /**
+ * When called, indicates that compression should end with the current
+ * contents of the input buffer.
+ */
+ @Override
+ public void finish() {
+ synchronized (zsRef) {
+ finish = true;
+ }
+ }
+
+ /**
+ * Returns true if the end of the compressed data output stream has
+ * been reached.
+ * @return true if the end of the compressed data output stream has
+ * been reached
+ */
+ @Override
+ public boolean finished() {
+ synchronized (zsRef) {
+ return finished;
+ }
+ }
+
+ /**
+ * Compresses the input data and fills specified buffer with compressed
+ * data. Returns actual number of bytes of compressed data. A return value
+ * of 0 indicates that {@link #needsInput() needsInput} should be called
+ * in order to determine if more input data is required.
+ *
+ * <p>This method uses {@link #NO_FLUSH} as its compression flush mode.
+ * An invocation of this method of the form {@code deflater.deflate(b, off, len)}
+ * yields the same result as the invocation of
+ * {@code deflater.deflate(b, off, len, IntelDeflater.NO_FLUSH)}.
+ *
+ * @param b the buffer for the compressed data
+ * @param off the start offset of the data
+ * @param len the maximum number of bytes of compressed data
+ * @return the actual number of bytes of compressed data written to the
+ * output buffer
+ */
+ @Override
+ public int deflate(byte[] b, int off, int len) {
+ return deflate(b, off, len, NO_FLUSH);
+ }
+
+ /**
+ * Compresses the input data and fills specified buffer with compressed
+ * data. Returns actual number of bytes of compressed data. A return value
+ * of 0 indicates that {@link #needsInput() needsInput} should be called
+ * in order to determine if more input data is required.
+ *
+ * <p>This method uses {@link #NO_FLUSH} as its compression flush mode.
+ * An invocation of this method of the form {@code deflater.deflate(b)}
+ * yields the same result as the invocation of
+ * {@code deflater.deflate(b, 0, b.length, IntelDeflater.NO_FLUSH)}.
+ *
+ * @param b the buffer for the compressed data
+ * @return the actual number of bytes of compressed data written to the
+ * output buffer
+ */
+ @Override
+ public int deflate(byte[] b) {
+ return deflate(b, 0, b.length, NO_FLUSH);
+ }
+
+ /**
+ * Compresses the input data and fills the specified buffer with compressed
+ * data. Returns actual number of bytes of data compressed.
+ *
+ * <p>Compression flush mode is one of the following three modes:
+ *
+ * <ul>
+ * <li>{@link #NO_FLUSH}: allows the deflater to decide how much data
+ * to accumulate, before producing output, in order to achieve the best
+ * compression (should be used in normal use scenario). A return value
+ * of 0 in this flush mode indicates that {@link #needsInput()} should
+ * be called in order to determine if more input data is required.
+ *
+ * <li>{@link #SYNC_FLUSH}: all pending output in the deflater is flushed,
+ * to the specified output buffer, so that an inflater that works on
+ * compressed data can get all input data available so far (In particular
+ * the {@link #needsInput()} returns {@code true} after this invocation
+ * if enough output space is provided). Flushing with {@link #SYNC_FLUSH}
+ * may degrade compression for some compression algorithms and so it
+ * should be used only when necessary.
+ *
+ * <li>{@link #FULL_FLUSH}: all pending output is flushed out as with
+ * {@link #SYNC_FLUSH}. The compression state is reset so that the inflater
+ * that works on the compressed output data can restart from this point
+ * if previous compressed data has been damaged or if random access is
+ * desired. Using {@link #FULL_FLUSH} too often can seriously degrade
+ * compression.
+ * </ul>
+ *
+ * <p>In the case of {@link #FULL_FLUSH} or {@link #SYNC_FLUSH}, if
+ * the return value is {@code len}, the space available in output
+ * buffer {@code b}, this method should be invoked again with the same
+ * {@code flush} parameter and more output space.
+ *
+ * @param b the buffer for the compressed data
+ * @param off the start offset of the data
+ * @param len the maximum number of bytes of compressed data
+ * @param flush the compression flush mode
+ * @return the actual number of bytes of compressed data written to
+ * the output buffer
+ *
+ * @throws IllegalArgumentException if the flush mode is invalid
+ * @since 1.7
+ */
+ public int deflate(byte[] b, int off, int len, int flush) {
+ //System.out.println("Inside IntelDeflater\n");
+ if (b == null) {
+ throw new NullPointerException();
+ }
+ if (off < 0 || len < 0 || off > b.length - len) {
+ throw new ArrayIndexOutOfBoundsException();
+ }
+ synchronized (zsRef) {
+ ensureOpen();
+ if (flush == NO_FLUSH || flush == SYNC_FLUSH ||
+ flush == FULL_FLUSH)
+ return deflateBytes(zsRef.address(), b, off, len, flush);
+ throw new IllegalArgumentException();
+ }
+ }
+
+ /**
+ * Returns the ADLER-32 value of the uncompressed data.
+ * @return the ADLER-32 value of the uncompressed data
+ */
+ @Override
+ public int getAdler() {
+ synchronized (zsRef) {
+ ensureOpen();
+ return getAdler(zsRef.address());
+ }
+ }
+
+ /**
+ * Returns the total number of uncompressed bytes input so far.
+ *
+ * <p>Since the number of bytes may be greater than
+ * Integer.MAX_VALUE, the {@link #getBytesRead()} method is now
+ * the preferred means of obtaining this information.</p>
+ *
+ * @return the total number of uncompressed bytes input so far
+ */
+ @Override
+ public int getTotalIn() {
+ return (int) getBytesRead();
+ }
+
+ /**
+ * Returns the total number of uncompressed bytes input so far.</p>
+ *
+ * @return the total (non-negative) number of uncompressed bytes input so far
+ * @since 1.5
+ */
+ @Override
+ public long getBytesRead() {
+ synchronized (zsRef) {
+ ensureOpen();
+ return getBytesRead(zsRef.address());
+ }
+ }
+
+ /**
+ * Returns the total number of compressed bytes output so far.
+ *
+ * <p>Since the number of bytes may be greater than
+ * Integer.MAX_VALUE, the {@link #getBytesWritten()} method is now
+ * the preferred means of obtaining this information.</p>
+ *
+ * @return the total number of compressed bytes output so far
+ */
+ @Override
+ public int getTotalOut() {
+ return (int) getBytesWritten();
+ }
+
+ /**
+ * Returns the total number of compressed bytes output so far.</p>
+ *
+ * @return the total (non-negative) number of compressed bytes output so far
+ * @since 1.5
+ */
+ @Override
+ public long getBytesWritten() {
+ synchronized (zsRef) {
+ ensureOpen();
+ return getBytesWritten(zsRef.address());
+ }
+ }
+
+ /**
+ * Resets deflater so that a new set of input data can be processed.
+ * Keeps current compression level and strategy settings.
+ */
+ @Override
+ public void reset() {
+ synchronized (zsRef) {
+ ensureOpen();
+ reset(zsRef.address());
+ finish = false;
+ finished = false;
+ off = len = 0;
+ }
+ }
+
+ /**
+ * Closes the compressor and discards any unprocessed input.
+ * This method should be called when the compressor is no longer
+ * being used, but will also be called automatically by the
+ * finalize() method. Once this method is called, the behavior
+ * of the IntelDeflater object is undefined.
+ */
+ @Override
+ public void end() {
+ synchronized (zsRef) {
+ long addr = zsRef.address();
+ zsRef.clear();
+ if (addr != 0) {
+ end(addr);
+ buf = null;
+ }
+ }
+ }
+
+ /**
+ * Closes the compressor when garbage is collected.
+ */
+ protected void finalize() {
+ end();
+ }
+
+ private void ensureOpen() {
+ assert Thread.holdsLock(zsRef);
+ if (zsRef.address() == 0)
+ throw new NullPointerException("IntelDeflater has been closed");
+ }
+
+ private static native void initIDs();
+ private native static long init(int level, int strategy, boolean nowrap);
+ private native static void setDictionary(long addr, byte[] b, int off, int len);
+ private native int deflateBytes(long addr, byte[] b, int off, int len,
+ int flush);
+ private native static int getAdler(long addr);
+ private native static long getBytesRead(long addr);
+ private native static long getBytesWritten(long addr);
+ private native static void reset(long addr);
+ private native static void end(long addr);
+}
+
diff --git a/src/java/net/sf/samtools/util/zip/ZStreamRef.java b/src/java/net/sf/samtools/util/zip/ZStreamRef.java
new file mode 100644
index 0000000..5a49d8a
--- /dev/null
+++ b/src/java/net/sf/samtools/util/zip/ZStreamRef.java
@@ -0,0 +1,48 @@
+/*
+ * Copyright (c) 2009, Oracle and/or its affiliates. All rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * This code is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU General Public License version 2 only, as
+ * published by the Free Software Foundation. Oracle designates this
+ * particular file as subject to the "Classpath" exception as provided
+ * by Oracle in the LICENSE file that accompanied this code.
+ *
+ * This code is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
+ * version 2 for more details (a copy is included in the LICENSE file that
+ * accompanied this code).
+ *
+ * You should have received a copy of the GNU General Public License version
+ * 2 along with this work; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
+ * or visit www.oracle.com if you need additional information or have any
+ * questions.
+ */
+package net.sf.samtools.util.zip;
+
+/**
+ * Copied from OpenJDK 7. Only change is package name, because IntelDeflater needs this and
+ * the original class is private to java.util.zip package.
+ *
+ * A reference to the native zlib's z_stream structure.
+ */
+
+class ZStreamRef {
+
+ private long address;
+ ZStreamRef (long address) {
+ this.address = address;
+ }
+
+ long address() {
+ return address;
+ }
+
+ void clear() {
+ address = 0;
+ }
+}
diff --git a/src/java/org/broad/tribble/AbstractFeatureReader.java b/src/java/org/broad/tribble/AbstractFeatureReader.java
index 2856578..4853375 100644
--- a/src/java/org/broad/tribble/AbstractFeatureReader.java
+++ b/src/java/org/broad/tribble/AbstractFeatureReader.java
@@ -41,22 +41,37 @@ public abstract class AbstractFeatureReader<T extends Feature, SOURCE> implement
protected final FeatureCodec<T, SOURCE> codec;
protected FeatureCodecHeader header;
- /** Convenience overload which defaults to requiring an index. */
+ private static ComponentMethods methods = new ComponentMethods();
+
+ /**
+ * Calls {@link #getFeatureReader(String, FeatureCodec, boolean)} with {@code requireIndex} = true
+ */
public static <FEATURE extends Feature, SOURCE> AbstractFeatureReader<FEATURE, SOURCE> getFeatureReader(final String featureFile, final FeatureCodec<FEATURE, SOURCE> codec) throws TribbleException {
return getFeatureReader(featureFile, codec, true);
}
/**
- * factory for unknown file type, could be ascii, binary, or could be tabix, or something else.
+ * {@link #getFeatureReader(String, String, FeatureCodec, boolean)} with {@code null} for indexResource
+ * @throws TribbleException
+ */
+ public static <FEATURE extends Feature, SOURCE> AbstractFeatureReader<FEATURE, SOURCE> getFeatureReader(final String featureResource, final FeatureCodec<FEATURE, SOURCE> codec, final boolean requireIndex) throws TribbleException {
+ return getFeatureReader(featureResource, null, codec, requireIndex);
+ }
+
+ /**
*
* @param featureResource the feature file to create from
- * @param codec the codec to read features with
+ * @param indexResource the index for the feature file. If null, will auto-generate (if necessary)
+ * @param codec
+ * @param requireIndex whether an index is required for this file
+ * @return
+ * @throws TribbleException
*/
- public static <FEATURE extends Feature, SOURCE> AbstractFeatureReader<FEATURE, SOURCE> getFeatureReader(final String featureResource, final FeatureCodec<FEATURE, SOURCE> codec, final boolean requireIndex) throws TribbleException {
+ public static <FEATURE extends Feature, SOURCE> AbstractFeatureReader<FEATURE, SOURCE> getFeatureReader(final String featureResource, String indexResource, final FeatureCodec<FEATURE, SOURCE> codec, final boolean requireIndex) throws TribbleException {
try {
// Test for tabix index
- if (featureResource.endsWith(".gz") && ParsingUtils.resourceExists(featureResource + ".tbi")) {
+ if (methods.isTabix(featureResource, indexResource)) {
if ( ! (codec instanceof AsciiFeatureCodec) )
throw new TribbleException("Tabix indexed files only work with ASCII codecs, but received non-Ascii codec " + codec.getClass().getSimpleName());
return new TabixFeatureReader<FEATURE, SOURCE>(featureResource, (AsciiFeatureCodec) codec);
@@ -96,6 +111,18 @@ public abstract class AbstractFeatureReader<T extends Feature, SOURCE> implement
this.codec = codec;
}
+ /**
+ * Whether the reader has an index or not
+ * Default implementation returns false
+ * @return
+ */
+ public boolean hasIndex(){
+ return false;
+ }
+
+ public static void setComponentMethods(ComponentMethods methods){
+ AbstractFeatureReader.methods = methods;
+ }
/**
* get the header
@@ -113,4 +140,14 @@ public abstract class AbstractFeatureReader<T extends Feature, SOURCE> implement
public void remove() { }
@Override public void close() { }
}
+
+ public static class ComponentMethods{
+
+ public boolean isTabix(String resourcePath, String indexPath) throws IOException{
+ if(indexPath == null){
+ indexPath = ParsingUtils.appendToPath(resourcePath, ".tbi");
+ }
+ return resourcePath.endsWith(".gz") && ParsingUtils.resourceExists(indexPath);
+ }
+ }
}
diff --git a/src/java/org/broad/tribble/TabixFeatureReader.java b/src/java/org/broad/tribble/TabixFeatureReader.java
index ad028e8..cdaba0b 100644
--- a/src/java/org/broad/tribble/TabixFeatureReader.java
+++ b/src/java/org/broad/tribble/TabixFeatureReader.java
@@ -76,6 +76,11 @@ public class TabixFeatureReader<T extends Feature, SOURCE> extends AbstractFeatu
}
}
+ @Override
+ public boolean hasIndex(){
+ return true;
+ }
+
public List<String> getSequenceNames() {
return sequenceNames;
diff --git a/src/java/org/broad/tribble/Tribble.java b/src/java/org/broad/tribble/Tribble.java
index 3544e14..abccbb7 100644
--- a/src/java/org/broad/tribble/Tribble.java
+++ b/src/java/org/broad/tribble/Tribble.java
@@ -23,6 +23,8 @@
*/
package org.broad.tribble;
+import org.broad.tribble.util.ParsingUtils;
+
import java.io.File;
/**
@@ -40,7 +42,7 @@ public class Tribble {
* @return
*/
public static String indexFile(String filename) {
- return filename + STANDARD_INDEX_EXTENSION;
+ return ParsingUtils.appendToPath(filename, STANDARD_INDEX_EXTENSION);
}
/**
@@ -52,4 +54,5 @@ public class Tribble {
public static File indexFile(File file) {
return new File(file.getAbsoluteFile() + STANDARD_INDEX_EXTENSION);
}
+
}
diff --git a/src/java/org/broad/tribble/TribbleIndexedFeatureReader.java b/src/java/org/broad/tribble/TribbleIndexedFeatureReader.java
index a243e4b..fd77a16 100644
--- a/src/java/org/broad/tribble/TribbleIndexedFeatureReader.java
+++ b/src/java/org/broad/tribble/TribbleIndexedFeatureReader.java
@@ -78,7 +78,7 @@ public class TribbleIndexedFeatureReader<T extends Feature, SOURCE> extends Abst
index = IndexFactory.loadIndex(indexFile);
} else {
// See if the index itself is gzipped
- indexFile = indexFile + ".gz";
+ indexFile = ParsingUtils.appendToPath(indexFile, ".gz");
if (ParsingUtils.resourceExists(indexFile)) {
index = IndexFactory.loadIndex(indexFile);
} else {
@@ -107,11 +107,11 @@ public class TribbleIndexedFeatureReader<T extends Feature, SOURCE> extends Abst
final SeekableStream result;
if (reuseStreamInQuery()) {
// if the stream points to an underlying file, only create the underlying seekable stream once
- if (seekableStream == null) seekableStream = SeekableStreamFactory.getStreamFor(path);
+ if (seekableStream == null) seekableStream = SeekableStreamFactory.getInstance().getStreamFor(path);
result = seekableStream;
} else {
// we are not reusing the stream, so make a fresh copy each time we request it
- result = SeekableStreamFactory.getStreamFor(path);
+ result = SeekableStreamFactory.getInstance().getStreamFor(path);
}
return result;
@@ -152,6 +152,10 @@ public class TribbleIndexedFeatureReader<T extends Feature, SOURCE> extends Abst
return index == null ? new ArrayList<String>() : new ArrayList<String>(index.getSequenceNames());
}
+ @Override
+ public boolean hasIndex() {
+ return index != null;
+ }
/**
* read the header from the file
diff --git a/src/java/org/broad/tribble/readers/TabixReader.java b/src/java/org/broad/tribble/readers/TabixReader.java
index 8c3c940..e7a3965 100644
--- a/src/java/org/broad/tribble/readers/TabixReader.java
+++ b/src/java/org/broad/tribble/readers/TabixReader.java
@@ -29,15 +29,19 @@ import java.util.HashMap;
import java.util.Arrays;
import java.lang.StringBuffer;
+import net.sf.samtools.seekablestream.ISeekableStreamFactory;
import net.sf.samtools.seekablestream.SeekableStream;
import net.sf.samtools.util.BlockCompressedInputStream;
import net.sf.samtools.seekablestream.SeekableStreamFactory;
+import org.broad.tribble.Tribble;
+import org.broad.tribble.util.ParsingUtils;
/**
* @author Heng Li <hengli at broadinstitute.org>
*/
public class TabixReader {
private String mFn;
+ private String mIdxFn;
BlockCompressedInputStream mFp;
private int mPreset;
@@ -91,7 +95,7 @@ public class TabixReader {
* @param fn File name of the data file
*/
public TabixReader(final String fn) throws IOException {
- this(fn, SeekableStreamFactory.getStreamFor(fn));
+ this(fn, SeekableStreamFactory.getInstance().getBufferedStream(SeekableStreamFactory.getInstance().getStreamFor(fn)));
}
/**
@@ -99,8 +103,20 @@ public class TabixReader {
* @param stream Seekable stream from which the data is read
*/
public TabixReader(final String fn, SeekableStream stream) throws IOException {
+ this(fn, null, stream);
+ }
+
+ /**
+ * @param fn File name of the data file (used for error messages only)
+ * @param idxFn Full path to the index file. Auto-generated if null
+ * @param stream Seekable stream from which the data is read
+ */
+ public TabixReader(final String fn, final String idxFn, SeekableStream stream) throws IOException {
mFn = fn;
- mFp = new BlockCompressedInputStream(stream); // new File(fn));
+ mFp = new BlockCompressedInputStream(stream);
+ if(idxFn == null){
+ mIdxFn = ParsingUtils.appendToPath(fn, ".tbi");
+ }
readIndex();
}
@@ -202,7 +218,8 @@ public class TabixReader {
* Read the Tabix index from the default file.
*/
public void readIndex() throws IOException {
- readIndex(SeekableStreamFactory.getStreamFor(mFn + ".tbi"));
+ ISeekableStreamFactory ssf = SeekableStreamFactory.getInstance();
+ readIndex(ssf.getBufferedStream(ssf.getStreamFor(mIdxFn), 128000));
}
/**
diff --git a/src/java/org/broad/tribble/util/ParsingUtils.java b/src/java/org/broad/tribble/util/ParsingUtils.java
index 42b4980..25bc9ce 100644
--- a/src/java/org/broad/tribble/util/ParsingUtils.java
+++ b/src/java/org/broad/tribble/util/ParsingUtils.java
@@ -23,6 +23,8 @@
*/
package org.broad.tribble.util;
+import net.sf.samtools.util.HttpUtils;
+
import java.awt.*;
import java.io.File;
import java.io.FileInputStream;
@@ -415,4 +417,31 @@ public class ParsingUtils {
}
urlHelperClass = helperClass;
}
+
+ /**
+ * Add the {@code indexExtension} to the {@code filepath}, preserving
+ * query string elements if present. Intended for use where {@code filepath}
+ * is a URL. Will behave correctly on regular file paths (just add the extension
+ * to the end)
+ * @param filepath
+ * @param indexExtension
+ * @return
+ */
+ public static String appendToPath(String filepath, String indexExtension) {
+ String tabxIndex = null;
+ URL url = null;
+ try{
+ url = new URL(filepath);
+ }catch (MalformedURLException e){
+ //pass
+ }
+ if (url != null) {
+ String path = url.getPath();
+ String indexPath = path + indexExtension;
+ tabxIndex = filepath.replace(path, indexPath);
+ } else {
+ tabxIndex = filepath + indexExtension;
+ }
+ return tabxIndex;
+ }
}
diff --git a/src/java/org/broadinstitute/variant/variantcontext/VariantContext.java b/src/java/org/broadinstitute/variant/variantcontext/VariantContext.java
index 52eb957..0709e2d 100644
--- a/src/java/org/broadinstitute/variant/variantcontext/VariantContext.java
+++ b/src/java/org/broadinstitute/variant/variantcontext/VariantContext.java
@@ -237,6 +237,53 @@ public class VariantContext implements Feature { // to enable tribble integratio
/* cached monomorphic value: null -> not yet computed, False, True */
private Boolean monomorphic = null;
+ /*
+* Determine which genotype fields are in use in the genotypes in VC
+* @return an ordered list of genotype fields in use in VC. If vc has genotypes this will always include GT first
+*/
+ public List<String> calcVCFGenotypeKeys(final VCFHeader header) {
+ final Set<String> keys = new HashSet<String>();
+
+ boolean sawGoodGT = false;
+ boolean sawGoodQual = false;
+ boolean sawGenotypeFilter = false;
+ boolean sawDP = false;
+ boolean sawAD = false;
+ boolean sawPL = false;
+ for (final Genotype g : this.getGenotypes()) {
+ keys.addAll(g.getExtendedAttributes().keySet());
+ if ( g.isAvailable() ) sawGoodGT = true;
+ if ( g.hasGQ() ) sawGoodQual = true;
+ if ( g.hasDP() ) sawDP = true;
+ if ( g.hasAD() ) sawAD = true;
+ if ( g.hasPL() ) sawPL = true;
+ if (g.isFiltered()) sawGenotypeFilter = true;
+ }
+
+ if ( sawGoodQual ) keys.add(VCFConstants.GENOTYPE_QUALITY_KEY);
+ if ( sawDP ) keys.add(VCFConstants.DEPTH_KEY);
+ if ( sawAD ) keys.add(VCFConstants.GENOTYPE_ALLELE_DEPTHS);
+ if ( sawPL ) keys.add(VCFConstants.GENOTYPE_PL_KEY);
+ if ( sawGenotypeFilter ) keys.add(VCFConstants.GENOTYPE_FILTER_KEY);
+
+ List<String> sortedList = ParsingUtils.sortList(new ArrayList<String>(keys));
+
+ // make sure the GT is first
+ if (sawGoodGT) {
+ final List<String> newList = new ArrayList<String>(sortedList.size()+1);
+ newList.add(VCFConstants.GENOTYPE_KEY);
+ newList.addAll(sortedList);
+ sortedList = newList;
+ }
+
+ if (sortedList.isEmpty() && header.hasGenotypingData()) {
+ // this needs to be done in case all samples are no-calls
+ return Collections.singletonList(VCFConstants.GENOTYPE_KEY);
+ } else {
+ return sortedList;
+ }
+ }
+
// ---------------------------------------------------------------------------------------------------------
//
// validation mode
diff --git a/src/java/org/broadinstitute/variant/variantcontext/VariantContextComparator.java b/src/java/org/broadinstitute/variant/variantcontext/VariantContextComparator.java
index 1f51e5c..7a8b9cb 100644
--- a/src/java/org/broadinstitute/variant/variantcontext/VariantContextComparator.java
+++ b/src/java/org/broadinstitute/variant/variantcontext/VariantContextComparator.java
@@ -1,15 +1,10 @@
package org.broadinstitute.variant.variantcontext;
+import net.sf.samtools.SAMSequenceDictionary;
+import net.sf.samtools.SAMSequenceRecord;
import org.broadinstitute.variant.vcf.VCFContigHeaderLine;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
/**
* A Comparator that orders VariantContexts by the ordering of the contigs/chromosomes in the List
@@ -17,6 +12,14 @@ import java.util.Set;
*/
public class VariantContextComparator implements Comparator<VariantContext> {
+ public static List<String> getSequenceNameList(final SAMSequenceDictionary dictionary) {
+ final List<String> list = new ArrayList<String>();
+ for (final SAMSequenceRecord record : dictionary.getSequences()) {
+ list.add(record.getSequenceName());
+ }
+ return list;
+ }
+
// For fast lookup of the contig's index in the contig list
private final Map<String, Integer> contigIndexLookup;
@@ -61,6 +64,10 @@ public class VariantContextComparator implements Comparator<VariantContext> {
this.contigIndexLookup = Collections.unmodifiableMap(protoContigIndexLookup);
}
+ public VariantContextComparator(final SAMSequenceDictionary dictionary) {
+ this(getSequenceNameList(dictionary));
+ }
+
@Override
public int compare(final VariantContext firstVariantContext, final VariantContext secondVariantContext) {
// Will throw NullPointerException -- happily -- if either of the chromosomes/contigs aren't
diff --git a/src/java/org/broadinstitute/variant/variantcontext/VariantContextUtils.java b/src/java/org/broadinstitute/variant/variantcontext/VariantContextUtils.java
index a5b7b6c..a23bcbb 100644
--- a/src/java/org/broadinstitute/variant/variantcontext/VariantContextUtils.java
+++ b/src/java/org/broadinstitute/variant/variantcontext/VariantContextUtils.java
@@ -27,6 +27,7 @@ package org.broadinstitute.variant.variantcontext;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
+import net.sf.samtools.util.Lazy;
import org.apache.commons.jexl2.Expression;
import org.apache.commons.jexl2.JexlEngine;
import org.broad.tribble.TribbleException;
@@ -36,18 +37,43 @@ import org.broadinstitute.variant.vcf.*;
import java.util.*;
public class VariantContextUtils {
-
private static Set<String> MISSING_KEYS_WARNED_ABOUT = new HashSet<String>();
- final public static JexlEngine engine = new JexlEngine();
+ /** Use a {@link Lazy} {@link JexlEngine} instance to avoid class-loading issues. (Applications that access this class are otherwise
+ * forced to build a {@link JexlEngine} instance, which depends on some apache logging libraries that mightn't be packaged.) */
+ final public static Lazy<JexlEngine> engine = new Lazy<JexlEngine>(new Lazy.LazyInitializer<JexlEngine>() {
+ @Override
+ public JexlEngine make() {
+ final JexlEngine jexl = new JexlEngine();
+ jexl.setSilent(false); // will throw errors now for selects that don't evaluate properly
+ jexl.setLenient(false);
+ jexl.setDebug(false);
+ return jexl;
+ }
+ });
private final static boolean ASSUME_MISSING_FIELDS_ARE_STRINGS = false;
-
- static {
- engine.setSilent(false); // will throw errors now for selects that don't evaluate properly
- engine.setLenient(false);
- engine.setDebug(false);
+
+ /**
+ * Computes the alternate allele frequency at the provided {@link VariantContext} by dividing its "AN" by its "AC".
+ * @param vc The variant whose alternate allele frequency is computed
+ * @return The alternate allele frequency in [0, 1]
+ * @throws AssertionError When either annotation is missing, or when the compuated frequency is outside the expected range
+ */
+ public static double calculateAltAlleleFrequency(final VariantContext vc) {
+ if (!vc.hasAttribute(VCFConstants.ALLELE_NUMBER_KEY) || !vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY))
+ throw new AssertionError(String.format(
+ "Cannot compute the provided variant's alt allele frequency because it does not have both %s and %s annotations: %s",
+ VCFConstants.ALLELE_NUMBER_KEY,
+ VCFConstants.ALLELE_COUNT_KEY,
+ vc));
+ final double altAlleleCount = vc.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY, 0);
+ final double totalCount = vc.getAttributeAsInt(VCFConstants.ALLELE_NUMBER_KEY, 0);
+ final double aaf = altAlleleCount / totalCount;
+ if (aaf > 1 || aaf < 0)
+ throw new AssertionError(String.format("Expected a minor allele frequency in the range [0, 1], but got %s. vc=%s", aaf, vc));
+ return aaf;
}
-
+
/**
* Update the attributes of the attributes map given the VariantContext to reflect the
* proper chromosome-based VCF tags
@@ -230,7 +256,7 @@ public class VariantContextUtils {
if ( name == null || expStr == null ) throw new IllegalArgumentException("Cannot create null expressions : " + name + " " + expStr);
try {
- Expression exp = engine.createExpression(expStr);
+ Expression exp = engine.get().createExpression(expStr);
exps.add(new JexlVCMatchExp(name, exp));
} catch (Exception e) {
throw new IllegalArgumentException("Argument " + name + "has a bad value. Invalid expression used (" + expStr + "). Please see the JEXL docs for correct syntax.") ;
@@ -316,26 +342,11 @@ public class VariantContextUtils {
return r;
}
- // TODO: remove that after testing
-// static private void verifyUniqueSampleNames(Collection<VariantContext> unsortedVCs) {
-// Set<String> names = new HashSet<String>();
-// for ( VariantContext vc : unsortedVCs ) {
-// for ( String name : vc.getSampleNames() ) {
-// //System.out.printf("Checking %s %b%n", name, names.contains(name));
-// if ( names.contains(name) )
-// throw new IllegalStateException("REQUIRE_UNIQUE sample names is true but duplicate names were discovered " + name);
-// }
-//
-// names.addAll(vc.getSampleNames());
-// }
-// }
-
-
public static int getSize( VariantContext vc ) {
return vc.getEnd() - vc.getStart() + 1;
}
- public static final Set<String> genotypeNames(final Collection<Genotype> genotypes) {
+ public static Set<String> genotypeNames(final Collection<Genotype> genotypes) {
final Set<String> names = new HashSet<String>(genotypes.size());
for ( final Genotype g : genotypes )
names.add(g.getSampleName());
diff --git a/src/java/org/broadinstitute/variant/variantcontext/writer/BCF2Writer.java b/src/java/org/broadinstitute/variant/variantcontext/writer/BCF2Writer.java
index c24ffec..462f32d 100644
--- a/src/java/org/broadinstitute/variant/variantcontext/writer/BCF2Writer.java
+++ b/src/java/org/broadinstitute/variant/variantcontext/writer/BCF2Writer.java
@@ -28,6 +28,7 @@ package org.broadinstitute.variant.variantcontext.writer;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import net.sf.samtools.SAMSequenceDictionary;
+import org.broad.tribble.index.IndexCreator;
import org.broadinstitute.variant.bcf2.BCF2Codec;
import org.broadinstitute.variant.bcf2.BCF2Type;
import org.broadinstitute.variant.bcf2.BCF2Utils;
@@ -107,13 +108,21 @@ class BCF2Writer extends IndexingVariantContextWriter {
private VCFHeader lastVCFHeaderOfUnparsedGenotypes = null;
private boolean canPassOnUnparsedGenotypeDataForLastVCFHeader = false;
-
- public BCF2Writer(final File location, final OutputStream output, final SAMSequenceDictionary refDict, final boolean enableOnTheFlyIndexing, final boolean doNotWriteGenotypes) {
+ public BCF2Writer(final File location, final OutputStream output, final SAMSequenceDictionary refDict,
+ final boolean enableOnTheFlyIndexing, final boolean doNotWriteGenotypes) {
super(writerName(location, output), location, output, refDict, enableOnTheFlyIndexing);
this.outputStream = getOutputStream();
this.doNotWriteGenotypes = doNotWriteGenotypes;
}
+ public BCF2Writer(final File location, final OutputStream output, final SAMSequenceDictionary refDict,
+ final IndexCreator indexCreator,
+ final boolean enableOnTheFlyIndexing, final boolean doNotWriteGenotypes) {
+ super(writerName(location, output), location, output, refDict, enableOnTheFlyIndexing, indexCreator);
+ this.outputStream = getOutputStream();
+ this.doNotWriteGenotypes = doNotWriteGenotypes;
+ }
+
// --------------------------------------------------------------------------------
//
// Interface functions
@@ -151,7 +160,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
fieldManager.setup(header, encoder, stringDictionaryMap);
try {
- // write out the header into a byte stream, get it's length, and write everything to the file
+ // write out the header into a byte stream, get its length, and write everything to the file
final ByteArrayOutputStream capture = new ByteArrayOutputStream();
final OutputStreamWriter writer = new OutputStreamWriter(capture);
this.header = VCFWriter.writeHeader(header, writer, doNotWriteGenotypes, VCFWriter.getVersionLine(), "BCF2 stream");
@@ -294,9 +303,9 @@ class BCF2Writer extends IndexingVariantContextWriter {
* @param vc
* @return
*/
- private final int getNGenotypeFormatFields(final VariantContext vc) {
+ private int getNGenotypeFormatFields(final VariantContext vc) {
final BCF2Codec.LazyData lazyData = getLazyData(vc);
- return lazyData != null ? lazyData.nGenotypeFields : VCFWriter.calcVCFGenotypeKeys(vc, header).size();
+ return lazyData != null ? lazyData.nGenotypeFields : vc.calcVCFGenotypeKeys(header).size();
}
private void buildID( VariantContext vc ) throws IOException {
@@ -341,7 +350,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
}
// we have to do work to convert the VC into a BCF2 byte stream
- final List<String> genotypeFields = VCFWriter.calcVCFGenotypeKeys(vc, header);
+ final List<String> genotypeFields = vc.calcVCFGenotypeKeys(header);
for ( final String field : genotypeFields ) {
final BCF2FieldWriter.GenotypesWriter writer = fieldManager.getGenotypeFieldWriter(field);
if ( writer == null ) errorUnexpectedFieldToWrite(vc, field, "FORMAT");
@@ -367,7 +376,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
* @param field
* @param fieldType
*/
- private final void errorUnexpectedFieldToWrite(final VariantContext vc, final String field, final String fieldType) {
+ private void errorUnexpectedFieldToWrite(final VariantContext vc, final String field, final String fieldType) {
throw new IllegalStateException("Found field " + field + " in the " + fieldType + " fields of VariantContext at " +
vc.getChr() + ":" + vc.getStart() + " from " + vc.getSource() + " but this hasn't been defined in the VCFHeader");
}
@@ -395,7 +404,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
@Requires("! strings.isEmpty()")
@Ensures("result.isIntegerType()")
- private final BCF2Type encodeStringsByRef(final Collection<String> strings) throws IOException {
+ private BCF2Type encodeStringsByRef(final Collection<String> strings) throws IOException {
final List<Integer> offsets = new ArrayList<Integer>(strings.size());
// iterate over strings until we find one that needs 16 bits, and break
@@ -417,7 +426,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
* @param contigLines
*/
@Requires("contigDictionary.isEmpty()")
- private final void createContigDictionary(final Collection<VCFContigHeaderLine> contigLines) {
+ private void createContigDictionary(final Collection<VCFContigHeaderLine> contigLines) {
int offset = 0;
for ( VCFContigHeaderLine contig : contigLines )
contigDictionary.put(contig.getID(), offset++);
diff --git a/src/java/org/broadinstitute/variant/variantcontext/writer/IndexingVariantContextWriter.java b/src/java/org/broadinstitute/variant/variantcontext/writer/IndexingVariantContextWriter.java
index 800cb84..c036d5d 100644
--- a/src/java/org/broadinstitute/variant/variantcontext/writer/IndexingVariantContextWriter.java
+++ b/src/java/org/broadinstitute/variant/variantcontext/writer/IndexingVariantContextWriter.java
@@ -32,6 +32,7 @@ import net.sf.samtools.SAMSequenceRecord;
import org.broad.tribble.Tribble;
import org.broad.tribble.index.DynamicIndexCreator;
import org.broad.tribble.index.Index;
+import org.broad.tribble.index.IndexCreator;
import org.broad.tribble.index.IndexFactory;
import org.broad.tribble.util.LittleEndianOutputStream;
import org.broadinstitute.variant.vcf.VCFHeader;
@@ -44,35 +45,80 @@ import java.io.*;
*/
abstract class IndexingVariantContextWriter implements VariantContextWriter {
private final String name;
+ private final File location;
private final SAMSequenceDictionary refDict;
private OutputStream outputStream;
private PositionalOutputStream positionalOutputStream = null;
- private DynamicIndexCreator indexer = null;
+ private IndexCreator indexer = null;
private LittleEndianOutputStream idxStream = null;
+ private IndexingVariantContextWriter(final String name, final File location, final OutputStream output, final SAMSequenceDictionary refDict) {
+ this.name = name;
+ this.location = location;
+ this.outputStream = output;
+ this.refDict = refDict;
+ }
+
+ /**
+ * Create a VariantContextWriter with an associated index using the default index creator
+ *
+ * @param name the name of this writer (i.e. the file name or stream)
+ * @param location the path to the output file
+ * @param output the output stream to write to
+ * @param refDict the reference dictionary
+ * @param enableOnTheFlyIndexing is OTF indexing enabled?
+ */
@Requires({"name != null",
"! ( location == null && output == null )",
"! ( enableOnTheFlyIndexing && location == null )"})
- protected IndexingVariantContextWriter(final String name, final File location, final OutputStream output, final SAMSequenceDictionary refDict, final boolean enableOnTheFlyIndexing) {
- outputStream = output;
- this.name = name;
- this.refDict = refDict;
+ protected IndexingVariantContextWriter(final String name, final File location, final OutputStream output, final SAMSequenceDictionary refDict,
+ final boolean enableOnTheFlyIndexing) {
+ this(name, location, output, refDict);
if ( enableOnTheFlyIndexing ) {
- try {
- idxStream = new LittleEndianOutputStream(new FileOutputStream(Tribble.indexFile(location)));
- //System.out.println("Creating index on the fly for " + location);
- indexer = new DynamicIndexCreator(IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME);
- indexer.initialize(location, indexer.defaultBinSize());
- positionalOutputStream = new PositionalOutputStream(output);
- outputStream = positionalOutputStream;
- } catch ( IOException ex ) {
- // No matter what we keep going, since we don't care if we can't create the index file
- idxStream = null;
- indexer = null;
- positionalOutputStream = null;
- }
+ final IndexCreator idxCreator = new DynamicIndexCreator(IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME);
+ idxCreator.initialize(location, idxCreator.defaultBinSize());
+ initIndexingWriter(idxCreator);
+ }
+ }
+
+ /**
+ * Create a VariantContextWriter with an associated index using a custom index creator
+ *
+ * @param name the name of this writer (i.e. the file name or stream)
+ * @param location the path to the output file
+ * @param output the output stream to write to
+ * @param refDict the reference dictionary
+ * @param enableOnTheFlyIndexing is OTF indexing enabled?
+ * @param idxCreator the custom index creator. NOTE: must be initialized
+ */
+ @Requires({"name != null",
+ "! ( location == null && output == null )",
+ "! ( enableOnTheFlyIndexing && location == null )",
+ "idxCreator != null"})
+ protected IndexingVariantContextWriter(final String name, final File location, final OutputStream output, final SAMSequenceDictionary refDict,
+ final boolean enableOnTheFlyIndexing, final IndexCreator idxCreator) {
+ this(name, location, output, refDict);
+
+ if ( enableOnTheFlyIndexing ) {
+ initIndexingWriter(idxCreator);
+ }
+ }
+
+ @Requires({"idxCreator != null"})
+ private void initIndexingWriter(final IndexCreator idxCreator) {
+ try {
+ indexer = idxCreator;
+ idxStream = new LittleEndianOutputStream(new FileOutputStream(Tribble.indexFile(location)));
+ //System.out.println("Creating index on the fly for " + location);
+ positionalOutputStream = new PositionalOutputStream(outputStream);
+ outputStream = positionalOutputStream;
+ } catch ( IOException ex ) {
+ // No matter what we keep going, since we don't care if we can't create the index file
+ idxStream = null;
+ indexer = null;
+ positionalOutputStream = null;
}
}
diff --git a/src/java/org/broadinstitute/variant/variantcontext/writer/IntGenotypeFieldAccessors.java b/src/java/org/broadinstitute/variant/variantcontext/writer/IntGenotypeFieldAccessors.java
index f02612b..9a485d2 100644
--- a/src/java/org/broadinstitute/variant/variantcontext/writer/IntGenotypeFieldAccessors.java
+++ b/src/java/org/broadinstitute/variant/variantcontext/writer/IntGenotypeFieldAccessors.java
@@ -38,7 +38,7 @@ import java.util.HashMap;
* @author Mark DePristo
* @since 6/12
*/
-class IntGenotypeFieldAccessors {
+public class IntGenotypeFieldAccessors {
// initialized once per writer to allow parallel writers to work
private final HashMap<String, Accessor> intGenotypeFieldEncoders = new HashMap<String, Accessor>();
diff --git a/src/java/org/broadinstitute/variant/variantcontext/writer/VCFWriter.java b/src/java/org/broadinstitute/variant/variantcontext/writer/VCFWriter.java
index c91dc79..7a43e83 100644
--- a/src/java/org/broadinstitute/variant/variantcontext/writer/VCFWriter.java
+++ b/src/java/org/broadinstitute/variant/variantcontext/writer/VCFWriter.java
@@ -26,36 +26,43 @@
package org.broadinstitute.variant.variantcontext.writer;
import net.sf.samtools.SAMSequenceDictionary;
-import org.broad.tribble.TribbleException;
-import org.broad.tribble.util.ParsingUtils;
-import org.broadinstitute.variant.vcf.*;
-import org.broadinstitute.variant.variantcontext.*;
-
-import java.io.*;
-import java.lang.reflect.Array;
-import java.nio.charset.Charset;
-import java.util.*;
+import org.broad.tribble.index.IndexCreator;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
+import org.broadinstitute.variant.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFEncoder;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.vcf.VCFHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderVersion;
+
+import java.io.BufferedWriter;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
+import java.io.Writer;
/**
* this class writes VCF files
*/
class VCFWriter extends IndexingVariantContextWriter {
- private final static String VERSION_LINE = VCFHeader.METADATA_INDICATOR + VCFHeaderVersion.VCF4_1.getFormatString() + "=" + VCFHeaderVersion.VCF4_1.getVersionString();
- /**
- * The encoding used for VCF files. ISO-8859-1
- */
- static final private Charset charset = Charset.forName("ISO-8859-1");
-
- // should we write genotypes or just sites?
- final protected boolean doNotWriteGenotypes;
+ private static final String VERSION_LINE =
+ VCFHeader.METADATA_INDICATOR + VCFHeaderVersion.VCF4_1.getFormatString() + "=" + VCFHeaderVersion.VCF4_1.getVersionString();
+
+ // Initialized when the header is written to the output stream
+ private VCFEncoder vcfEncoder = null;
// the VCF header we're storing
protected VCFHeader mHeader = null;
- final private boolean allowMissingFieldsInHeader;
+ private final boolean allowMissingFieldsInHeader;
- /**
+ // should we write genotypes or just sites?
+ private final boolean doNotWriteGenotypes;
+
+ /*
* The VCF writer uses an internal Writer, based by the ByteArrayOutputStream lineBuffer,
* to temp. buffer the header and per-site output before flushing the per line output
* in one go to the super.getOutputStream. This results in high-performance, proper encoding,
@@ -65,28 +72,34 @@ class VCFWriter extends IndexingVariantContextWriter {
*/
private static final int INITIAL_BUFFER_SIZE = 1024 * 16;
private final ByteArrayOutputStream lineBuffer = new ByteArrayOutputStream(INITIAL_BUFFER_SIZE);
- /** Wrapping in a {@link BufferedWriter} avoids frequent conversions with individual writes to OutputStreamWriter. */
- private final Writer writer = new BufferedWriter(new OutputStreamWriter(lineBuffer, charset));
- private IntGenotypeFieldAccessors intGenotypeFieldAccessors = new IntGenotypeFieldAccessors();
+ /* Wrapping in a {@link BufferedWriter} avoids frequent conversions with individual writes to OutputStreamWriter. */
+ private final Writer writer = new BufferedWriter(new OutputStreamWriter(lineBuffer, VCFEncoder.VCF_CHARSET));
public VCFWriter(final File location, final OutputStream output, final SAMSequenceDictionary refDict,
- final boolean enableOnTheFlyIndexing, boolean doNotWriteGenotypes,
- final boolean allowMissingFieldsInHeader ) {
+ final boolean enableOnTheFlyIndexing,
+ final boolean doNotWriteGenotypes, final boolean allowMissingFieldsInHeader ) {
super(writerName(location, output), location, output, refDict, enableOnTheFlyIndexing);
this.doNotWriteGenotypes = doNotWriteGenotypes;
- this.allowMissingFieldsInHeader = allowMissingFieldsInHeader;
+ this.allowMissingFieldsInHeader = allowMissingFieldsInHeader;
}
+ public VCFWriter(final File location, final OutputStream output, final SAMSequenceDictionary refDict,
+ final IndexCreator indexCreator, final boolean enableOnTheFlyIndexing,
+ final boolean doNotWriteGenotypes, final boolean allowMissingFieldsInHeader ) {
+ super(writerName(location, output), location, output, refDict, enableOnTheFlyIndexing, indexCreator);
+ this.doNotWriteGenotypes = doNotWriteGenotypes;
+ this.allowMissingFieldsInHeader = allowMissingFieldsInHeader;
+ }
// --------------------------------------------------------------------------------
//
// VCFWriter interface functions
//
// --------------------------------------------------------------------------------
- /**
+ /*
* Write String s to the internal buffered writer.
*
- * flushBuffer() must be called to actually write the data to the true output stream.
+ * writeAndResetBuffer() must be called to actually write the data to the true output stream.
*
* @param s the string to write
* @throws IOException
@@ -95,26 +108,25 @@ class VCFWriter extends IndexingVariantContextWriter {
writer.write(s);
}
- /**
- * Actually write the line buffer contents to the destination output stream.
- *
- * After calling this function the line buffer is reset, so the contents of the buffer can be reused
- *
- * @throws IOException
+ /*
+ * Actually write the line buffer contents to the destination output stream. After calling this function
+ * the line buffer is reset so the contents of the buffer can be reused
*/
- private void flushBuffer() throws IOException {
+ private void writeAndResetBuffer() throws IOException {
writer.flush();
getOutputStream().write(lineBuffer.toByteArray());
lineBuffer.reset();
}
@Override
- public void writeHeader(VCFHeader header) {
+ public void writeHeader(final VCFHeader header) {
// note we need to update the mHeader object after this call because they header
// may have genotypes trimmed out of it, if doNotWriteGenotypes is true
try {
- mHeader = writeHeader(header, writer, doNotWriteGenotypes, getVersionLine(), getStreamName());
- flushBuffer();
+ this.mHeader = writeHeader(header, writer, doNotWriteGenotypes, getVersionLine(), getStreamName());
+ this.vcfEncoder = new VCFEncoder(this.mHeader, this.allowMissingFieldsInHeader);
+ writeAndResetBuffer();
+
} catch ( IOException e ) {
throw new RuntimeException("Couldn't write file " + getStreamName(), e);
}
@@ -135,7 +147,7 @@ class VCFWriter extends IndexingVariantContextWriter {
// the file format field needs to be written first
writer.write(versionLine + "\n");
- for ( VCFHeaderLine line : header.getMetaDataInSortedOrder() ) {
+ for (final VCFHeaderLine line : header.getMetaDataInSortedOrder() ) {
if ( VCFHeaderVersion.isFormatString(line.getKey()) )
continue;
@@ -147,7 +159,7 @@ class VCFWriter extends IndexingVariantContextWriter {
// write out the column line
writer.write(VCFHeader.HEADER_INDICATOR);
boolean isFirst = true;
- for ( VCFHeader.HEADER_FIELDS field : header.getHeaderFields() ) {
+ for (final VCFHeader.HEADER_FIELDS field : header.getHeaderFields() ) {
if ( isFirst )
isFirst = false; // don't write out a field separator
else
@@ -158,7 +170,7 @@ class VCFWriter extends IndexingVariantContextWriter {
if ( header.hasGenotypingData() ) {
writer.write(VCFConstants.FIELD_SEPARATOR);
writer.write("FORMAT");
- for ( String sample : header.getGenotypeSamples() ) {
+ for (final String sample : header.getGenotypeSamples() ) {
writer.write(VCFConstants.FIELD_SEPARATOR);
writer.write(sample);
}
@@ -191,414 +203,21 @@ class VCFWriter extends IndexingVariantContextWriter {
}
/**
- * add a record to the file
- *
- * @param vc the Variant Context object
+ * Add a record to the file
*/
@Override
- public void add(VariantContext vc) {
- if ( mHeader == null )
- throw new IllegalStateException("The VCF Header must be written before records can be added: " + getStreamName());
-
- if ( doNotWriteGenotypes )
- vc = new VariantContextBuilder(vc).noGenotypes().make();
-
+ public void add(final VariantContext context) {
try {
- super.add(vc);
-
- Map<Allele, String> alleleMap = buildAlleleMap(vc);
-
- // CHROM
- write(vc.getChr());
- write(VCFConstants.FIELD_SEPARATOR);
-
- // POS
- write(String.valueOf(vc.getStart()));
- write(VCFConstants.FIELD_SEPARATOR);
-
- // ID
- String ID = vc.getID();
- write(ID);
- write(VCFConstants.FIELD_SEPARATOR);
-
- // REF
- String refString = vc.getReference().getDisplayString();
- write(refString);
- write(VCFConstants.FIELD_SEPARATOR);
-
- // ALT
- if ( vc.isVariant() ) {
- Allele altAllele = vc.getAlternateAllele(0);
- String alt = altAllele.getDisplayString();
- write(alt);
-
- for (int i = 1; i < vc.getAlternateAlleles().size(); i++) {
- altAllele = vc.getAlternateAllele(i);
- alt = altAllele.getDisplayString();
- write(",");
- write(alt);
- }
- } else {
- write(VCFConstants.EMPTY_ALTERNATE_ALLELE_FIELD);
- }
- write(VCFConstants.FIELD_SEPARATOR);
-
- // QUAL
- if ( !vc.hasLog10PError() )
- write(VCFConstants.MISSING_VALUE_v4);
- else
- write(formatQualValue(vc.getPhredScaledQual()));
- write(VCFConstants.FIELD_SEPARATOR);
-
- // FILTER
- String filters = getFilterString(vc);
- write(filters);
- write(VCFConstants.FIELD_SEPARATOR);
+ super.add(context);
- // INFO
- Map<String, String> infoFields = new TreeMap<String, String>();
- for ( Map.Entry<String, Object> field : vc.getAttributes().entrySet() ) {
- String key = field.getKey();
+ if (this.doNotWriteGenotypes) write(this.vcfEncoder.encode(new VariantContextBuilder(context).noGenotypes().make()));
+ else write(this.vcfEncoder.encode(context));
+ write("\n");
- if ( ! mHeader.hasInfoLine(key) )
- fieldIsMissingFromHeaderError(vc, key, "INFO");
+ writeAndResetBuffer();
- String outputValue = formatVCFField(field.getValue());
- if ( outputValue != null )
- infoFields.put(key, outputValue);
- }
- writeInfoString(infoFields);
-
- // FORMAT
- final GenotypesContext gc = vc.getGenotypes();
- if ( gc.isLazyWithData() && ((LazyGenotypesContext)gc).getUnparsedGenotypeData() instanceof String ) {
- write(VCFConstants.FIELD_SEPARATOR);
- write(((LazyGenotypesContext) gc).getUnparsedGenotypeData().toString());
- } else {
- List<String> genotypeAttributeKeys = calcVCFGenotypeKeys(vc, mHeader);
- if ( ! genotypeAttributeKeys.isEmpty() ) {
- for ( final String format : genotypeAttributeKeys )
- if ( ! mHeader.hasFormatLine(format) )
- fieldIsMissingFromHeaderError(vc, format, "FORMAT");
-
- final String genotypeFormatString = ParsingUtils.join(VCFConstants.GENOTYPE_FIELD_SEPARATOR, genotypeAttributeKeys);
-
- write(VCFConstants.FIELD_SEPARATOR);
- write(genotypeFormatString);
-
- addGenotypeData(vc, alleleMap, genotypeAttributeKeys);
- }
- }
-
- write("\n");
- // note that we cannot call flush here if we want block gzipping to work properly
- // calling flush results in all gzipped blocks for each variant
- flushBuffer();
} catch (IOException e) {
throw new RuntimeException("Unable to write the VCF object to " + getStreamName(), e);
}
}
-
- private static Map<Allele, String> buildAlleleMap(final VariantContext vc) {
- final Map<Allele, String> alleleMap = new HashMap<Allele, String>(vc.getAlleles().size()+1);
- alleleMap.put(Allele.NO_CALL, VCFConstants.EMPTY_ALLELE); // convenience for lookup
-
- final List<Allele> alleles = vc.getAlleles();
- for ( int i = 0; i < alleles.size(); i++ ) {
- alleleMap.put(alleles.get(i), String.valueOf(i));
- }
-
- return alleleMap;
- }
-
- // --------------------------------------------------------------------------------
- //
- // implementation functions
- //
- // --------------------------------------------------------------------------------
-
- private final String getFilterString(final VariantContext vc) {
- if ( vc.isFiltered() ) {
- for ( final String filter : vc.getFilters() )
- if ( ! mHeader.hasFilterLine(filter) )
- fieldIsMissingFromHeaderError(vc, filter, "FILTER");
-
- return ParsingUtils.join(";", ParsingUtils.sortList(vc.getFilters()));
- }
- else if ( vc.filtersWereApplied() )
- return VCFConstants.PASSES_FILTERS_v4;
- else
- return VCFConstants.UNFILTERED;
- }
-
- private static final String QUAL_FORMAT_STRING = "%.2f";
- private static final String QUAL_FORMAT_EXTENSION_TO_TRIM = ".00";
-
- private String formatQualValue(double qual) {
- String s = String.format(QUAL_FORMAT_STRING, qual);
- if ( s.endsWith(QUAL_FORMAT_EXTENSION_TO_TRIM) )
- s = s.substring(0, s.length() - QUAL_FORMAT_EXTENSION_TO_TRIM.length());
- return s;
- }
-
- /**
- * create the info string; assumes that no values are null
- *
- * @param infoFields a map of info fields
- * @throws IOException for writer
- */
- private void writeInfoString(Map<String, String> infoFields) throws IOException {
- if ( infoFields.isEmpty() ) {
- write(VCFConstants.EMPTY_INFO_FIELD);
- return;
- }
-
- boolean isFirst = true;
- for ( Map.Entry<String, String> entry : infoFields.entrySet() ) {
- if ( isFirst )
- isFirst = false;
- else
- write(VCFConstants.INFO_FIELD_SEPARATOR);
-
- String key = entry.getKey();
- write(key);
-
- if ( !entry.getValue().equals("") ) {
- VCFInfoHeaderLine metaData = mHeader.getInfoHeaderLine(key);
- if ( metaData == null || metaData.getCountType() != VCFHeaderLineCount.INTEGER || metaData.getCount() != 0 ) {
- write("=");
- write(entry.getValue());
- }
- }
- }
- }
-
- /**
- * add the genotype data
- *
- * @param vc the variant context
- * @param genotypeFormatKeys Genotype formatting string
- * @param alleleMap alleles for this context
- * @throws IOException for writer
- */
- private void addGenotypeData(VariantContext vc, Map<Allele, String> alleleMap, List<String> genotypeFormatKeys)
- throws IOException {
- final int ploidy = vc.getMaxPloidy(2);
-
- for ( String sample : mHeader.getGenotypeSamples() ) {
- write(VCFConstants.FIELD_SEPARATOR);
-
- Genotype g = vc.getGenotype(sample);
- if ( g == null ) g = GenotypeBuilder.createMissing(sample, ploidy);
-
- final List<String> attrs = new ArrayList<String>(genotypeFormatKeys.size());
- for ( String field : genotypeFormatKeys ) {
- if ( field.equals(VCFConstants.GENOTYPE_KEY) ) {
- if ( !g.isAvailable() ) {
- throw new IllegalStateException("GTs cannot be missing for some samples if they are available for others in the record");
- }
-
- writeAllele(g.getAllele(0), alleleMap);
- for (int i = 1; i < g.getPloidy(); i++) {
- write(g.isPhased() ? VCFConstants.PHASED : VCFConstants.UNPHASED);
- writeAllele(g.getAllele(i), alleleMap);
- }
-
- continue;
- } else {
- String outputValue;
- if ( field.equals(VCFConstants.GENOTYPE_FILTER_KEY ) ) {
- outputValue = g.isFiltered() ? g.getFilters() : VCFConstants.PASSES_FILTERS_v4;
- } else {
- final IntGenotypeFieldAccessors.Accessor accessor = intGenotypeFieldAccessors.getAccessor(field);
- if ( accessor != null ) {
- final int[] intValues = accessor.getValues(g);
- if ( intValues == null )
- outputValue = VCFConstants.MISSING_VALUE_v4;
- else if ( intValues.length == 1 ) // fast path
- outputValue = Integer.toString(intValues[0]);
- else {
- StringBuilder sb = new StringBuilder();
- sb.append(intValues[0]);
- for ( int i = 1; i < intValues.length; i++) {
- sb.append(",");
- sb.append(intValues[i]);
- }
- outputValue = sb.toString();
- }
- } else {
- Object val = g.hasExtendedAttribute(field) ? g.getExtendedAttribute(field) : VCFConstants.MISSING_VALUE_v4;
-
- VCFFormatHeaderLine metaData = mHeader.getFormatHeaderLine(field);
- if ( metaData != null ) {
- int numInFormatField = metaData.getCount(vc);
- if ( numInFormatField > 1 && val.equals(VCFConstants.MISSING_VALUE_v4) ) {
- // If we have a missing field but multiple values are expected, we need to construct a new string with all fields.
- // For example, if Number=2, the string has to be ".,."
- StringBuilder sb = new StringBuilder(VCFConstants.MISSING_VALUE_v4);
- for ( int i = 1; i < numInFormatField; i++ ) {
- sb.append(",");
- sb.append(VCFConstants.MISSING_VALUE_v4);
- }
- val = sb.toString();
- }
- }
-
- // assume that if key is absent, then the given string encoding suffices
- outputValue = formatVCFField(val);
- }
- }
-
- if ( outputValue != null )
- attrs.add(outputValue);
- }
- }
-
- // strip off trailing missing values
- for (int i = attrs.size()-1; i >= 0; i--) {
- if ( isMissingValue(attrs.get(i)) )
- attrs.remove(i);
- else
- break;
- }
-
- for (int i = 0; i < attrs.size(); i++) {
- if ( i > 0 || genotypeFormatKeys.contains(VCFConstants.GENOTYPE_KEY) )
- write(VCFConstants.GENOTYPE_FIELD_SEPARATOR);
- write(attrs.get(i));
- }
- }
- }
-
- private boolean isMissingValue(String s) {
- // we need to deal with the case that it's a list of missing values
- return (countOccurrences(VCFConstants.MISSING_VALUE_v4.charAt(0), s) + countOccurrences(',', s) == s.length());
- }
-
- private void writeAllele(Allele allele, Map<Allele, String> alleleMap) throws IOException {
- String encoding = alleleMap.get(allele);
- if ( encoding == null )
- throw new TribbleException.InternalCodecException("Allele " + allele + " is not an allele in the variant context");
- write(encoding);
- }
-
- /**
- * Takes a double value and pretty prints it to a String for display
- *
- * Large doubles => gets %.2f style formatting
- * Doubles < 1 / 10 but > 1/100 </>=> get %.3f style formatting
- * Double < 1/100 => %.3e formatting
- * @param d
- * @return
- */
- public static final String formatVCFDouble(final double d) {
- String format;
- if ( d < 1 ) {
- if ( d < 0.01 ) {
- if ( Math.abs(d) >= 1e-20 )
- format = "%.3e";
- else {
- // return a zero format
- return "0.00";
- }
- } else {
- format = "%.3f";
- }
- } else {
- format = "%.2f";
- }
-
- return String.format(format, d);
- }
-
- public static String formatVCFField(Object val) {
- String result;
- if ( val == null )
- result = VCFConstants.MISSING_VALUE_v4;
- else if ( val instanceof Double )
- result = formatVCFDouble((Double) val);
- else if ( val instanceof Boolean )
- result = (Boolean)val ? "" : null; // empty string for true, null for false
- else if ( val instanceof List ) {
- result = formatVCFField(((List)val).toArray());
- } else if ( val.getClass().isArray() ) {
- final int length = Array.getLength(val);
- if ( length == 0 )
- return formatVCFField(null);
- final StringBuilder sb = new StringBuilder(formatVCFField(Array.get(val, 0)));
- for ( int i = 1; i < length; i++) {
- sb.append(",");
- sb.append(formatVCFField(Array.get(val, i)));
- }
- result = sb.toString();
- } else
- result = val.toString();
-
- return result;
- }
-
- /**
- * Determine which genotype fields are in use in the genotypes in VC
- * @param vc
- * @return an ordered list of genotype fields in use in VC. If vc has genotypes this will always include GT first
- */
- public static List<String> calcVCFGenotypeKeys(final VariantContext vc, final VCFHeader header) {
- Set<String> keys = new HashSet<String>();
-
- boolean sawGoodGT = false;
- boolean sawGoodQual = false;
- boolean sawGenotypeFilter = false;
- boolean sawDP = false;
- boolean sawAD = false;
- boolean sawPL = false;
- for ( final Genotype g : vc.getGenotypes() ) {
- keys.addAll(g.getExtendedAttributes().keySet());
- if ( g.isAvailable() ) sawGoodGT = true;
- if ( g.hasGQ() ) sawGoodQual = true;
- if ( g.hasDP() ) sawDP = true;
- if ( g.hasAD() ) sawAD = true;
- if ( g.hasPL() ) sawPL = true;
- if (g.isFiltered()) sawGenotypeFilter = true;
- }
-
- if ( sawGoodQual ) keys.add(VCFConstants.GENOTYPE_QUALITY_KEY);
- if ( sawDP ) keys.add(VCFConstants.DEPTH_KEY);
- if ( sawAD ) keys.add(VCFConstants.GENOTYPE_ALLELE_DEPTHS);
- if ( sawPL ) keys.add(VCFConstants.GENOTYPE_PL_KEY);
- if ( sawGenotypeFilter ) keys.add(VCFConstants.GENOTYPE_FILTER_KEY);
-
- List<String> sortedList = ParsingUtils.sortList(new ArrayList<String>(keys));
-
- // make sure the GT is first
- if ( sawGoodGT ) {
- List<String> newList = new ArrayList<String>(sortedList.size()+1);
- newList.add(VCFConstants.GENOTYPE_KEY);
- newList.addAll(sortedList);
- sortedList = newList;
- }
-
- if ( sortedList.isEmpty() && header.hasGenotypingData() ) {
- // this needs to be done in case all samples are no-calls
- return Collections.singletonList(VCFConstants.GENOTYPE_KEY);
- } else {
- return sortedList;
- }
- }
-
-
- private static int countOccurrences(char c, String s) {
- int count = 0;
- for (int i = 0; i < s.length(); i++) {
- count += s.charAt(i) == c ? 1 : 0;
- }
- return count;
- }
-
- private final void fieldIsMissingFromHeaderError(final VariantContext vc, final String id, final String field) {
- if ( !allowMissingFieldsInHeader)
- throw new IllegalStateException("Key " + id + " found in VariantContext field " + field
- + " at " + vc.getChr() + ":" + vc.getStart()
- + " but this key isn't defined in the VCFHeader. We require all VCFs to have"
- + " complete VCF headers by default.");
- }
}
diff --git a/src/java/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterFactory.java b/src/java/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterFactory.java
index 57e69d2..ee23333 100644
--- a/src/java/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterFactory.java
+++ b/src/java/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterFactory.java
@@ -25,8 +25,8 @@
package org.broadinstitute.variant.variantcontext.writer;
-import net.sf.samtools.Defaults;
import net.sf.samtools.SAMSequenceDictionary;
+import org.broad.tribble.index.IndexCreator;
import java.io.*;
import java.util.EnumSet;
@@ -82,6 +82,25 @@ public class VariantContextWriterFactory {
}
}
+ public static VariantContextWriter create(final File location,
+ final OutputStream output,
+ final SAMSequenceDictionary refDict,
+ final IndexCreator indexCreator,
+ final EnumSet<Options> options) {
+ final boolean enableBCF = isBCFOutput(location, options);
+
+ if ( enableBCF )
+ return new BCF2Writer(location, output, refDict, indexCreator,
+ options.contains(Options.INDEX_ON_THE_FLY),
+ options.contains(Options.DO_NOT_WRITE_GENOTYPES));
+ else {
+ return new VCFWriter(location, output, refDict, indexCreator,
+ options.contains(Options.INDEX_ON_THE_FLY),
+ options.contains(Options.DO_NOT_WRITE_GENOTYPES),
+ options.contains(Options.ALLOW_MISSING_FIELDS_IN_HEADER));
+ }
+ }
+
/**
* Should we output a BCF file based solely on the name of the file at location?
*
diff --git a/src/java/org/broadinstitute/variant/vcf/AbstractVCFCodec.java b/src/java/org/broadinstitute/variant/vcf/AbstractVCFCodec.java
index b23aaf6..7049d8b 100644
--- a/src/java/org/broadinstitute/variant/vcf/AbstractVCFCodec.java
+++ b/src/java/org/broadinstitute/variant/vcf/AbstractVCFCodec.java
@@ -195,6 +195,21 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
return this.header;
}
+ /**
+ * Explicitly set the VCFHeader on this codec. This will overwrite the header read from the file
+ * and the version state stored in this instance; conversely, reading the header from a file will
+ * overwrite whatever is set here. The returned header may not be identical to the header argument
+ * since the header lines may be "repaired" (i.e., rewritten) if doOnTheFlyModifications is set.
+ */
+ public VCFHeader setVCFHeader(final VCFHeader header, final VCFHeaderVersion version) {
+ this.version = version;
+
+ if (this.doOnTheFlyModifications) this.header = VCFStandardHeaderLines.repairStandardHeaderLines(header);
+ else this.header = header;
+
+ return this.header;
+ }
+
/**
* the fast decode function
* @param line the line of text for the record
@@ -213,7 +228,7 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
return decodeLine(line, true);
}
- private final VariantContext decodeLine(final String line, final boolean includeGenotypes) {
+ private VariantContext decodeLine(final String line, final boolean includeGenotypes) {
// the same line reader is not used for parsing the header and parsing lines, if we see a #, we've seen a header line
if (line.startsWith(VCFHeader.HEADER_INDICATOR)) return null;
@@ -223,9 +238,10 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
if (parts == null)
parts = new String[Math.min(header.getColumnCount(), NUM_STANDARD_FIELDS+1)];
- int nParts = ParsingUtils.split(line, parts, VCFConstants.FIELD_SEPARATOR_CHAR, true);
+ final int nParts = ParsingUtils.split(line, parts, VCFConstants.FIELD_SEPARATOR_CHAR, true);
- // if we have don't have a header, or we have a header with no genotyping data check that we have eight columns. Otherwise check that we have nine (normal colummns + genotyping data)
+ // if we have don't have a header, or we have a header with no genotyping data check that we
+ // have eight columns. Otherwise check that we have nine (normal columns + genotyping data)
if (( (header == null || !header.hasGenotypingData()) && nParts != NUM_STANDARD_FIELDS) ||
(header != null && header.hasGenotypingData() && nParts != (NUM_STANDARD_FIELDS + 1)) )
throw new TribbleException("Line " + lineNo + ": there aren't enough columns for line " + line + " (we expected " + (header == null ? NUM_STANDARD_FIELDS : NUM_STANDARD_FIELDS + 1) +
@@ -354,11 +370,11 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
Map<String, Object> attributes = new HashMap<String, Object>();
if ( infoField.length() == 0 )
- generateException("The VCF specification requires a valid info field");
+ generateException("The VCF specification requires a valid (non-zero length) info field");
if ( !infoField.equals(VCFConstants.EMPTY_INFO_FIELD) ) {
if ( infoField.indexOf("\t") != -1 || infoField.indexOf(" ") != -1 )
- generateException("The VCF specification does not allow for whitespace in the INFO field");
+ generateException("The VCF specification does not allow for whitespace in the INFO field. Offending field value was \"" + infoField + "\"");
int infoFieldSplitSize = ParsingUtils.split(infoField, infoFieldArray, VCFConstants.INFO_FIELD_SEPARATOR_CHAR, false);
for (int i = 0; i < infoFieldSplitSize; i++) {
diff --git a/src/java/org/broadinstitute/variant/vcf/VCFContigHeaderLine.java b/src/java/org/broadinstitute/variant/vcf/VCFContigHeaderLine.java
index abb6a67..d65c56a 100644
--- a/src/java/org/broadinstitute/variant/vcf/VCFContigHeaderLine.java
+++ b/src/java/org/broadinstitute/variant/vcf/VCFContigHeaderLine.java
@@ -59,7 +59,7 @@ public class VCFContigHeaderLine extends VCFSimpleHeaderLine {
}
VCFContigHeaderLine(final SAMSequenceRecord sequenceRecord, final String assembly) {
- super(sequenceRecord.getId(), new HashMap<String, String>() {{
+ super(VCFHeader.CONTIG_KEY, new HashMap<String, String>() {{
// Now inside an init block in an anon HashMap subclass
this.put("ID", sequenceRecord.getSequenceName());
this.put("length", Integer.toString(sequenceRecord.getSequenceLength()));
diff --git a/src/java/org/broadinstitute/variant/vcf/VCFEncoder.java b/src/java/org/broadinstitute/variant/vcf/VCFEncoder.java
new file mode 100644
index 0000000..fdb5883
--- /dev/null
+++ b/src/java/org/broadinstitute/variant/vcf/VCFEncoder.java
@@ -0,0 +1,381 @@
+package org.broadinstitute.variant.vcf;
+
+import org.broad.tribble.util.ParsingUtils;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
+import org.broadinstitute.variant.variantcontext.GenotypesContext;
+import org.broadinstitute.variant.variantcontext.LazyGenotypesContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.writer.IntGenotypeFieldAccessors;
+
+import java.lang.reflect.Array;
+import java.nio.charset.Charset;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
+/**
+ * Functions specific to encoding VCF records.
+ */
+public class VCFEncoder {
+
+ /**
+ * The encoding used for VCF files: ISO-8859-1
+ */
+ public static final Charset VCF_CHARSET = Charset.forName("ISO-8859-1");
+ private static final String QUAL_FORMAT_STRING = "%.2f";
+ private static final String QUAL_FORMAT_EXTENSION_TO_TRIM = ".00";
+
+ private final IntGenotypeFieldAccessors GENOTYPE_FIELD_ACCESSORS = new IntGenotypeFieldAccessors();
+
+ private VCFHeader header;
+
+ private boolean allowMissingFieldsInHeader = false;
+
+ /**
+ * Prepare a VCFEncoder that will encode records appropriate to the given VCF header, optionally
+ * allowing missing fields in the header.
+ */
+ public VCFEncoder(final VCFHeader header, final boolean allowMissingFieldsInHeader) {
+ if (header == null) throw new NullPointerException("The VCF header must not be null.");
+ this.header = header;
+ this.allowMissingFieldsInHeader = allowMissingFieldsInHeader;
+ }
+
+ /**
+ * Please see the notes in the default constructor
+ */
+ @Deprecated
+ public void setVCFHeader(final VCFHeader header) {
+ this.header = header;
+ }
+
+ /**
+ * Please see the notes in the default constructor
+ */
+ @Deprecated
+ public void setAllowMissingFieldsInHeader(final boolean allow) {
+ this.allowMissingFieldsInHeader = allow;
+ }
+
+ public String encode(final VariantContext context) {
+ if (this.header == null) {
+ throw new NullPointerException("The header field must be set on the VCFEncoder before encoding records.");
+ }
+
+ final StringBuilder stringBuilder = new StringBuilder();
+
+ // CHROM
+ stringBuilder.append(context.getChr()).append(VCFConstants.FIELD_SEPARATOR);
+
+ // POS
+ stringBuilder.append(String.valueOf(context.getStart())).append(VCFConstants.FIELD_SEPARATOR);
+
+ // ID
+ stringBuilder.append(context.getID()).append(VCFConstants.FIELD_SEPARATOR);
+
+ // REF
+ stringBuilder.append(context.getReference().getDisplayString()).append(VCFConstants.FIELD_SEPARATOR);
+
+ // ALT
+ if ( context.isVariant() ) {
+ Allele altAllele = context.getAlternateAllele(0);
+ String alt = altAllele.getDisplayString();
+ stringBuilder.append(alt);
+
+ for (int i = 1; i < context.getAlternateAlleles().size(); i++) {
+ altAllele = context.getAlternateAllele(i);
+ alt = altAllele.getDisplayString();
+ stringBuilder.append(",");
+ stringBuilder.append(alt);
+ }
+ } else {
+ stringBuilder.append(VCFConstants.EMPTY_ALTERNATE_ALLELE_FIELD);
+ }
+
+ stringBuilder.append(VCFConstants.FIELD_SEPARATOR);
+
+ // QUAL
+ if ( ! context.hasLog10PError()) stringBuilder.append(VCFConstants.MISSING_VALUE_v4);
+ else stringBuilder.append(formatQualValue(context.getPhredScaledQual()));
+ stringBuilder.append(VCFConstants.FIELD_SEPARATOR);
+
+ // FILTER
+ stringBuilder.append(getFilterString(context)).append(VCFConstants.FIELD_SEPARATOR);
+
+ // INFO
+ final Map<String, String> infoFields = new TreeMap<String, String>();
+ for (final Map.Entry<String, Object> field : context.getAttributes().entrySet() ) {
+ if ( ! this.header.hasInfoLine(field.getKey())) fieldIsMissingFromHeaderError(context, field.getKey(), "INFO");
+
+ final String outputValue = formatVCFField(field.getValue());
+ if (outputValue != null) infoFields.put(field.getKey(), outputValue);
+ }
+ writeInfoString(infoFields, stringBuilder);
+
+ // FORMAT
+ final GenotypesContext gc = context.getGenotypes();
+ if (gc.isLazyWithData() && ((LazyGenotypesContext) gc).getUnparsedGenotypeData() instanceof String) {
+ stringBuilder.append(VCFConstants.FIELD_SEPARATOR);
+ stringBuilder.append(((LazyGenotypesContext) gc).getUnparsedGenotypeData().toString());
+ } else {
+ final List<String> genotypeAttributeKeys = context.calcVCFGenotypeKeys(this.header);
+ if ( ! genotypeAttributeKeys.isEmpty()) {
+ for (final String format : genotypeAttributeKeys)
+ if ( ! this.header.hasFormatLine(format))
+ fieldIsMissingFromHeaderError(context, format, "FORMAT");
+
+ final String genotypeFormatString = ParsingUtils.join(VCFConstants.GENOTYPE_FIELD_SEPARATOR, genotypeAttributeKeys);
+
+ stringBuilder.append(VCFConstants.FIELD_SEPARATOR);
+ stringBuilder.append(genotypeFormatString);
+
+ final Map<Allele, String> alleleStrings = buildAlleleStrings(context);
+ addGenotypeData(context, alleleStrings, genotypeAttributeKeys, stringBuilder);
+ }
+ }
+
+ return stringBuilder.toString();
+ }
+
+ VCFHeader getVCFHeader() {
+ return this.header;
+ }
+
+ boolean getAllowMissingFieldsInHeader() {
+ return this.allowMissingFieldsInHeader;
+ }
+
+ private String getFilterString(final VariantContext vc) {
+ if (vc.isFiltered()) {
+ for (final String filter : vc.getFilters()) {
+ if ( ! this.header.hasFilterLine(filter)) fieldIsMissingFromHeaderError(vc, filter, "FILTER");
+ }
+
+ return ParsingUtils.join(";", ParsingUtils.sortList(vc.getFilters()));
+ }
+ else if (vc.filtersWereApplied()) return VCFConstants.PASSES_FILTERS_v4;
+ else return VCFConstants.UNFILTERED;
+ }
+
+ private String formatQualValue(final double qual) {
+ String s = String.format(QUAL_FORMAT_STRING, qual);
+ if ( s.endsWith(QUAL_FORMAT_EXTENSION_TO_TRIM) )
+ s = s.substring(0, s.length() - QUAL_FORMAT_EXTENSION_TO_TRIM.length());
+ return s;
+ }
+
+ private void fieldIsMissingFromHeaderError(final VariantContext vc, final String id, final String field) {
+ if ( ! allowMissingFieldsInHeader)
+ throw new IllegalStateException("Key " + id + " found in VariantContext field " + field
+ + " at " + vc.getChr() + ":" + vc.getStart()
+ + " but this key isn't defined in the VCFHeader. We require all VCFs to have"
+ + " complete VCF headers by default.");
+ }
+
+ String formatVCFField(final Object val) {
+ final String result;
+ if ( val == null )
+ result = VCFConstants.MISSING_VALUE_v4;
+ else if ( val instanceof Double )
+ result = formatVCFDouble((Double) val);
+ else if ( val instanceof Boolean )
+ result = (Boolean)val ? "" : null; // empty string for true, null for false
+ else if ( val instanceof List ) {
+ result = formatVCFField(((List)val).toArray());
+ } else if ( val.getClass().isArray() ) {
+ final int length = Array.getLength(val);
+ if ( length == 0 )
+ return formatVCFField(null);
+ final StringBuilder sb = new StringBuilder(formatVCFField(Array.get(val, 0)));
+ for ( int i = 1; i < length; i++) {
+ sb.append(",");
+ sb.append(formatVCFField(Array.get(val, i)));
+ }
+ result = sb.toString();
+ } else
+ result = val.toString();
+
+ return result;
+ }
+
+ /**
+ * Takes a double value and pretty prints it to a String for display
+ *
+ * Large doubles => gets %.2f style formatting
+ * Doubles < 1 / 10 but > 1/100 </>=> get %.3f style formatting
+ * Double < 1/100 => %.3e formatting
+ * @param d
+ * @return
+ */
+ public static String formatVCFDouble(final double d) {
+ final String format;
+ if ( d < 1 ) {
+ if ( d < 0.01 ) {
+ if ( Math.abs(d) >= 1e-20 )
+ format = "%.3e";
+ else {
+ // return a zero format
+ return "0.00";
+ }
+ } else {
+ format = "%.3f";
+ }
+ } else {
+ format = "%.2f";
+ }
+
+ return String.format(format, d);
+ }
+
+ static int countOccurrences(final char c, final String s) {
+ int count = 0;
+ for (int i = 0; i < s.length(); i++) {
+ count += s.charAt(i) == c ? 1 : 0;
+ }
+ return count;
+ }
+
+ static boolean isMissingValue(final String s) {
+ // we need to deal with the case that it's a list of missing values
+ return (countOccurrences(VCFConstants.MISSING_VALUE_v4.charAt(0), s) + countOccurrences(',', s) == s.length());
+ }
+
+ /*
+ * Add the genotype data
+ */
+ private void addGenotypeData(final VariantContext vc, final Map<Allele, String> alleleMap, final List<String> genotypeFormatKeys, final StringBuilder builder) {
+ final int ploidy = vc.getMaxPloidy(2);
+
+ for (final String sample : this.header.getGenotypeSamples()) {
+ builder.append(VCFConstants.FIELD_SEPARATOR);
+
+ Genotype g = vc.getGenotype(sample);
+ if (g == null) g = GenotypeBuilder.createMissing(sample, ploidy);
+
+ final List<String> attrs = new ArrayList<String>(genotypeFormatKeys.size());
+ for (final String field : genotypeFormatKeys) {
+ if (field.equals(VCFConstants.GENOTYPE_KEY)) {
+ if ( ! g.isAvailable()) {
+ throw new IllegalStateException("GTs cannot be missing for some samples if they are available for others in the record");
+ }
+
+ writeAllele(g.getAllele(0), alleleMap, builder);
+ for (int i = 1; i < g.getPloidy(); i++) {
+ builder.append(g.isPhased() ? VCFConstants.PHASED : VCFConstants.UNPHASED);
+ writeAllele(g.getAllele(i), alleleMap, builder);
+ }
+ continue;
+
+ } else {
+ final String outputValue;
+ if ( field.equals(VCFConstants.GENOTYPE_FILTER_KEY ) ) {
+ outputValue = g.isFiltered() ? g.getFilters() : VCFConstants.PASSES_FILTERS_v4;
+ } else {
+ final IntGenotypeFieldAccessors.Accessor accessor = GENOTYPE_FIELD_ACCESSORS.getAccessor(field);
+ if ( accessor != null ) {
+ final int[] intValues = accessor.getValues(g);
+ if ( intValues == null )
+ outputValue = VCFConstants.MISSING_VALUE_v4;
+ else if ( intValues.length == 1 ) // fast path
+ outputValue = Integer.toString(intValues[0]);
+ else {
+ final StringBuilder sb = new StringBuilder();
+ sb.append(intValues[0]);
+ for ( int i = 1; i < intValues.length; i++) {
+ sb.append(",");
+ sb.append(intValues[i]);
+ }
+ outputValue = sb.toString();
+ }
+ } else {
+ Object val = g.hasExtendedAttribute(field) ? g.getExtendedAttribute(field) : VCFConstants.MISSING_VALUE_v4;
+
+ final VCFFormatHeaderLine metaData = this.header.getFormatHeaderLine(field);
+ if ( metaData != null ) {
+ final int numInFormatField = metaData.getCount(vc);
+ if ( numInFormatField > 1 && val.equals(VCFConstants.MISSING_VALUE_v4) ) {
+ // If we have a missing field but multiple values are expected, we need to construct a new string with all fields.
+ // For example, if Number=2, the string has to be ".,."
+ final StringBuilder sb = new StringBuilder(VCFConstants.MISSING_VALUE_v4);
+ for ( int i = 1; i < numInFormatField; i++ ) {
+ sb.append(",");
+ sb.append(VCFConstants.MISSING_VALUE_v4);
+ }
+ val = sb.toString();
+ }
+ }
+
+ // assume that if key is absent, then the given string encoding suffices
+ outputValue = formatVCFField(val);
+ }
+ }
+
+ if ( outputValue != null )
+ attrs.add(outputValue);
+ }
+ }
+
+ // strip off trailing missing values
+ for (int i = attrs.size()-1; i >= 0; i--) {
+ if ( isMissingValue(attrs.get(i))) attrs.remove(i);
+ else break;
+ }
+
+ for (int i = 0; i < attrs.size(); i++) {
+ if ( i > 0 || genotypeFormatKeys.contains(VCFConstants.GENOTYPE_KEY)) {
+ builder.append(VCFConstants.GENOTYPE_FIELD_SEPARATOR);
+ }
+ builder.append(attrs.get(i));
+ }
+ }
+ }
+
+ /*
+ * Create the info string; assumes that no values are null
+ */
+ private void writeInfoString(final Map<String, String> infoFields, final StringBuilder builder) {
+ if ( infoFields.isEmpty() ) {
+ builder.append(VCFConstants.EMPTY_INFO_FIELD);
+ return;
+ }
+
+ boolean isFirst = true;
+ for (final Map.Entry<String, String> entry : infoFields.entrySet()) {
+ if (isFirst) isFirst = false;
+ else builder.append(VCFConstants.INFO_FIELD_SEPARATOR);
+
+ builder.append(entry.getKey());
+
+ if ( ! entry.getValue().equals("")) {
+ final VCFInfoHeaderLine metaData = this.header.getInfoHeaderLine(entry.getKey());
+ if ( metaData == null || metaData.getCountType() != VCFHeaderLineCount.INTEGER || metaData.getCount() != 0 ) {
+ builder.append("=");
+ builder.append(entry.getValue());
+ }
+ }
+ }
+ }
+
+ private Map<Allele, String> buildAlleleStrings(final VariantContext vc) {
+ final Map<Allele, String> alleleMap = new HashMap<Allele, String>(vc.getAlleles().size()+1);
+ alleleMap.put(Allele.NO_CALL, VCFConstants.EMPTY_ALLELE); // convenience for lookup
+
+ final List<Allele> alleles = vc.getAlleles();
+ for ( int i = 0; i < alleles.size(); i++ ) {
+ alleleMap.put(alleles.get(i), String.valueOf(i));
+ }
+
+ return alleleMap;
+ }
+
+ private void writeAllele(final Allele allele, final Map<Allele, String> alleleMap, final StringBuilder builder) {
+ final String encoding = alleleMap.get(allele);
+ if ( encoding == null )
+ throw new RuntimeException("Allele " + allele + " is not an allele in the variant context");
+ builder.append(encoding);
+ }
+}
diff --git a/src/java/org/broadinstitute/variant/vcf/VCFHeader.java b/src/java/org/broadinstitute/variant/vcf/VCFHeader.java
index 59c5f27..42365e3 100644
--- a/src/java/org/broadinstitute/variant/vcf/VCFHeader.java
+++ b/src/java/org/broadinstitute/variant/vcf/VCFHeader.java
@@ -208,8 +208,10 @@ public class VCFHeader {
public void setSequenceDictionary(final SAMSequenceDictionary dictionary) {
this.contigMetaData.clear();
for (final SAMSequenceRecord record : dictionary.getSequences()) {
- this.contigMetaData.add(new VCFContigHeaderLine(record, null));
+ contigMetaData.add(new VCFContigHeaderLine(record, null));
}
+
+ this.mMetaData.addAll(contigMetaData);
}
public VariantContextComparator getVCFRecordComparator() {
diff --git a/src/java/org/broadinstitute/variant/vcf/VCFRecordCodec.java b/src/java/org/broadinstitute/variant/vcf/VCFRecordCodec.java
new file mode 100644
index 0000000..15cbf59
--- /dev/null
+++ b/src/java/org/broadinstitute/variant/vcf/VCFRecordCodec.java
@@ -0,0 +1,63 @@
+package org.broadinstitute.variant.vcf;
+
+import net.sf.samtools.util.SortingCollection;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStream;
+import java.io.PrintStream;
+
+/**
+ * Writes VariantContext instances to an OutputStream without headers or metadata. For use
+ * with SortingCollection ONLY.
+ */
+public class VCFRecordCodec implements SortingCollection.Codec<VariantContext> {
+
+ final VCFCodec vcfDecoder = new VCFCodec();
+
+ final VCFEncoder vcfEncoder;
+
+ private PrintStream outputStream = null;
+
+ private BufferedReader inputReader = null;
+
+ public VCFRecordCodec(final VCFHeader header) {
+ this.vcfEncoder = new VCFEncoder(header, false);
+ // Explicitly set the version because it's not available in the header itself.
+ this.vcfDecoder.setVCFHeader(header, VCFHeaderVersion.VCF4_1);
+ }
+
+ @Override
+ public void setOutputStream(final OutputStream stream) {
+ this.outputStream = new PrintStream(stream);
+ }
+
+ @Override
+ public void setInputStream(final InputStream stream) {
+ this.inputReader = new BufferedReader(new InputStreamReader(stream));
+ }
+
+ @Override
+ public void encode(final VariantContext context) {
+ this.outputStream.println(this.vcfEncoder.encode(context));
+ }
+
+ @Override
+ public VariantContext decode() {
+ try {
+ final String line;
+ return ((line = inputReader.readLine()) != null) ? this.vcfDecoder.decode(line) : null;
+ } catch (final IOException ioe) {
+ throw new RuntimeException("Could not decode/read a VCF record for a sorting collection: " + ioe.getMessage(), ioe);
+ }
+ }
+
+ @Override
+ public VCFRecordCodec clone() {
+ return new VCFRecordCodec(this.vcfEncoder.getVCFHeader());
+ }
+}
+
diff --git a/src/scripts/build_intel_deflater.sh b/src/scripts/build_intel_deflater.sh
new file mode 100644
index 0000000..49d018c
--- /dev/null
+++ b/src/scripts/build_intel_deflater.sh
@@ -0,0 +1,64 @@
+#! /bin/bash
+#
+# The MIT License
+#
+# Copyright (c) 2013 The Broad Institute
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+
+# Build libIntelDeflater.so, the JNI library that wraps Intel IPP compression library.
+# Note that this is not built as part of standard release process. Rather, it is built manually and then
+# copied to Picard-public/lib/jni.
+
+# Assumes OpenJDK exists at $OPENJDK. I used openjdk-7-fcs-src-b147-27_jun_2011.zip
+# Assumes that Picard-public java sources have been compiled
+# Assumes IPP8_CODE_SAMPLES_DIR points to Intel IPP sample code built with -fPIC
+set -e
+
+if [ "$OPENJDK" = "" ]
+then echo "ERROR: OPENJDK environment variable not defined." >&2
+ exit 1
+fi
+
+if [ "$IPP8_CODE_SAMPLES_DIR" = "" ]
+then echo "ERROR: IPP8_CODE_SAMPLES_DIR environment variable not defined." >&2
+ exit 1
+fi
+
+rootdir=$(dirname $(dirname $(dirname $0)))
+
+
+builddir=$rootdir/lib_build
+rm -rf $builddir
+mkdir -p $builddir
+
+# Create JNI C header file
+javah -jni -classpath $rootdir/classes -d $builddir net.sf.samtools.util.zip.IntelDeflater
+
+# Compile source and create library.
+gcc -I$builddir -I$JAVA_HOME/include/ -I$JAVA_HOME/include/linux/ -I$OPENJDK/jdk/src/share/native/common/ \
+-I$OPENJDK/jdk/src/solaris/native/common/ -c -O3 -fPIC IntelDeflater.c
+gcc -shared -o $builddir/libIntelDeflater.so IntelDeflater.o -L${IPP8_CODE_SAMPLES_DIR}/__cmake/data-compression.intel64.make.static.release/__lib/release \
+-lzlib -lstdc++ -Wl,-Bstatic -lbfp754 -ldecimal -liomp5 -liompstubs5 -lipgo -lippac -lippcc -lippch -lippcv \
+-lippdc -lippdi -lippgen -lippi -lippj -lippm -lippr -lippsc -lippvc -lippvm -lirng -lmatmul -lpdbx \
+-lpdbxinst -lsvml -lipps -limf -lirc -lirc_s -lippcore -Wl,-Bdynamic
+
+
+
diff --git a/src/scripts/net/sf/picard/analysis/rnaSeqCoverage.R b/src/scripts/net/sf/picard/analysis/rnaSeqCoverage.R
index db64b0f..1cf004e 100644
--- a/src/scripts/net/sf/picard/analysis/rnaSeqCoverage.R
+++ b/src/scripts/net/sf/picard/analysis/rnaSeqCoverage.R
@@ -3,7 +3,7 @@
# @author Tim Fennell
# Parse the arguments
-args <- commandArgs(trailing=T)
+args <- commandArgs(trailing = TRUE)
metricsFile <- args[1]
outputFile <- args[2]
bamName <- args[3]
@@ -26,7 +26,6 @@ for (i in 1:length(startFinder)) {
}
data <- read.table(metricsFile, header=T, sep="\t", skip=secondBlankLine, check.names=FALSE)
-pdf(outputFile)
# The histogram has a normalized_position and normalized_coverage column for each metric "level"
# This code parses out the distinct levels so we can output one graph per level
@@ -38,34 +37,34 @@ headers <- sapply(sub(".normalized_coverage","",names(data),fixed=TRUE), "[[" ,1
if (any(duplicated(headers))) {
print(paste("Not creating insert size PDF as there are duplicated header names:", headers[which(duplicated(headers))]))
} else {
+ pdf(outputFile)
levels <- c()
for (i in 2:length(headers)) {
if (!(headers[i] %in% levels)) {
levels[length(levels)+1] <- headers[i]
}
}
-}
-
-# Some constants that are used below
-COLORS = c("royalblue", "#FFAAAA", "palegreen3");
-# For each level, plot of the normalized coverage by GC
-for (i in 1:length(levels)) {
+ # Some constants that are used below
+ COLORS = c("royalblue", "#FFAAAA", "palegreen3");
- # Reconstitutes the histogram column header for this level
- nc <- paste(levels[i], "normalized_coverage", sep=".")
+ # For each level, plot of the normalized coverage by GC
+ for (i in 1:length(levels)) {
- plot(x=data$normalized_position, y=as.matrix(data[nc]),
- type="o",
- xlab="Normalized Distance Along Transcript",
- ylab="Normalized Coverage",
- xlim=c(0, 100),
- ylim=range(0, max(data[nc])),
- col="royalblue",
- main=paste("RNA-Seq Coverage vs. Transcript Position\n", levels[i], " ", ifelse(subtitle=="", "", paste("(", subtitle, ")", sep="")), "\nin file ", bamName,sep=""))
+ # Reconstitutes the histogram column header for this level
+ nc <- paste(levels[i], "normalized_coverage", sep=".")
- # Add a horizontal line at coverage=1
- abline(h=1, col="lightgrey");
-}
+ plot(x=data$normalized_position, y=as.matrix(data[nc]),
+ type="o",
+ xlab="Normalized Distance Along Transcript",
+ ylab="Normalized Coverage",
+ xlim=c(0, 100),
+ ylim=range(0, max(data[nc])),
+ col="royalblue",
+ main=paste("RNA-Seq Coverage vs. Transcript Position\n", levels[i], " ", ifelse(subtitle=="", "", paste("(", subtitle, ")", sep="")), "\nin file ", bamName,sep=""))
-dev.off();
\ No newline at end of file
+ # Add a horizontal line at coverage=1
+ abline(h=1, col="lightgrey");
+ }
+ dev.off();
+}
\ No newline at end of file
diff --git a/src/scripts/release_picard.sh b/src/scripts/release_picard.sh
index a77c9a0..340a0d2 100755
--- a/src/scripts/release_picard.sh
+++ b/src/scripts/release_picard.sh
@@ -75,7 +75,8 @@ SVNROOT=svn+ssh://$USERNAME@svn.code.sf.net/p/picard/code
RELEASE_ID=$1
-PREV_RELEASE_ID=`svn --username $USERNAME ls $SVNROOT/tags | tail -1 | sed 's/\/$//'`
+# Since releases are lexically sorted, need to filter in order to have 1.1xx be at the bottom.
+PREV_RELEASE_ID=`svn --username $USERNAME ls $SVNROOT/tags | egrep '[.]\d\d\d' | tail -1 | sed 's/\/$//'`
if branch_exists $SVNROOT/branches/$RELEASE_ID
then echo "ERROR: $SVNROOT/branches/$RELEASE_ID already exists.">&2
diff --git a/src/tests/java/net/sf/picard/illumina/IlluminaBasecallsToFastqTest.java b/src/tests/java/net/sf/picard/illumina/IlluminaBasecallsToFastqTest.java
index e278174..d20c8ec 100644
--- a/src/tests/java/net/sf/picard/illumina/IlluminaBasecallsToFastqTest.java
+++ b/src/tests/java/net/sf/picard/illumina/IlluminaBasecallsToFastqTest.java
@@ -29,7 +29,6 @@ import net.sf.samtools.util.BufferedLineReader;
import net.sf.samtools.util.LineReader;
import net.sf.samtools.util.StringUtil;
import net.sf.samtools.util.TestUtil;
-import org.testng.Assert;
import org.testng.annotations.Test;
import java.io.File;
@@ -58,14 +57,16 @@ public class IlluminaBasecallsToFastqTest {
"LANE=" + lane,
"READ_STRUCTURE=76T76T",
"OUTPUT_PREFIX=" + outputPrefix,
- "RUN_BARCODE=HiMom"
+ "RUN_BARCODE=HiMom",
+ "MACHINE_NAME=machine1",
+ "FLOWCELL_BARCODE=abcdeACXX"
});
IoUtil.assertFilesEqual(outputFastq1, new File(TEST_DATA_DIR, "nonBarcoded.1.fastq"));
IoUtil.assertFilesEqual(outputFastq2, new File(TEST_DATA_DIR, "nonBarcoded.2.fastq"));
}
@Test
- public void testMultiplex() throws Exception {
+ public void testMultiplexWithIlluminaReadNameHeaders() throws Exception {
final File outputDir = File.createTempFile("testMultiplex.", ".dir");
try {
outputDir.delete();
@@ -80,7 +81,10 @@ public class IlluminaBasecallsToFastqTest {
"LANE=" + 7,
"RUN_BARCODE=HiMom",
"READ_STRUCTURE=" + "30T8B",
- "OUTPUT_PREFIX=" + outputPrefix.getAbsolutePath()
+ "OUTPUT_PREFIX=" + outputPrefix.getAbsolutePath(),
+ "MACHINE_NAME=machine1",
+ "FLOWCELL_BARCODE=abcdeACXX",
+ "READ_NAME_FORMAT=" + IlluminaBasecallsToFastq.ReadNameFormat.ILLUMINA
});
final String[] filenames = new String[]{
@@ -148,7 +152,9 @@ public class IlluminaBasecallsToFastqTest {
"LANE=" + lane,
"RUN_BARCODE=HiMom",
"READ_STRUCTURE=" + readStructureString,
- "MULTIPLEX_PARAMS=" + libraryParams
+ "MULTIPLEX_PARAMS=" + libraryParams,
+ "MACHINE_NAME=machine1",
+ "FLOWCELL_BARCODE=abcdeACXX"
});
final ReadStructure readStructure = new ReadStructure(readStructureString);
diff --git a/src/tests/java/net/sf/picard/io/IoUtilTest.java b/src/tests/java/net/sf/picard/io/IoUtilTest.java
index 04cdf2d..7e8373b 100644
--- a/src/tests/java/net/sf/picard/io/IoUtilTest.java
+++ b/src/tests/java/net/sf/picard/io/IoUtilTest.java
@@ -37,6 +37,8 @@ import java.util.List;
public class IoUtilTest {
private static final File SLURP_TEST_FILE = new File("testdata/net/sf/picard/io/slurptest.txt");
+ private static final File EMPTY_FILE = new File("testdata/net/sf/picard/io/empty.txt");;
+ private static final File FIVE_SPACES_THEN_A_NEWLINE_THEN_FIVE_SPACES_FILE = new File("testdata/net/sf/picard/io/5newline5.txt");
private static final List<String> SLURP_TEST_LINES = Arrays.asList("bacon and rice ","for breakfast ","wont you join me");
private static final String SLURP_TEST_LINE_SEPARATOR = "\n";
private static final String TEST_FILE_PREFIX = "foo";
@@ -119,6 +121,16 @@ public class IoUtilTest {
public void slurpLinesTest() throws FileNotFoundException {
Assert.assertEquals(IoUtil.slurpLines(SLURP_TEST_FILE), SLURP_TEST_LINES);
}
+
+ @Test
+ public void slurpWhitespaceOnlyFileTest() throws FileNotFoundException {
+ Assert.assertEquals(IoUtil.slurp(FIVE_SPACES_THEN_A_NEWLINE_THEN_FIVE_SPACES_FILE), " \n ");
+ }
+
+ @Test
+ public void slurpEmptyFileTest() throws FileNotFoundException {
+ Assert.assertEquals(IoUtil.slurp(EMPTY_FILE), "");
+ }
@Test
public void slurpTest() throws FileNotFoundException {
diff --git a/src/tests/java/net/sf/picard/sam/FastqToSamTest.java b/src/tests/java/net/sf/picard/sam/FastqToSamTest.java
index 3da1ba1..fbb679d 100644
--- a/src/tests/java/net/sf/picard/sam/FastqToSamTest.java
+++ b/src/tests/java/net/sf/picard/sam/FastqToSamTest.java
@@ -33,6 +33,8 @@ import org.testng.annotations.Test;
import java.io.File;
import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
/**
* Tests for FastqToBam
@@ -80,6 +82,22 @@ public class FastqToSamTest {
};
}
+ // permissive fastq format, i.e. contain blank lines at various places
+ @DataProvider(name = "permissiveFormatFiles")
+ public Object[][] permissiveFormatFiles() {
+ return new Object[][] {
+ {"permissive-format/pair1.txt", "permissive-format/pair2.txt", FastqQualityFormat.Standard },
+ {"permissive-format/s_1_1_sequence.txt", "permissive-format/s_1_2_sequence.txt", FastqQualityFormat.Illumina},
+ {"permissive-format/pair1.txt", null, FastqQualityFormat.Standard},
+ {"permissive-format/pair2.txt", null, FastqQualityFormat.Standard},
+ {"permissive-format/s_1_1_sequence.txt", null, FastqQualityFormat.Illumina},
+ {"permissive-format/s_1_2_sequence.txt", null, FastqQualityFormat.Illumina},
+ {"permissive-format/s_1_sequence.txt", null, FastqQualityFormat.Illumina},
+
+ };
+ }
+
+
// OK paired fastq files
@DataProvider(name = "okPairedFiles")
public Object[][] okPairedFiles() {
@@ -102,15 +120,24 @@ public class FastqToSamTest {
};
}
+ @Test(dataProvider = "permissiveFormatFiles")
+ public void testPermissiveOk(final String filename1, final String filename2, final FastqQualityFormat version) throws IOException {
+ convertFile(filename1,filename2,version,true);
+ }
+
+ @Test(dataProvider = "permissiveFormatFiles",expectedExceptions = PicardException.class)
+ public void testPermissiveFail(final String filename1, final String filename2, final FastqQualityFormat version) throws IOException {
+ convertFile(filename1,filename2,version,false);
+ }
@Test(dataProvider = "okVersionFiles")
public void testFastqVersionOk(final String fastqVersionFilename, final FastqQualityFormat version) throws IOException {
- final File fastqVersionSamFile = convertFile(fastqVersionFilename, version);
+ convertFile(fastqVersionFilename, version);
}
@Test(dataProvider = "badVersionFiles", expectedExceptions= PicardException.class)
public void testFastqVersionBad(final String fastqVersionFilename, final FastqQualityFormat version) throws IOException {
- final File fastqVersionSamFile = convertFile(fastqVersionFilename, version);
+ convertFile(fastqVersionFilename, version);
}
@Test(dataProvider = "badFormatFiles", expectedExceptions= PicardException.class)
@@ -132,35 +159,28 @@ public class FastqToSamTest {
return convertFile(filename, null, version);
}
- private File convertFile(final String fastqFilename1, final String fastqFilename2, final FastqQualityFormat version) throws IOException {
+ private File convertFile(final String fastqFilename1, final String fastqFilename2, final FastqQualityFormat version) throws IOException{
+ return convertFile(fastqFilename1, fastqFilename2, version,false);
+ }
+
+ private File convertFile(final String fastqFilename1, final String fastqFilename2, final FastqQualityFormat version,final boolean permissiveFormat) throws IOException {
final File fastq1 = new File(TEST_DATA_DIR, fastqFilename1);
final File fastq2 = (fastqFilename2 != null) ? new File(TEST_DATA_DIR, fastqFilename2) : null;
final File samFile = newTempSamFile(fastq1.getName());
- String [] args;
-
- if(fastqFilename2 != null) {
- args = new String[] {
- "FASTQ=" + fastq1.getAbsolutePath(),
- "FASTQ2=" + fastq2.getAbsolutePath(),
- "OUTPUT=" + samFile.getAbsolutePath(),
- "QUALITY_FORMAT=" + version,
- "READ_GROUP_NAME=rg",
- "SAMPLE_NAME=s1"
- };
- } else {
- args = new String[] {
- "FASTQ=" + fastq1.getAbsolutePath(),
- "OUTPUT=" + samFile.getAbsolutePath(),
- "QUALITY_FORMAT=" + version,
- "READ_GROUP_NAME=rg",
- "SAMPLE_NAME=s1"
- };
-
- }
-
- FastqToSam fqToSam = new FastqToSam();
- Assert.assertEquals(fqToSam.instanceMain(args), 0);
+ final List<String> args =new ArrayList<String>();
+
+ args.add("FASTQ=" + fastq1.getAbsolutePath());
+ args.add("OUTPUT=" + samFile.getAbsolutePath());
+ args.add("QUALITY_FORMAT=" + version);
+ args.add("READ_GROUP_NAME=rg");
+ args.add("SAMPLE_NAME=s1");
+
+ if(fastqFilename2 != null) args.add("FASTQ2=" + fastq2.getAbsolutePath());
+ if(permissiveFormat) args.add("ALLOW_AND_IGNORE_EMPTY_LINES=true");
+
+ final FastqToSam fqToSam = new FastqToSam();
+ Assert.assertEquals(fqToSam.instanceMain(args.toArray(new String[args.size()])), 0);
return samFile ;
}
@@ -181,13 +201,12 @@ public class FastqToSamTest {
// an existing file.
private static final FastqToSam fastqToSam = new FastqToSam();
- private static File dummyFile ;
private static FastqReader freader1 ;
private static FastqReader freader2 ;
@BeforeClass
public static void beforeClass() throws IOException {
- dummyFile = newTempFile("dummy");
+ final File dummyFile = newTempFile("dummy");
freader1 = new FastqReader(dummyFile);
freader2 = new FastqReader(dummyFile);
}
diff --git a/src/tests/java/net/sf/picard/sam/SamToFastqTest.java b/src/tests/java/net/sf/picard/sam/SamToFastqTest.java
index ea929e8..7f052ed 100644
--- a/src/tests/java/net/sf/picard/sam/SamToFastqTest.java
+++ b/src/tests/java/net/sf/picard/sam/SamToFastqTest.java
@@ -30,6 +30,7 @@ import net.sf.picard.fastq.FastqReader;
import net.sf.picard.fastq.FastqRecord;
import net.sf.picard.io.IoUtil;
import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMFormatException;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.util.IOUtil;
import org.testng.Assert;
@@ -183,7 +184,7 @@ public class SamToFastqTest {
}
- @Test (dataProvider = "badFiles", expectedExceptions= PicardException.class)
+ @Test (dataProvider = "badFiles", expectedExceptions= SAMFormatException.class)
public void testBadFile(final String samFilename) throws IOException {
final File samFile = new File(TEST_DATA_DIR,samFilename);
final File pair1 = File.createTempFile("tt-pair1.", ".fastq");
diff --git a/src/tests/java/net/sf/picard/util/MathUtilTest.java b/src/tests/java/net/sf/picard/util/MathUtilTest.java
new file mode 100644
index 0000000..ea17612
--- /dev/null
+++ b/src/tests/java/net/sf/picard/util/MathUtilTest.java
@@ -0,0 +1,45 @@
+package net.sf.picard.util;
+
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.Arrays;
+
+/**
+ * @author mccowan
+ */
+public class MathUtilTest {
+ @Test
+ public void logMathTest() {
+ Assert.assertEquals(MathUtil.LOG_10_MATH.getLogValue(10), 1d, 0.00001d);
+ Assert.assertEquals(MathUtil.LOG_10_MATH.getNonLogValue(1), 10d, 0.00001d);
+ Assert.assertEquals(MathUtil.LOG_10_MATH.mean(5, 5, 5), 5d, 0.00001d);
+ // http://www.wolframalpha.com/input/?i=log10%2810%5E1.23%2B10%5E4.56%2B10%5E99999%29
+ Assert.assertEquals(MathUtil.LOG_10_MATH.sum(1.23, 4.56, 2), 4.5613970317323586660874152202433434022756298235604568d, 0.00001d);
+ // http://www.wolframalpha.com/input/?i=log10%2810%5E1.23+*+10%5E4.56+*+10%5E2%29
+ Assert.assertEquals(MathUtil.LOG_10_MATH.product(1.23, 4.56, 2), 7.7899999999999999999999999999999999999999999999999999d, 0.00001d);
+ }
+
+ @DataProvider
+ public Object[][] seqMethodTestCases() {
+ return new Object[][] {
+ new Object[] {0d, 5d, 1d, new double[] {0,1,2,3,4,5}},
+ new Object[] {0d, 0.5d, 0.1d, new double[] {0, 0.1, 0.2, 0.3, 0.4, 0.5}},
+ new Object[] {0d, 0.5d, 0.11d,new double[] {0, 0.11, 0.22, 0.33, 0.44}},
+ new Object[] {50d, 55d, 1.25d,new double[] {50, 51.25, 52.5, 53.75, 55}},
+ new Object[] {10d, 0d, 02d, new double[] {}},
+ new Object[] {10d, 0d, -2d, new double[] {10, 8, 6, 4, 2, 0}},
+ };
+ }
+
+ @Test(dataProvider="seqMethodTestCases")
+ public void testSeqGeneration(final double from, final double to, final double by, final double[] expected) {
+ final double[] actual = MathUtil.seq(from, to, by);
+ Assert.assertEquals(actual.length, expected.length);
+
+ for (int i=0; i<expected.length; ++i) {
+ Assert.assertTrue(Math.abs(actual[i] - expected[i]) < 0.0000001);
+ }
+ }
+}
diff --git a/src/tests/java/net/sf/picard/vcf/SplitVcfsTest.java b/src/tests/java/net/sf/picard/vcf/SplitVcfsTest.java
index ad0092a..18caa9c 100644
--- a/src/tests/java/net/sf/picard/vcf/SplitVcfsTest.java
+++ b/src/tests/java/net/sf/picard/vcf/SplitVcfsTest.java
@@ -1,5 +1,6 @@
package net.sf.picard.vcf;
+import net.sf.picard.io.IoUtil;
import net.sf.samtools.util.CloseableIterator;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext.Type;
@@ -7,6 +8,7 @@ import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
import org.broadinstitute.variant.vcf.VCFFileReader;
import org.testng.Assert;
+import org.testng.annotations.AfterClass;
import org.testng.annotations.Test;
import java.io.File;
@@ -16,13 +18,19 @@ import java.util.Queue;
public class SplitVcfsTest {
- private static final String TEST_DATA_PATH = "testdata/net/sf/picard/vcf/";
+ private static final File OUTPUT_DATA_PATH = IoUtil.createTempDir("SplitVcfsTest", null);
+ private static final File TEST_DATA_PATH = new File("testdata/net/sf/picard/vcf/");
+
+ @AfterClass
+ public void teardown() {
+ IoUtil.deleteDirectoryTree(OUTPUT_DATA_PATH);
+ }
@Test
public void testSplit() {
- final File indelOutputFile = new File(TEST_DATA_PATH + "split-vcfs-test-indels-delete-me.vcf");
- final File snpOutputFile = new File(TEST_DATA_PATH + "split-vcfs-test-snps-delete-me.vcf");
- final File input = new File(TEST_DATA_PATH + "CEUTrio-merged-indels-snps.vcf");
+ final File indelOutputFile = new File(OUTPUT_DATA_PATH, "split-vcfs-test-indels-delete-me.vcf");
+ final File snpOutputFile = new File(OUTPUT_DATA_PATH, "split-vcfs-test-snps-delete-me.vcf");
+ final File input = new File(TEST_DATA_PATH, "CEUTrio-merged-indels-snps.vcf");
indelOutputFile.deleteOnExit();
snpOutputFile.deleteOnExit();
diff --git a/src/tests/java/org/broadinstitute/variant/variantcontext/VariantJEXLContextUnitTest.java b/src/tests/java/org/broadinstitute/variant/variantcontext/VariantJEXLContextUnitTest.java
index 8d25697..e92df8a 100644
--- a/src/tests/java/org/broadinstitute/variant/variantcontext/VariantJEXLContextUnitTest.java
+++ b/src/tests/java/org/broadinstitute/variant/variantcontext/VariantJEXLContextUnitTest.java
@@ -59,7 +59,7 @@ public class VariantJEXLContextUnitTest extends VariantBaseTest {
@BeforeClass
public void beforeClass() {
try {
- exp = new VariantContextUtils.JexlVCMatchExp("name", VariantContextUtils.engine.createExpression(expression));
+ exp = new VariantContextUtils.JexlVCMatchExp("name", VariantContextUtils.engine.get().createExpression(expression));
} catch (Exception e) {
Assert.fail("Unable to create expression" + e.getMessage());
}
diff --git a/src/tests/java/org/broadinstitute/variant/variantcontext/writer/VCFWriterUnitTest.java b/src/tests/java/org/broadinstitute/variant/variantcontext/writer/VCFWriterUnitTest.java
index 5b963dd..653d5a0 100644
--- a/src/tests/java/org/broadinstitute/variant/variantcontext/writer/VCFWriterUnitTest.java
+++ b/src/tests/java/org/broadinstitute/variant/variantcontext/writer/VCFWriterUnitTest.java
@@ -31,17 +31,30 @@ import org.broad.tribble.AbstractFeatureReader;
import org.broad.tribble.FeatureReader;
import org.broad.tribble.Tribble;
import org.broadinstitute.variant.VariantBaseTest;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
+import org.broadinstitute.variant.variantcontext.GenotypesContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
import org.broadinstitute.variant.vcf.VCFCodec;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderVersion;
-import org.broadinstitute.variant.variantcontext.*;
import org.testng.Assert;
-import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
-import java.io.*;
-import java.util.*;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.EnumSet;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
/**
@@ -155,39 +168,6 @@ public class VCFWriterUnitTest extends VariantBaseTest {
Assert.assertEquals(index, additionalColumns.size());
}
- @DataProvider(name = "VCFWriterDoubleFormatTestData")
- public Object[][] makeVCFWriterDoubleFormatTestData() {
- List<Object[]> tests = new ArrayList<Object[]>();
- tests.add(new Object[]{1.0, "1.00"});
- tests.add(new Object[]{10.1, "10.10"});
- tests.add(new Object[]{10.01, "10.01"});
- tests.add(new Object[]{10.012, "10.01"});
- tests.add(new Object[]{10.015, "10.02"});
- tests.add(new Object[]{0.0, "0.00"});
- tests.add(new Object[]{0.5, "0.500"});
- tests.add(new Object[]{0.55, "0.550"});
- tests.add(new Object[]{0.555, "0.555"});
- tests.add(new Object[]{0.5555, "0.556"});
- tests.add(new Object[]{0.1, "0.100"});
- tests.add(new Object[]{0.050, "0.050"});
- tests.add(new Object[]{0.010, "0.010"});
- tests.add(new Object[]{0.012, "0.012"});
- tests.add(new Object[]{0.0012, "1.200e-03"});
- tests.add(new Object[]{1.2e-4, "1.200e-04"});
- tests.add(new Object[]{1.21e-4, "1.210e-04"});
- tests.add(new Object[]{1.212e-5, "1.212e-05"});
- tests.add(new Object[]{1.2123e-6, "1.212e-06"});
- tests.add(new Object[]{Double.POSITIVE_INFINITY, "Infinity"});
- tests.add(new Object[]{Double.NEGATIVE_INFINITY, "-Infinity"});
- tests.add(new Object[]{Double.NaN, "NaN"});
- return tests.toArray(new Object[][]{});
- }
-
- @Test(dataProvider = "VCFWriterDoubleFormatTestData")
- public void testVCFWriterDoubleFormatTestData(final double d, final String expected) {
- Assert.assertEquals(VCFWriter.formatVCFDouble(d), expected, "Failed to pretty print double in VCFWriter");
- }
-
@Test(enabled=true)
public void TestWritingLargeVCF() throws FileNotFoundException, InterruptedException {
diff --git a/src/tests/java/org/broadinstitute/variant/vcf/VCFEncoderTest.java b/src/tests/java/org/broadinstitute/variant/vcf/VCFEncoderTest.java
new file mode 100644
index 0000000..d9fa13e
--- /dev/null
+++ b/src/tests/java/org/broadinstitute/variant/vcf/VCFEncoderTest.java
@@ -0,0 +1,45 @@
+package org.broadinstitute.variant.vcf;
+
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class VCFEncoderTest {
+
+ @DataProvider(name = "VCFWriterDoubleFormatTestData")
+ public Object[][] makeVCFWriterDoubleFormatTestData() {
+ List<Object[]> tests = new ArrayList<Object[]>();
+ tests.add(new Object[]{1.0, "1.00"});
+ tests.add(new Object[]{10.1, "10.10"});
+ tests.add(new Object[]{10.01, "10.01"});
+ tests.add(new Object[]{10.012, "10.01"});
+ tests.add(new Object[]{10.015, "10.02"});
+ tests.add(new Object[]{0.0, "0.00"});
+ tests.add(new Object[]{0.5, "0.500"});
+ tests.add(new Object[]{0.55, "0.550"});
+ tests.add(new Object[]{0.555, "0.555"});
+ tests.add(new Object[]{0.5555, "0.556"});
+ tests.add(new Object[]{0.1, "0.100"});
+ tests.add(new Object[]{0.050, "0.050"});
+ tests.add(new Object[]{0.010, "0.010"});
+ tests.add(new Object[]{0.012, "0.012"});
+ tests.add(new Object[]{0.0012, "1.200e-03"});
+ tests.add(new Object[]{1.2e-4, "1.200e-04"});
+ tests.add(new Object[]{1.21e-4, "1.210e-04"});
+ tests.add(new Object[]{1.212e-5, "1.212e-05"});
+ tests.add(new Object[]{1.2123e-6, "1.212e-06"});
+ tests.add(new Object[]{Double.POSITIVE_INFINITY, "Infinity"});
+ tests.add(new Object[]{Double.NEGATIVE_INFINITY, "-Infinity"});
+ tests.add(new Object[]{Double.NaN, "NaN"});
+ return tests.toArray(new Object[][]{});
+ }
+
+ @Test(dataProvider = "VCFWriterDoubleFormatTestData")
+ public void testVCFWriterDoubleFormatTestData(final double d, final String expected) {
+ Assert.assertEquals(VCFEncoder.formatVCFDouble(d), expected, "Failed to pretty print double in VCFWriter");
+ }
+
+}
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGAC.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGAC.1.fastq
index b90b0bd..7c7dde1 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGAC.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGAC.1.fastq
@@ -1,52 +1,52 @@
- at HiMom:7:1:2:358
+ at machine1:HiMom:abcdeACXX:7:1:2:358 :N:0:AACTTGAC
NTCTGTTGTTATTTCCCTGTTACTTTTGGT
+
##############################
- at HiMom:7:1:3:1222
+ at machine1:HiMom:abcdeACXX:7:1:3:1222 :Y:0:AACTTGAC
TGGCATCCAGCTTTGTACTCATGAAAATTG
+
A?=@CBA@=7A@>@9 at BBA?>B=;<=@?B@
- at HiMom:7:1:3:1450
+ at machine1:HiMom:abcdeACXX:7:1:3:1450 :N:0:AACTTGAC
NGATTCGATTAGAATCATCGAATGGACTCG
+
##############################
- at HiMom:7:1:3:162
+ at machine1:HiMom:abcdeACXX:7:1:3:162 :Y:0:AACTTGAC
AATGAAGGCCACAGAGTGGTCCAAATAGCC
+
?@@5@@@>>A<0?;=0839:2<AAABA=##
- at HiMom:7:1:3:1677
+ at machine1:HiMom:abcdeACXX:7:1:3:1677 :Y:0:AACTTGAC
AGTGCAGTGGCGTGATCTTGGCTCACTGCA
+
A?7BBB@?9969A7B7;@;1>9:'=7;7 at B
- at HiMom:7:1:3:1760
+ at machine1:HiMom:abcdeACXX:7:1:3:1760 :Y:0:AACTTGAC
ACAAGAGACCCTAACATTAGGTAGGAATAT
+
A:@@5A<B<48 at B@=>?A?:;:?5>AB?@@
- at HiMom:7:1:3:985
+ at machine1:HiMom:abcdeACXX:7:1:3:985 :Y:0:AACTTGAC
AGGTTTAATTGGTTCCAGGAGGTCACACTG
+
?898 at BBB?@6<;@>;B::>:-79BA at A@:
- at HiMom:7:2:2:1365
+ at machine1:HiMom:abcdeACXX:7:2:2:1365 :N:0:AACTTGAC
NATAAAGATTATCCGTGAATGGCGCCTCCA
+
##############################
- at HiMom:7:2:3:1209
+ at machine1:HiMom:abcdeACXX:7:2:3:1209 :Y:0:AACTTGAC
NTTGAGGATGTTACTACATTATTATACAAA
+
%/3370/010.55#################
- at HiMom:7:2:3:1326
+ at machine1:HiMom:abcdeACXX:7:2:3:1326 :N:0:AACTTGAC
AGGAGGGAATGATGAACCAGTAGGTTAAGG
+
B>=<28+<B5%9:/;A78>+/=A#######
- at HiMom:7:2:3:1807
+ at machine1:HiMom:abcdeACXX:7:2:3:1807 :N:0:AACTTGAC
NGCATACTTCTTTCTTTCTTATTTTTCTTT
+
##############################
- at HiMom:7:2:3:1941
+ at machine1:HiMom:abcdeACXX:7:2:3:1941 :Y:0:AACTTGAC
TGTACTCGTGTAGCCTTTCACAGGCACAGC
+
B<.ACBBB2;9C>@5ABBBCBCBABCCC5B
- at HiMom:7:2:3:2038
+ at machine1:HiMom:abcdeACXX:7:2:3:2038 :N:0:AACTTGAC
NANAGATAGATAGATAGATAGATAGATAGA
+
##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGAC.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGAC.barcode_1.fastq
index 6db8795..d1921ed 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGAC.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGAC.barcode_1.fastq
@@ -1,52 +1,52 @@
- at HiMom:7:1:2:358
+ at machine1:HiMom:abcdeACXX:7:1:2:358 :N:0:AACTTGAC
AACTTGAC
+
A?;65173
- at HiMom:7:1:3:1222
+ at machine1:HiMom:abcdeACXX:7:1:3:1222 :Y:0:AACTTGAC
AACTTGAC
+
@CC=@@>B
- at HiMom:7:1:3:1450
+ at machine1:HiMom:abcdeACXX:7:1:3:1450 :N:0:AACTTGAC
AACTTGAC
+
BC1'<7A#
- at HiMom:7:1:3:162
+ at machine1:HiMom:abcdeACXX:7:1:3:162 :Y:0:AACTTGAC
AACTTGAC
+
BBBC at 5>?
- at HiMom:7:1:3:1677
+ at machine1:HiMom:abcdeACXX:7:1:3:1677 :Y:0:AACTTGAC
AACTTGAC
+
BCA>=4=B
- at HiMom:7:1:3:1760
+ at machine1:HiMom:abcdeACXX:7:1:3:1760 :Y:0:AACTTGAC
AACTTGAC
+
BABBABAA
- at HiMom:7:1:3:985
+ at machine1:HiMom:abcdeACXX:7:1:3:985 :Y:0:AACTTGAC
AACTTGAC
+
BBBB@>@B
- at HiMom:7:2:2:1365
+ at machine1:HiMom:abcdeACXX:7:2:2:1365 :N:0:AACTTGAC
AACTTGAC
+
BCAB>>AB
- at HiMom:7:2:3:1209
+ at machine1:HiMom:abcdeACXX:7:2:3:1209 :Y:0:AACTTGAC
AACTTGAC
+
3?@?92;B
- at HiMom:7:2:3:1326
+ at machine1:HiMom:abcdeACXX:7:2:3:1326 :N:0:AACTTGAC
AACTTGAC
+
BCBBB3BB
- at HiMom:7:2:3:1807
+ at machine1:HiMom:abcdeACXX:7:2:3:1807 :N:0:AACTTGAC
AACTTGAC
+
B?4=B@><
- at HiMom:7:2:3:1941
+ at machine1:HiMom:abcdeACXX:7:2:3:1941 :Y:0:AACTTGAC
AACTTGAC
+
BCBBBBBB
- at HiMom:7:2:3:2038
+ at machine1:HiMom:abcdeACXX:7:2:3:2038 :N:0:AACTTGAC
AACTTGAC
+
BA@;(1>B
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGACTTGAGCCT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGACTTGAGCCT.1.fastq
index 5889e62..c2dcba1 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGACTTGAGCCT.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGACTTGAGCCT.1.fastq
@@ -1,52 +1,52 @@
- at HiMom:9:1:2:358
+ at machine1:HiMom:abcdeACXX:9:1:2:358 :N:0:AACTTGACTTGAGCCT
NTCTGTTGTTATTTCCCTGTTACTTTTGGT
+
##############################
- at HiMom:9:1:3:1222
+ at machine1:HiMom:abcdeACXX:9:1:3:1222 :Y:0:AACTTGACTTGAGCCT
TGGCATCCAGCTTTGTACTCATGAAAATTG
+
A?=@CBA@=7A@>@9 at BBA?>B=;<=@?B@
- at HiMom:9:1:3:1450
+ at machine1:HiMom:abcdeACXX:9:1:3:1450 :N:0:AACTTGACTTGAGCCT
NGATTCGATTAGAATCATCGAATGGACTCG
+
##############################
- at HiMom:9:1:3:162
+ at machine1:HiMom:abcdeACXX:9:1:3:162 :Y:0:AACTTGACTTGAGCCT
AATGAAGGCCACAGAGTGGTCCAAATAGCC
+
?@@5@@@>>A<0?;=0839:2<AAABA=##
- at HiMom:9:1:3:1677
+ at machine1:HiMom:abcdeACXX:9:1:3:1677 :Y:0:AACTTGACTTGAGCCT
AGTGCAGTGGCGTGATCTTGGCTCACTGCA
+
A?7BBB@?9969A7B7;@;1>9:'=7;7 at B
- at HiMom:9:1:3:1760
+ at machine1:HiMom:abcdeACXX:9:1:3:1760 :Y:0:AACTTGACTTGAGCCT
ACAAGAGACCCTAACATTAGGTAGGAATAT
+
A:@@5A<B<48 at B@=>?A?:;:?5>AB?@@
- at HiMom:9:1:3:985
+ at machine1:HiMom:abcdeACXX:9:1:3:985 :Y:0:AACTTGACTTGAGCCT
AGGTTTAATTGGTTCCAGGAGGTCACACTG
+
?898 at BBB?@6<;@>;B::>:-79BA at A@:
- at HiMom:9:2:2:1365
+ at machine1:HiMom:abcdeACXX:9:2:2:1365 :N:0:AACTTGACTTGAGCCT
NATAAAGATTATCCGTGAATGGCGCCTCCA
+
##############################
- at HiMom:9:2:3:1209
+ at machine1:HiMom:abcdeACXX:9:2:3:1209 :Y:0:AACTTGACTTGAGCCT
NTTGAGGATGTTACTACATTATTATACAAA
+
%/3370/010.55#################
- at HiMom:9:2:3:1326
+ at machine1:HiMom:abcdeACXX:9:2:3:1326 :N:0:AACTTGACTTGAGCCT
AGGAGGGAATGATGAACCAGTAGGTTAAGG
+
B>=<28+<B5%9:/;A78>+/=A#######
- at HiMom:9:2:3:1807
+ at machine1:HiMom:abcdeACXX:9:2:3:1807 :N:0:AACTTGACTTGAGCCT
NGCATACTTCTTTCTTTCTTATTTTTCTTT
+
##############################
- at HiMom:9:2:3:1941
+ at machine1:HiMom:abcdeACXX:9:2:3:1941 :Y:0:AACTTGACTTGAGCCT
TGTACTCGTGTAGCCTTTCACAGGCACAGC
+
B<.ACBBB2;9C>@5ABBBCBCBABCCC5B
- at HiMom:9:2:3:2038
+ at machine1:HiMom:abcdeACXX:9:2:3:2038 :N:0:AACTTGACTTGAGCCT
NANAGATAGATAGATAGATAGATAGATAGA
+
##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGACTTGAGCCT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGACTTGAGCCT.barcode_1.fastq
index 2ba42e1..34ef16f 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGACTTGAGCCT.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGACTTGAGCCT.barcode_1.fastq
@@ -1,52 +1,52 @@
- at HiMom:9:1:2:358
+ at machine1:HiMom:abcdeACXX:9:1:2:358 :N:0:AACTTGACTTGAGCCT
AACTTGAC
+
A?;65173
- at HiMom:9:1:3:1222
+ at machine1:HiMom:abcdeACXX:9:1:3:1222 :Y:0:AACTTGACTTGAGCCT
AACTTGAC
+
@CC=@@>B
- at HiMom:9:1:3:1450
+ at machine1:HiMom:abcdeACXX:9:1:3:1450 :N:0:AACTTGACTTGAGCCT
AACTTGAC
+
BC1'<7A#
- at HiMom:9:1:3:162
+ at machine1:HiMom:abcdeACXX:9:1:3:162 :Y:0:AACTTGACTTGAGCCT
AACTTGAC
+
BBBC at 5>?
- at HiMom:9:1:3:1677
+ at machine1:HiMom:abcdeACXX:9:1:3:1677 :Y:0:AACTTGACTTGAGCCT
AACTTGAC
+
BCA>=4=B
- at HiMom:9:1:3:1760
+ at machine1:HiMom:abcdeACXX:9:1:3:1760 :Y:0:AACTTGACTTGAGCCT
AACTTGAC
+
BABBABAA
- at HiMom:9:1:3:985
+ at machine1:HiMom:abcdeACXX:9:1:3:985 :Y:0:AACTTGACTTGAGCCT
AACTTGAC
+
BBBB@>@B
- at HiMom:9:2:2:1365
+ at machine1:HiMom:abcdeACXX:9:2:2:1365 :N:0:AACTTGACTTGAGCCT
AACTTGAC
+
BCAB>>AB
- at HiMom:9:2:3:1209
+ at machine1:HiMom:abcdeACXX:9:2:3:1209 :Y:0:AACTTGACTTGAGCCT
AACTTGAC
+
3?@?92;B
- at HiMom:9:2:3:1326
+ at machine1:HiMom:abcdeACXX:9:2:3:1326 :N:0:AACTTGACTTGAGCCT
AACTTGAC
+
BCBBB3BB
- at HiMom:9:2:3:1807
+ at machine1:HiMom:abcdeACXX:9:2:3:1807 :N:0:AACTTGACTTGAGCCT
AACTTGAC
+
B?4=B@><
- at HiMom:9:2:3:1941
+ at machine1:HiMom:abcdeACXX:9:2:3:1941 :Y:0:AACTTGACTTGAGCCT
AACTTGAC
+
BCBBBBBB
- at HiMom:9:2:3:2038
+ at machine1:HiMom:abcdeACXX:9:2:3:2038 :N:0:AACTTGACTTGAGCCT
AACTTGAC
+
BA@;(1>B
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGACTTGAGCCT.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGACTTGAGCCT.barcode_2.fastq
index 42df6cb..068fcfd 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGACTTGAGCCT.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGACTTGAGCCT.barcode_2.fastq
@@ -1,52 +1,52 @@
- at HiMom:9:1:2:358
+ at machine1:HiMom:abcdeACXX:9:1:2:358 :N:0:AACTTGACTTGAGCCT
TTGAGCCT
+
A?;65173
- at HiMom:9:1:3:1222
+ at machine1:HiMom:abcdeACXX:9:1:3:1222 :Y:0:AACTTGACTTGAGCCT
TTGAGCCT
+
@CC=@@>B
- at HiMom:9:1:3:1450
+ at machine1:HiMom:abcdeACXX:9:1:3:1450 :N:0:AACTTGACTTGAGCCT
TTGAGCCT
+
BC1'<7A#
- at HiMom:9:1:3:162
+ at machine1:HiMom:abcdeACXX:9:1:3:162 :Y:0:AACTTGACTTGAGCCT
TTGAGCCT
+
BBBC at 5>?
- at HiMom:9:1:3:1677
+ at machine1:HiMom:abcdeACXX:9:1:3:1677 :Y:0:AACTTGACTTGAGCCT
TTGAGCCT
+
BCA>=4=B
- at HiMom:9:1:3:1760
+ at machine1:HiMom:abcdeACXX:9:1:3:1760 :Y:0:AACTTGACTTGAGCCT
TTGAGCCT
+
BABBABAA
- at HiMom:9:1:3:985
+ at machine1:HiMom:abcdeACXX:9:1:3:985 :Y:0:AACTTGACTTGAGCCT
TTGAGCCT
+
BBBB@>@B
- at HiMom:9:2:2:1365
+ at machine1:HiMom:abcdeACXX:9:2:2:1365 :N:0:AACTTGACTTGAGCCT
TTGAGCCT
+
BCAB>>AB
- at HiMom:9:2:3:1209
+ at machine1:HiMom:abcdeACXX:9:2:3:1209 :Y:0:AACTTGACTTGAGCCT
TTGAGCCT
+
3?@?92;B
- at HiMom:9:2:3:1326
+ at machine1:HiMom:abcdeACXX:9:2:3:1326 :N:0:AACTTGACTTGAGCCT
TTGAGCCT
+
BCBBB3BB
- at HiMom:9:2:3:1807
+ at machine1:HiMom:abcdeACXX:9:2:3:1807 :N:0:AACTTGACTTGAGCCT
TTGAGCCT
+
B?4=B@><
- at HiMom:9:2:3:1941
+ at machine1:HiMom:abcdeACXX:9:2:3:1941 :Y:0:AACTTGACTTGAGCCT
TTGAGCCT
+
BCBBBBBB
- at HiMom:9:2:3:2038
+ at machine1:HiMom:abcdeACXX:9:2:3:2038 :N:0:AACTTGACTTGAGCCT
TTGAGCCT
+
BA@;(1>B
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGT.1.fastq
index a19858d..c0696c6 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGT.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGT.1.fastq
@@ -1,52 +1,52 @@
- at HiMom:7:1:2:1417
+ at machine1:HiMom:abcdeACXX:7:1:2:1417 :Y:0:AAGGATGT
NATTCCATTCGATGATTCCATTCGAGTCCA
+
%-::567;93-510788014:8538122##
- at HiMom:7:1:2:1889
+ at machine1:HiMom:abcdeACXX:7:1:2:1889 :Y:0:AAGGATGT
NGAAATGTATCAAGGTTTGTATAATTGCTG
+
%-7<<:::<2:::8:4<<:07547765978
- at HiMom:7:1:3:1764
+ at machine1:HiMom:abcdeACXX:7:1:3:1764 :N:0:AAGGATGT
NTCTATGGGGTGTGTATCTGTTTCTGGACT
+
%09::845(4586/6666884;8851.314
- at HiMom:7:1:3:2027
+ at machine1:HiMom:abcdeACXX:7:1:3:2027 :Y:0:AAGGATGT
AATGTATTATGTTTCATAAGAAAACAAAAG
+
BA7/- at 8=@4,*1=>?:A@:>B at BBCB@8#
- at HiMom:7:1:3:273
+ at machine1:HiMom:abcdeACXX:7:1:3:273 :N:0:AAGGATGT
NAATTGACATAAATCAATATTGTTAAAATG
+
##############################
- at HiMom:7:1:3:608
+ at machine1:HiMom:abcdeACXX:7:1:3:608 :Y:0:AAGGATGT
NTGTGCTTCAATGATGCTATCAGGTGTGTT
+
%.9675:747:766553::9:7119::8::
- at HiMom:7:2:2:1842
+ at machine1:HiMom:abcdeACXX:7:2:2:1842 :N:0:AAGGATGT
NGGTGGATCCCCTGAGGTCAGGAGTTCAAG
+
##############################
- at HiMom:7:2:2:1944
+ at machine1:HiMom:abcdeACXX:7:2:2:1944 :Y:0:AAGGATGT
NATTAAATATATATTTTATTCTGAACATAA
+
%09::<<<<<;:<<<:99<<9<<;<;<:<<
- at HiMom:7:2:2:1985
+ at machine1:HiMom:abcdeACXX:7:2:2:1985 :N:0:AAGGATGT
NGACTATCACTCTAGGGCCTCCACCCTTGC
+
%%2266466667186(66############
- at HiMom:7:2:3:1952
+ at machine1:HiMom:abcdeACXX:7:2:3:1952 :Y:0:AAGGATGT
NATAGATGATAAAAACATTTGACAGTGAAA
+
%.8737868:::<;<;9;9979::9858;;
- at HiMom:7:2:3:470
+ at machine1:HiMom:abcdeACXX:7:2:3:470 :Y:0:AAGGATGT
TGTGGATTCCATTCGAATTCATTCGATTAT
+
BBCBBACC at CCCC>)@CBA>@CB?BCCCCC
- at HiMom:7:2:3:490
+ at machine1:HiMom:abcdeACXX:7:2:3:490 :N:0:AAGGATGT
NCTAATTGATGGGTAAGAGGCAAAGCATGA
+
##############################
- at HiMom:7:2:3:589
+ at machine1:HiMom:abcdeACXX:7:2:3:589 :Y:0:AAGGATGT
TGAATGCAGGTGCCAGGGAGACGTGACTTC
+
=8ACBB??>@=?<ACB9<;?A>??;A<>?3
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGT.barcode_1.fastq
index 878aacb..f4f317f 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGT.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGT.barcode_1.fastq
@@ -1,52 +1,52 @@
- at HiMom:7:1:2:1417
+ at machine1:HiMom:abcdeACXX:7:1:2:1417 :Y:0:AAGGATGT
AAGGATGT
+
B?5??BC?
- at HiMom:7:1:2:1889
+ at machine1:HiMom:abcdeACXX:7:1:2:1889 :Y:0:AAGGATGT
NAGGATGT
+
%.46:;;9
- at HiMom:7:1:3:1764
+ at machine1:HiMom:abcdeACXX:7:1:3:1764 :N:0:AAGGATGT
AAGGATGT
+
BB?BB@:A
- at HiMom:7:1:3:2027
+ at machine1:HiMom:abcdeACXX:7:1:3:2027 :Y:0:AAGGATGT
AAGGATGT
+
B>7-<::#
- at HiMom:7:1:3:273
+ at machine1:HiMom:abcdeACXX:7:1:3:273 :N:0:AAGGATGT
AAGGATGT
+
38=5+AC7
- at HiMom:7:1:3:608
+ at machine1:HiMom:abcdeACXX:7:1:3:608 :Y:0:AAGGATGT
AAGGATGT
+
AA5B?BB@
- at HiMom:7:2:2:1842
+ at machine1:HiMom:abcdeACXX:7:2:2:1842 :N:0:AAGGATGT
AAGGATGT
+
@:1;39B>
- at HiMom:7:2:2:1944
+ at machine1:HiMom:abcdeACXX:7:2:2:1944 :Y:0:AAGGATGT
AAGGATGT
+
BB9BBA:#
- at HiMom:7:2:2:1985
+ at machine1:HiMom:abcdeACXX:7:2:2:1985 :N:0:AAGGATGT
AAGGATGT
+
BC?7>2<8
- at HiMom:7:2:3:1952
+ at machine1:HiMom:abcdeACXX:7:2:3:1952 :Y:0:AAGGATGT
AAGGATGT
+
BB?BB at B<
- at HiMom:7:2:3:470
+ at machine1:HiMom:abcdeACXX:7:2:3:470 :Y:0:AAGGATGT
AAGGATGT
+
B at 6::=B:
- at HiMom:7:2:3:490
+ at machine1:HiMom:abcdeACXX:7:2:3:490 :N:0:AAGGATGT
AAGGATGT
+
?#######
- at HiMom:7:2:3:589
+ at machine1:HiMom:abcdeACXX:7:2:3:589 :Y:0:AAGGATGT
AAGGATGT
+
?BB9BB at 9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGTTTCGCTGA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGTTTCGCTGA.1.fastq
index 6485a6d..377ac1f 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGTTTCGCTGA.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGTTTCGCTGA.1.fastq
@@ -1,52 +1,52 @@
- at HiMom:9:1:2:1417
+ at machine1:HiMom:abcdeACXX:9:1:2:1417 :Y:0:AAGGATGTTTCGCTGA
NATTCCATTCGATGATTCCATTCGAGTCCA
+
%-::567;93-510788014:8538122##
- at HiMom:9:1:2:1889
+ at machine1:HiMom:abcdeACXX:9:1:2:1889 :Y:0:AAGGATGTTTCGCTGA
NGAAATGTATCAAGGTTTGTATAATTGCTG
+
%-7<<:::<2:::8:4<<:07547765978
- at HiMom:9:1:3:1764
+ at machine1:HiMom:abcdeACXX:9:1:3:1764 :N:0:AAGGATGTTTCGCTGA
NTCTATGGGGTGTGTATCTGTTTCTGGACT
+
%09::845(4586/6666884;8851.314
- at HiMom:9:1:3:2027
+ at machine1:HiMom:abcdeACXX:9:1:3:2027 :Y:0:AAGGATGTTTCGCTGA
AATGTATTATGTTTCATAAGAAAACAAAAG
+
BA7/- at 8=@4,*1=>?:A@:>B at BBCB@8#
- at HiMom:9:1:3:273
+ at machine1:HiMom:abcdeACXX:9:1:3:273 :N:0:AAGGATGTTTCGCTGA
NAATTGACATAAATCAATATTGTTAAAATG
+
##############################
- at HiMom:9:1:3:608
+ at machine1:HiMom:abcdeACXX:9:1:3:608 :Y:0:AAGGATGTTTCGCTGA
NTGTGCTTCAATGATGCTATCAGGTGTGTT
+
%.9675:747:766553::9:7119::8::
- at HiMom:9:2:2:1842
+ at machine1:HiMom:abcdeACXX:9:2:2:1842 :N:0:AAGGATGTTTCGCTGA
NGGTGGATCCCCTGAGGTCAGGAGTTCAAG
+
##############################
- at HiMom:9:2:2:1944
+ at machine1:HiMom:abcdeACXX:9:2:2:1944 :Y:0:AAGGATGTTTCGCTGA
NATTAAATATATATTTTATTCTGAACATAA
+
%09::<<<<<;:<<<:99<<9<<;<;<:<<
- at HiMom:9:2:2:1985
+ at machine1:HiMom:abcdeACXX:9:2:2:1985 :N:0:AAGGATGTTTCGCTGA
NGACTATCACTCTAGGGCCTCCACCCTTGC
+
%%2266466667186(66############
- at HiMom:9:2:3:1952
+ at machine1:HiMom:abcdeACXX:9:2:3:1952 :Y:0:AAGGATGTTTCGCTGA
NATAGATGATAAAAACATTTGACAGTGAAA
+
%.8737868:::<;<;9;9979::9858;;
- at HiMom:9:2:3:470
+ at machine1:HiMom:abcdeACXX:9:2:3:470 :Y:0:AAGGATGTTTCGCTGA
TGTGGATTCCATTCGAATTCATTCGATTAT
+
BBCBBACC at CCCC>)@CBA>@CB?BCCCCC
- at HiMom:9:2:3:490
+ at machine1:HiMom:abcdeACXX:9:2:3:490 :N:0:AAGGATGTTTCGCTGA
NCTAATTGATGGGTAAGAGGCAAAGCATGA
+
##############################
- at HiMom:9:2:3:589
+ at machine1:HiMom:abcdeACXX:9:2:3:589 :Y:0:AAGGATGTTTCGCTGA
TGAATGCAGGTGCCAGGGAGACGTGACTTC
+
=8ACBB??>@=?<ACB9<;?A>??;A<>?3
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGTTTCGCTGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGTTTCGCTGA.barcode_1.fastq
index dca7f0b..99ac8f1 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGTTTCGCTGA.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGTTTCGCTGA.barcode_1.fastq
@@ -1,52 +1,52 @@
- at HiMom:9:1:2:1417
+ at machine1:HiMom:abcdeACXX:9:1:2:1417 :Y:0:AAGGATGTTTCGCTGA
AAGGATGT
+
B?5??BC?
- at HiMom:9:1:2:1889
+ at machine1:HiMom:abcdeACXX:9:1:2:1889 :Y:0:AAGGATGTTTCGCTGA
NAGGATGT
+
%.46:;;9
- at HiMom:9:1:3:1764
+ at machine1:HiMom:abcdeACXX:9:1:3:1764 :N:0:AAGGATGTTTCGCTGA
AAGGATGT
+
BB?BB@:A
- at HiMom:9:1:3:2027
+ at machine1:HiMom:abcdeACXX:9:1:3:2027 :Y:0:AAGGATGTTTCGCTGA
AAGGATGT
+
B>7-<::#
- at HiMom:9:1:3:273
+ at machine1:HiMom:abcdeACXX:9:1:3:273 :N:0:AAGGATGTTTCGCTGA
AAGGATGT
+
38=5+AC7
- at HiMom:9:1:3:608
+ at machine1:HiMom:abcdeACXX:9:1:3:608 :Y:0:AAGGATGTTTCGCTGA
AAGGATGT
+
AA5B?BB@
- at HiMom:9:2:2:1842
+ at machine1:HiMom:abcdeACXX:9:2:2:1842 :N:0:AAGGATGTTTCGCTGA
AAGGATGT
+
@:1;39B>
- at HiMom:9:2:2:1944
+ at machine1:HiMom:abcdeACXX:9:2:2:1944 :Y:0:AAGGATGTTTCGCTGA
AAGGATGT
+
BB9BBA:#
- at HiMom:9:2:2:1985
+ at machine1:HiMom:abcdeACXX:9:2:2:1985 :N:0:AAGGATGTTTCGCTGA
AAGGATGT
+
BC?7>2<8
- at HiMom:9:2:3:1952
+ at machine1:HiMom:abcdeACXX:9:2:3:1952 :Y:0:AAGGATGTTTCGCTGA
AAGGATGT
+
BB?BB at B<
- at HiMom:9:2:3:470
+ at machine1:HiMom:abcdeACXX:9:2:3:470 :Y:0:AAGGATGTTTCGCTGA
AAGGATGT
+
B at 6::=B:
- at HiMom:9:2:3:490
+ at machine1:HiMom:abcdeACXX:9:2:3:490 :N:0:AAGGATGTTTCGCTGA
AAGGATGT
+
?#######
- at HiMom:9:2:3:589
+ at machine1:HiMom:abcdeACXX:9:2:3:589 :Y:0:AAGGATGTTTCGCTGA
AAGGATGT
+
?BB9BB at 9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGTTTCGCTGA.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGTTTCGCTGA.barcode_2.fastq
index c6a434b..b4130ae 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGTTTCGCTGA.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGTTTCGCTGA.barcode_2.fastq
@@ -1,52 +1,52 @@
- at HiMom:9:1:2:1417
+ at machine1:HiMom:abcdeACXX:9:1:2:1417 :Y:0:AAGGATGTTTCGCTGA
TTCGCTGA
+
B?5??BC?
- at HiMom:9:1:2:1889
+ at machine1:HiMom:abcdeACXX:9:1:2:1889 :Y:0:AAGGATGTTTCGCTGA
TTCGCTGA
+
%.46:;;9
- at HiMom:9:1:3:1764
+ at machine1:HiMom:abcdeACXX:9:1:3:1764 :N:0:AAGGATGTTTCGCTGA
TTCGCTGA
+
BB?BB@:A
- at HiMom:9:1:3:2027
+ at machine1:HiMom:abcdeACXX:9:1:3:2027 :Y:0:AAGGATGTTTCGCTGA
TTCGCTGA
+
B>7-<::#
- at HiMom:9:1:3:273
+ at machine1:HiMom:abcdeACXX:9:1:3:273 :N:0:AAGGATGTTTCGCTGA
TTCGCTGA
+
38=5+AC7
- at HiMom:9:1:3:608
+ at machine1:HiMom:abcdeACXX:9:1:3:608 :Y:0:AAGGATGTTTCGCTGA
TTCGCTGA
+
AA5B?BB@
- at HiMom:9:2:2:1842
+ at machine1:HiMom:abcdeACXX:9:2:2:1842 :N:0:AAGGATGTTTCGCTGA
TTCGCTGA
+
@:1;39B>
- at HiMom:9:2:2:1944
+ at machine1:HiMom:abcdeACXX:9:2:2:1944 :Y:0:AAGGATGTTTCGCTGA
TTCGCTGA
+
BB9BBA:#
- at HiMom:9:2:2:1985
+ at machine1:HiMom:abcdeACXX:9:2:2:1985 :N:0:AAGGATGTTTCGCTGA
TTCGCTGA
+
BC?7>2<8
- at HiMom:9:2:3:1952
+ at machine1:HiMom:abcdeACXX:9:2:3:1952 :Y:0:AAGGATGTTTCGCTGA
TTCGCTGA
+
BB?BB at B<
- at HiMom:9:2:3:470
+ at machine1:HiMom:abcdeACXX:9:2:3:470 :Y:0:AAGGATGTTTCGCTGA
TTCGCTGA
+
B at 6::=B:
- at HiMom:9:2:3:490
+ at machine1:HiMom:abcdeACXX:9:2:3:490 :N:0:AAGGATGTTTCGCTGA
TTCGCTGA
+
?#######
- at HiMom:9:2:3:589
+ at machine1:HiMom:abcdeACXX:9:2:3:589 :Y:0:AAGGATGTTTCGCTGA
TTCGCTGA
+
?BB9BB at 9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTG.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTG.1.fastq
index 1b524a9..9cc5451 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTG.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTG.1.fastq
@@ -1,36 +1,36 @@
- at HiMom:7:1:3:1219
+ at machine1:HiMom:abcdeACXX:7:1:3:1219 :Y:0:ACCAACTG
AGTTACTTATAGTGAATGGTTATTACTCCA
+
BA>BBBBBBA@?:?AA;;<8 at B9=97>9>A
- at HiMom:7:1:3:1319
+ at machine1:HiMom:abcdeACXX:7:1:3:1319 :N:0:ACCAACTG
TAAATGATTGCCTTCCACAGTATACATGTG
+
BAAA<::=B at 7:89)>=>B+)B at B@=####
- at HiMom:7:1:3:795
+ at machine1:HiMom:abcdeACXX:7:1:3:795 :N:0:ACCAACTG
NGTAATGGAAGTCCTAGTACTAAAAATTAG
+
##############################
- at HiMom:7:2:2:1298
+ at machine1:HiMom:abcdeACXX:7:2:2:1298 :N:0:ACCAACTG
NGATTCCATTCAATGAATCCATTCGATTCC
+
%.235+22976###################
- at HiMom:7:2:2:1745
+ at machine1:HiMom:abcdeACXX:7:2:2:1745 :Y:0:ACCAACTG
NGGGAGCTAAGTAACTGGAACAAGTTTTTG
+
%-5237789999:8886689:9:9569887
- at HiMom:7:2:2:1874
+ at machine1:HiMom:abcdeACXX:7:2:2:1874 :Y:0:ACCAACTG
NGGCATATATCCTTTTACATACCCAACACA
+
%,0137:949699;9;88798789717996
- at HiMom:7:2:2:904
+ at machine1:HiMom:abcdeACXX:7:2:2:904 :N:0:ACCAACTG
NTTAGACACCATGAAGGTAACTTCCTACTC
+
%0:62667999/&.6058::5978489366
- at HiMom:7:2:3:207
+ at machine1:HiMom:abcdeACXX:7:2:3:207 :Y:0:ACCAACTG
AGTTAGAAACAGAATACGGGTAATAATGTA
+
BBCCCA at BA@AAABC at CC@AACBCBBBCBC
- at HiMom:7:2:3:577
+ at machine1:HiMom:abcdeACXX:7:2:3:577 :N:0:ACCAACTG
NTTCAACTCTGGGAGTTGAATGCAAACATC
+
##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTG.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTG.barcode_1.fastq
index f5b5b30..a43dd6e 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTG.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTG.barcode_1.fastq
@@ -1,36 +1,36 @@
- at HiMom:7:1:3:1219
+ at machine1:HiMom:abcdeACXX:7:1:3:1219 :Y:0:ACCAACTG
ACCAACTG
+
B?@@A??9
- at HiMom:7:1:3:1319
+ at machine1:HiMom:abcdeACXX:7:1:3:1319 :N:0:ACCAACTG
ACCAACTG
+
??8 at A>8:
- at HiMom:7:1:3:795
+ at machine1:HiMom:abcdeACXX:7:1:3:795 :N:0:ACCAACTG
ACCAACTG
+
>88 at A>##
- at HiMom:7:2:2:1298
+ at machine1:HiMom:abcdeACXX:7:2:2:1298 :N:0:ACCAACTG
ACCAACTG
+
A7><<%;<
- at HiMom:7:2:2:1745
+ at machine1:HiMom:abcdeACXX:7:2:2:1745 :Y:0:ACCAACTG
ACCAACTG
+
BA>BBABB
- at HiMom:7:2:2:1874
+ at machine1:HiMom:abcdeACXX:7:2:2:1874 :Y:0:ACCAACTG
ACCAACTG
+
B>>>?8@=
- at HiMom:7:2:2:904
+ at machine1:HiMom:abcdeACXX:7:2:2:904 :N:0:ACCAACTG
ACCAACTG
+
A?ABB?;7
- at HiMom:7:2:3:207
+ at machine1:HiMom:abcdeACXX:7:2:3:207 :Y:0:ACCAACTG
ACCAACTG
+
BA;6@??@
- at HiMom:7:2:3:577
+ at machine1:HiMom:abcdeACXX:7:2:3:577 :N:0:ACCAACTG
ACCAACTG
+
B?:4<A??
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTGTGTCGGAT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTGTGTCGGAT.1.fastq
index 92ff10f..c9771ab 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTGTGTCGGAT.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTGTGTCGGAT.1.fastq
@@ -1,36 +1,36 @@
- at HiMom:9:1:3:1219
+ at machine1:HiMom:abcdeACXX:9:1:3:1219 :Y:0:ACCAACTGTGTCGGAT
AGTTACTTATAGTGAATGGTTATTACTCCA
+
BA>BBBBBBA@?:?AA;;<8 at B9=97>9>A
- at HiMom:9:1:3:1319
+ at machine1:HiMom:abcdeACXX:9:1:3:1319 :N:0:ACCAACTGTGTCGGAT
TAAATGATTGCCTTCCACAGTATACATGTG
+
BAAA<::=B at 7:89)>=>B+)B at B@=####
- at HiMom:9:1:3:795
+ at machine1:HiMom:abcdeACXX:9:1:3:795 :N:0:ACCAACTGTGTCGGAT
NGTAATGGAAGTCCTAGTACTAAAAATTAG
+
##############################
- at HiMom:9:2:2:1298
+ at machine1:HiMom:abcdeACXX:9:2:2:1298 :N:0:ACCAACTGTGTCGGAT
NGATTCCATTCAATGAATCCATTCGATTCC
+
%.235+22976###################
- at HiMom:9:2:2:1745
+ at machine1:HiMom:abcdeACXX:9:2:2:1745 :Y:0:ACCAACTGTGTCGGAT
NGGGAGCTAAGTAACTGGAACAAGTTTTTG
+
%-5237789999:8886689:9:9569887
- at HiMom:9:2:2:1874
+ at machine1:HiMom:abcdeACXX:9:2:2:1874 :Y:0:ACCAACTGTGTCGGAT
NGGCATATATCCTTTTACATACCCAACACA
+
%,0137:949699;9;88798789717996
- at HiMom:9:2:2:904
+ at machine1:HiMom:abcdeACXX:9:2:2:904 :N:0:ACCAACTGTGTCGGAT
NTTAGACACCATGAAGGTAACTTCCTACTC
+
%0:62667999/&.6058::5978489366
- at HiMom:9:2:3:207
+ at machine1:HiMom:abcdeACXX:9:2:3:207 :Y:0:ACCAACTGTGTCGGAT
AGTTAGAAACAGAATACGGGTAATAATGTA
+
BBCCCA at BA@AAABC at CC@AACBCBBBCBC
- at HiMom:9:2:3:577
+ at machine1:HiMom:abcdeACXX:9:2:3:577 :N:0:ACCAACTGTGTCGGAT
NTTCAACTCTGGGAGTTGAATGCAAACATC
+
##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTGTGTCGGAT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTGTGTCGGAT.barcode_1.fastq
index 0dcb66f..bdc8147 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTGTGTCGGAT.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTGTGTCGGAT.barcode_1.fastq
@@ -1,36 +1,36 @@
- at HiMom:9:1:3:1219
+ at machine1:HiMom:abcdeACXX:9:1:3:1219 :Y:0:ACCAACTGTGTCGGAT
ACCAACTG
+
B?@@A??9
- at HiMom:9:1:3:1319
+ at machine1:HiMom:abcdeACXX:9:1:3:1319 :N:0:ACCAACTGTGTCGGAT
ACCAACTG
+
??8 at A>8:
- at HiMom:9:1:3:795
+ at machine1:HiMom:abcdeACXX:9:1:3:795 :N:0:ACCAACTGTGTCGGAT
ACCAACTG
+
>88 at A>##
- at HiMom:9:2:2:1298
+ at machine1:HiMom:abcdeACXX:9:2:2:1298 :N:0:ACCAACTGTGTCGGAT
ACCAACTG
+
A7><<%;<
- at HiMom:9:2:2:1745
+ at machine1:HiMom:abcdeACXX:9:2:2:1745 :Y:0:ACCAACTGTGTCGGAT
ACCAACTG
+
BA>BBABB
- at HiMom:9:2:2:1874
+ at machine1:HiMom:abcdeACXX:9:2:2:1874 :Y:0:ACCAACTGTGTCGGAT
ACCAACTG
+
B>>>?8@=
- at HiMom:9:2:2:904
+ at machine1:HiMom:abcdeACXX:9:2:2:904 :N:0:ACCAACTGTGTCGGAT
ACCAACTG
+
A?ABB?;7
- at HiMom:9:2:3:207
+ at machine1:HiMom:abcdeACXX:9:2:3:207 :Y:0:ACCAACTGTGTCGGAT
ACCAACTG
+
BA;6@??@
- at HiMom:9:2:3:577
+ at machine1:HiMom:abcdeACXX:9:2:3:577 :N:0:ACCAACTGTGTCGGAT
ACCAACTG
+
B?:4<A??
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTGTGTCGGAT.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTGTGTCGGAT.barcode_2.fastq
index e4b4fd7..95db720 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTGTGTCGGAT.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTGTGTCGGAT.barcode_2.fastq
@@ -1,36 +1,36 @@
- at HiMom:9:1:3:1219
+ at machine1:HiMom:abcdeACXX:9:1:3:1219 :Y:0:ACCAACTGTGTCGGAT
TGTCGGAT
+
B?@@A??9
- at HiMom:9:1:3:1319
+ at machine1:HiMom:abcdeACXX:9:1:3:1319 :N:0:ACCAACTGTGTCGGAT
TGTCGGAT
+
??8 at A>8:
- at HiMom:9:1:3:795
+ at machine1:HiMom:abcdeACXX:9:1:3:795 :N:0:ACCAACTGTGTCGGAT
TGTCGGAT
+
>88 at A>##
- at HiMom:9:2:2:1298
+ at machine1:HiMom:abcdeACXX:9:2:2:1298 :N:0:ACCAACTGTGTCGGAT
TGTCGGAT
+
A7><<%;<
- at HiMom:9:2:2:1745
+ at machine1:HiMom:abcdeACXX:9:2:2:1745 :Y:0:ACCAACTGTGTCGGAT
TGTCGGAT
+
BA>BBABB
- at HiMom:9:2:2:1874
+ at machine1:HiMom:abcdeACXX:9:2:2:1874 :Y:0:ACCAACTGTGTCGGAT
TGTCGGAT
+
B>>>?8@=
- at HiMom:9:2:2:904
+ at machine1:HiMom:abcdeACXX:9:2:2:904 :N:0:ACCAACTGTGTCGGAT
TGTCGGAT
+
A?ABB?;7
- at HiMom:9:2:3:207
+ at machine1:HiMom:abcdeACXX:9:2:3:207 :Y:0:ACCAACTGTGTCGGAT
TGTCGGAT
+
BA;6@??@
- at HiMom:9:2:3:577
+ at machine1:HiMom:abcdeACXX:9:2:3:577 :N:0:ACCAACTGTGTCGGAT
TGTCGGAT
+
B?:4<A??
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTC.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTC.1.fastq
index e6d4d68..d967158 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTC.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTC.1.fastq
@@ -1,32 +1,32 @@
- at HiMom:7:1:2:1507
+ at machine1:HiMom:abcdeACXX:7:1:2:1507 :Y:0:AGCAATTC
NGGCTTGGAAAGTGTAGGAGGGAGAGTCAC
+
##############################
- at HiMom:7:1:2:658
+ at machine1:HiMom:abcdeACXX:7:1:2:658 :Y:0:AGCAATTC
NGATGCTTCTGTCCTAAGAAGCTTGAGACA
+
%%2632887412107753560555542255
- at HiMom:7:2:2:599
+ at machine1:HiMom:abcdeACXX:7:2:2:599 :N:0:AGCAATTC
NAAACAAAAAAGCTGATGGCCTGGCGGGGT
+
%.836844751583,38-)/8638######
- at HiMom:7:2:3:1133
+ at machine1:HiMom:abcdeACXX:7:2:3:1133 :Y:0:AGCAATTC
AGAAGCTTTCTATTCTGATCCCCAAGGAGT
+
BACBA>BB=1;?BA??5A>:@25<=.43;?
- at HiMom:7:2:3:157
+ at machine1:HiMom:abcdeACXX:7:2:3:157 :Y:0:AGCAATTC
TGGGTGGTTCAAACTAAGCAGTCCAACTGC
+
BACC at BBABBBBCBBCBBBBBB?AAB?B?A
- at HiMom:7:2:3:1602
+ at machine1:HiMom:abcdeACXX:7:2:3:1602 :Y:0:AGCAATTC
AATTCATGAATACTTTTCAGTCTTTAAAAA
+
BCBAAABBBBB?<@BAB?AA=?BBBBBBBB
- at HiMom:7:2:3:808
+ at machine1:HiMom:abcdeACXX:7:2:3:808 :N:0:AGCAATTC
NGAGTGTAATACAATGGTATGGATTTTAAC
+
##############################
- at HiMom:7:2:3:991
+ at machine1:HiMom:abcdeACXX:7:2:3:991 :Y:0:AGCAATTC
TGGAAGCCAGCCAAAGATACACTCTTGGCA
+
BABC>6BBCBBBBCAAA at BACB<<?BABBB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTC.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTC.barcode_1.fastq
index 96f11c2..f6603a3 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTC.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTC.barcode_1.fastq
@@ -1,32 +1,32 @@
- at HiMom:7:1:2:1507
+ at machine1:HiMom:abcdeACXX:7:1:2:1507 :Y:0:AGCAATTC
AGCAATTC
+
?2=@9A<>
- at HiMom:7:1:2:658
+ at machine1:HiMom:abcdeACXX:7:1:2:658 :Y:0:AGCAATTC
AGCAATTC
+
@7=@@@=;
- at HiMom:7:2:2:599
+ at machine1:HiMom:abcdeACXX:7:2:2:599 :N:0:AGCAATTC
AGCAATTC
+
:-8BABB?
- at HiMom:7:2:3:1133
+ at machine1:HiMom:abcdeACXX:7:2:3:1133 :Y:0:AGCAATTC
AGCAATTC
+
??9 at 5AB;
- at HiMom:7:2:3:157
+ at machine1:HiMom:abcdeACXX:7:2:3:157 :Y:0:AGCAATTC
AGCAATTC
+
BBB??CBA
- at HiMom:7:2:3:1602
+ at machine1:HiMom:abcdeACXX:7:2:3:1602 :Y:0:AGCAATTC
AGCAATTC
+
?6<A at B>8
- at HiMom:7:2:3:808
+ at machine1:HiMom:abcdeACXX:7:2:3:808 :N:0:AGCAATTC
AGCAATTC
+
>25:9?##
- at HiMom:7:2:3:991
+ at machine1:HiMom:abcdeACXX:7:2:3:991 :Y:0:AGCAATTC
AGCAATTC
+
BBAB at BB<
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTCTGCTCGAC.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTCTGCTCGAC.1.fastq
index baaeb61..f3139dd 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTCTGCTCGAC.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTCTGCTCGAC.1.fastq
@@ -1,32 +1,32 @@
- at HiMom:9:1:2:1507
+ at machine1:HiMom:abcdeACXX:9:1:2:1507 :Y:0:AGCAATTCTGCTCGAC
NGGCTTGGAAAGTGTAGGAGGGAGAGTCAC
+
##############################
- at HiMom:9:1:2:658
+ at machine1:HiMom:abcdeACXX:9:1:2:658 :Y:0:AGCAATTCTGCTCGAC
NGATGCTTCTGTCCTAAGAAGCTTGAGACA
+
%%2632887412107753560555542255
- at HiMom:9:2:2:599
+ at machine1:HiMom:abcdeACXX:9:2:2:599 :N:0:AGCAATTCTGCTCGAC
NAAACAAAAAAGCTGATGGCCTGGCGGGGT
+
%.836844751583,38-)/8638######
- at HiMom:9:2:3:1133
+ at machine1:HiMom:abcdeACXX:9:2:3:1133 :Y:0:AGCAATTCTGCTCGAC
AGAAGCTTTCTATTCTGATCCCCAAGGAGT
+
BACBA>BB=1;?BA??5A>:@25<=.43;?
- at HiMom:9:2:3:157
+ at machine1:HiMom:abcdeACXX:9:2:3:157 :Y:0:AGCAATTCTGCTCGAC
TGGGTGGTTCAAACTAAGCAGTCCAACTGC
+
BACC at BBABBBBCBBCBBBBBB?AAB?B?A
- at HiMom:9:2:3:1602
+ at machine1:HiMom:abcdeACXX:9:2:3:1602 :Y:0:AGCAATTCTGCTCGAC
AATTCATGAATACTTTTCAGTCTTTAAAAA
+
BCBAAABBBBB?<@BAB?AA=?BBBBBBBB
- at HiMom:9:2:3:808
+ at machine1:HiMom:abcdeACXX:9:2:3:808 :N:0:AGCAATTCTGCTCGAC
NGAGTGTAATACAATGGTATGGATTTTAAC
+
##############################
- at HiMom:9:2:3:991
+ at machine1:HiMom:abcdeACXX:9:2:3:991 :Y:0:AGCAATTCTGCTCGAC
TGGAAGCCAGCCAAAGATACACTCTTGGCA
+
BABC>6BBCBBBBCAAA at BACB<<?BABBB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTCTGCTCGAC.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTCTGCTCGAC.barcode_1.fastq
index 5b7c119..8d51016 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTCTGCTCGAC.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTCTGCTCGAC.barcode_1.fastq
@@ -1,32 +1,32 @@
- at HiMom:9:1:2:1507
+ at machine1:HiMom:abcdeACXX:9:1:2:1507 :Y:0:AGCAATTCTGCTCGAC
AGCAATTC
+
?2=@9A<>
- at HiMom:9:1:2:658
+ at machine1:HiMom:abcdeACXX:9:1:2:658 :Y:0:AGCAATTCTGCTCGAC
AGCAATTC
+
@7=@@@=;
- at HiMom:9:2:2:599
+ at machine1:HiMom:abcdeACXX:9:2:2:599 :N:0:AGCAATTCTGCTCGAC
AGCAATTC
+
:-8BABB?
- at HiMom:9:2:3:1133
+ at machine1:HiMom:abcdeACXX:9:2:3:1133 :Y:0:AGCAATTCTGCTCGAC
AGCAATTC
+
??9 at 5AB;
- at HiMom:9:2:3:157
+ at machine1:HiMom:abcdeACXX:9:2:3:157 :Y:0:AGCAATTCTGCTCGAC
AGCAATTC
+
BBB??CBA
- at HiMom:9:2:3:1602
+ at machine1:HiMom:abcdeACXX:9:2:3:1602 :Y:0:AGCAATTCTGCTCGAC
AGCAATTC
+
?6<A at B>8
- at HiMom:9:2:3:808
+ at machine1:HiMom:abcdeACXX:9:2:3:808 :N:0:AGCAATTCTGCTCGAC
AGCAATTC
+
>25:9?##
- at HiMom:9:2:3:991
+ at machine1:HiMom:abcdeACXX:9:2:3:991 :Y:0:AGCAATTCTGCTCGAC
AGCAATTC
+
BBAB at BB<
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTCTGCTCGAC.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTCTGCTCGAC.barcode_2.fastq
index f8c2096..93196d5 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTCTGCTCGAC.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTCTGCTCGAC.barcode_2.fastq
@@ -1,32 +1,32 @@
- at HiMom:9:1:2:1507
+ at machine1:HiMom:abcdeACXX:9:1:2:1507 :Y:0:AGCAATTCTGCTCGAC
TGCTCGAC
+
?2=@9A<>
- at HiMom:9:1:2:658
+ at machine1:HiMom:abcdeACXX:9:1:2:658 :Y:0:AGCAATTCTGCTCGAC
TGCTCGAC
+
@7=@@@=;
- at HiMom:9:2:2:599
+ at machine1:HiMom:abcdeACXX:9:2:2:599 :N:0:AGCAATTCTGCTCGAC
TGCTCGAC
+
:-8BABB?
- at HiMom:9:2:3:1133
+ at machine1:HiMom:abcdeACXX:9:2:3:1133 :Y:0:AGCAATTCTGCTCGAC
TGCTCGAC
+
??9 at 5AB;
- at HiMom:9:2:3:157
+ at machine1:HiMom:abcdeACXX:9:2:3:157 :Y:0:AGCAATTCTGCTCGAC
TGCTCGAC
+
BBB??CBA
- at HiMom:9:2:3:1602
+ at machine1:HiMom:abcdeACXX:9:2:3:1602 :Y:0:AGCAATTCTGCTCGAC
TGCTCGAC
+
?6<A at B>8
- at HiMom:9:2:3:808
+ at machine1:HiMom:abcdeACXX:9:2:3:808 :N:0:AGCAATTCTGCTCGAC
TGCTCGAC
+
>25:9?##
- at HiMom:9:2:3:991
+ at machine1:HiMom:abcdeACXX:9:2:3:991 :Y:0:AGCAATTCTGCTCGAC
TGCTCGAC
+
BBAB at BB<
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTT.1.fastq
index 6864836..efd45c4 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTT.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTT.1.fastq
@@ -1,32 +1,32 @@
- at HiMom:7:1:3:1341
+ at machine1:HiMom:abcdeACXX:7:1:3:1341 :Y:0:AGTTGCTT
TGAAGAGTTTCTGGCACATAGGCACTCAAC
+
B7AACB;>C7A??4AB<B>B:':@CAAAAB
- at HiMom:7:1:3:1861
+ at machine1:HiMom:abcdeACXX:7:1:3:1861 :Y:0:AGTTGCTT
NGATTAATGAATAGAGTGAATAGTGTCTGA
+
%-07:::5.3<<7788529:<<530:9646
- at HiMom:7:1:3:699
+ at machine1:HiMom:abcdeACXX:7:1:3:699 :N:0:AGTTGCTT
NTGTCTTCTTACACTATTTTTTTTAAAATC
+
##############################
- at HiMom:7:2:3:1962
+ at machine1:HiMom:abcdeACXX:7:2:3:1962 :Y:0:AGTTGCTT
ACTAAATCCAAGAGCACATCAAAATGTTAA
+
B5;BBB@@8 at BAB9>BBBABACB@@B;@BB
- at HiMom:7:2:3:274
+ at machine1:HiMom:abcdeACXX:7:2:3:274 :Y:0:AGTTGCTT
AGTGAAGTGCTTAGCACCTGGGCCAGCAGC
+
:57.:@@>96=@97>@=;=>;@;@=@9=9;
- at HiMom:7:2:3:640
+ at machine1:HiMom:abcdeACXX:7:2:3:640 :Y:0:AGTTGCTT
AGATTAAAAAAAAATGACGTGACAAATTAA
+
=6CBC at CABCBBCBC@>@=@ABBCCBBBCC
- at HiMom:7:2:3:691
+ at machine1:HiMom:abcdeACXX:7:2:3:691 :Y:0:AGTTGCTT
ATTTTCAAATCATAAATATGGATTGCTGTG
+
BBBABACBBA at ABBBBBBB727AB8+;B55
- at HiMom:7:2:3:72
+ at machine1:HiMom:abcdeACXX:7:2:3:72 :Y:0:AGTTGCTT
CTAGTCTTTGACTTATATCAATTCAGTATT
+
BBC?ACCCCCB at CCCCCCCBCCCCCA@BCC
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTT.barcode_1.fastq
index 49ea5fe..d3c3fdc 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTT.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTT.barcode_1.fastq
@@ -1,32 +1,32 @@
- at HiMom:7:1:3:1341
+ at machine1:HiMom:abcdeACXX:7:1:3:1341 :Y:0:AGTTGCTT
AGATGCTT
+
B#######
- at HiMom:7:1:3:1861
+ at machine1:HiMom:abcdeACXX:7:1:3:1861 :Y:0:AGTTGCTT
AGTTGCTT
+
B9@><A<C
- at HiMom:7:1:3:699
+ at machine1:HiMom:abcdeACXX:7:1:3:699 :N:0:AGTTGCTT
AGTTGCTT
+
98?>8>##
- at HiMom:7:2:3:1962
+ at machine1:HiMom:abcdeACXX:7:2:3:1962 :Y:0:AGTTGCTT
AGTTGCTT
+
A76 at 8=0=
- at HiMom:7:2:3:274
+ at machine1:HiMom:abcdeACXX:7:2:3:274 :Y:0:AGTTGCTT
AGTTGCTT
+
@@??<?BC
- at HiMom:7:2:3:640
+ at machine1:HiMom:abcdeACXX:7:2:3:640 :Y:0:AGTTGCTT
AGTTGCTT
+
A=BBB;<A
- at HiMom:7:2:3:691
+ at machine1:HiMom:abcdeACXX:7:2:3:691 :Y:0:AGTTGCTT
AGTTGCTT
+
@=8@>@?A
- at HiMom:7:2:3:72
+ at machine1:HiMom:abcdeACXX:7:2:3:72 :Y:0:AGTTGCTT
AGTTGCTT
+
BCBCA>BB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTTTCTGGCGA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTTTCTGGCGA.1.fastq
index d074f97..0e8e846 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTTTCTGGCGA.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTTTCTGGCGA.1.fastq
@@ -1,32 +1,32 @@
- at HiMom:9:1:3:1341
+ at machine1:HiMom:abcdeACXX:9:1:3:1341 :Y:0:AGTTGCTTTCTGGCGA
TGAAGAGTTTCTGGCACATAGGCACTCAAC
+
B7AACB;>C7A??4AB<B>B:':@CAAAAB
- at HiMom:9:1:3:1861
+ at machine1:HiMom:abcdeACXX:9:1:3:1861 :Y:0:AGTTGCTTTCTGGCGA
NGATTAATGAATAGAGTGAATAGTGTCTGA
+
%-07:::5.3<<7788529:<<530:9646
- at HiMom:9:1:3:699
+ at machine1:HiMom:abcdeACXX:9:1:3:699 :N:0:AGTTGCTTTCTGGCGA
NTGTCTTCTTACACTATTTTTTTTAAAATC
+
##############################
- at HiMom:9:2:3:1962
+ at machine1:HiMom:abcdeACXX:9:2:3:1962 :Y:0:AGTTGCTTTCTGGCGA
ACTAAATCCAAGAGCACATCAAAATGTTAA
+
B5;BBB@@8 at BAB9>BBBABACB@@B;@BB
- at HiMom:9:2:3:274
+ at machine1:HiMom:abcdeACXX:9:2:3:274 :Y:0:AGTTGCTTTCTGGCGA
AGTGAAGTGCTTAGCACCTGGGCCAGCAGC
+
:57.:@@>96=@97>@=;=>;@;@=@9=9;
- at HiMom:9:2:3:640
+ at machine1:HiMom:abcdeACXX:9:2:3:640 :Y:0:AGTTGCTTTCTGGCGA
AGATTAAAAAAAAATGACGTGACAAATTAA
+
=6CBC at CABCBBCBC@>@=@ABBCCBBBCC
- at HiMom:9:2:3:691
+ at machine1:HiMom:abcdeACXX:9:2:3:691 :Y:0:AGTTGCTTTCTGGCGA
ATTTTCAAATCATAAATATGGATTGCTGTG
+
BBBABACBBA at ABBBBBBB727AB8+;B55
- at HiMom:9:2:3:72
+ at machine1:HiMom:abcdeACXX:9:2:3:72 :Y:0:AGTTGCTTTCTGGCGA
CTAGTCTTTGACTTATATCAATTCAGTATT
+
BBC?ACCCCCB at CCCCCCCBCCCCCA@BCC
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTTTCTGGCGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTTTCTGGCGA.barcode_1.fastq
index f658475..de4d00e 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTTTCTGGCGA.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTTTCTGGCGA.barcode_1.fastq
@@ -1,32 +1,32 @@
- at HiMom:9:1:3:1341
+ at machine1:HiMom:abcdeACXX:9:1:3:1341 :Y:0:AGTTGCTTTCTGGCGA
AGATGCTT
+
B#######
- at HiMom:9:1:3:1861
+ at machine1:HiMom:abcdeACXX:9:1:3:1861 :Y:0:AGTTGCTTTCTGGCGA
AGTTGCTT
+
B9@><A<C
- at HiMom:9:1:3:699
+ at machine1:HiMom:abcdeACXX:9:1:3:699 :N:0:AGTTGCTTTCTGGCGA
AGTTGCTT
+
98?>8>##
- at HiMom:9:2:3:1962
+ at machine1:HiMom:abcdeACXX:9:2:3:1962 :Y:0:AGTTGCTTTCTGGCGA
AGTTGCTT
+
A76 at 8=0=
- at HiMom:9:2:3:274
+ at machine1:HiMom:abcdeACXX:9:2:3:274 :Y:0:AGTTGCTTTCTGGCGA
AGTTGCTT
+
@@??<?BC
- at HiMom:9:2:3:640
+ at machine1:HiMom:abcdeACXX:9:2:3:640 :Y:0:AGTTGCTTTCTGGCGA
AGTTGCTT
+
A=BBB;<A
- at HiMom:9:2:3:691
+ at machine1:HiMom:abcdeACXX:9:2:3:691 :Y:0:AGTTGCTTTCTGGCGA
AGTTGCTT
+
@=8@>@?A
- at HiMom:9:2:3:72
+ at machine1:HiMom:abcdeACXX:9:2:3:72 :Y:0:AGTTGCTTTCTGGCGA
AGTTGCTT
+
BCBCA>BB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTTTCTGGCGA.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTTTCTGGCGA.barcode_2.fastq
index 86cb86c..17ca9ad 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTTTCTGGCGA.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTTTCTGGCGA.barcode_2.fastq
@@ -1,32 +1,32 @@
- at HiMom:9:1:3:1341
+ at machine1:HiMom:abcdeACXX:9:1:3:1341 :Y:0:AGTTGCTTTCTGGCGA
TCTGGCGA
+
B#######
- at HiMom:9:1:3:1861
+ at machine1:HiMom:abcdeACXX:9:1:3:1861 :Y:0:AGTTGCTTTCTGGCGA
TCTGGCGA
+
B9@><A<C
- at HiMom:9:1:3:699
+ at machine1:HiMom:abcdeACXX:9:1:3:699 :N:0:AGTTGCTTTCTGGCGA
TCTGGCGA
+
98?>8>##
- at HiMom:9:2:3:1962
+ at machine1:HiMom:abcdeACXX:9:2:3:1962 :Y:0:AGTTGCTTTCTGGCGA
TCTGGCGA
+
A76 at 8=0=
- at HiMom:9:2:3:274
+ at machine1:HiMom:abcdeACXX:9:2:3:274 :Y:0:AGTTGCTTTCTGGCGA
TCTGGCGA
+
@@??<?BC
- at HiMom:9:2:3:640
+ at machine1:HiMom:abcdeACXX:9:2:3:640 :Y:0:AGTTGCTTTCTGGCGA
TCTGGCGA
+
A=BBB;<A
- at HiMom:9:2:3:691
+ at machine1:HiMom:abcdeACXX:9:2:3:691 :Y:0:AGTTGCTTTCTGGCGA
TCTGGCGA
+
@=8@>@?A
- at HiMom:9:2:3:72
+ at machine1:HiMom:abcdeACXX:9:2:3:72 :Y:0:AGTTGCTTTCTGGCGA
TCTGGCGA
+
BCBCA>BB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTT.1.fastq
index 1643100..2ae8e10 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTT.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTT.1.fastq
@@ -1,12 +1,12 @@
- at HiMom:7:1:3:1867
+ at machine1:HiMom:abcdeACXX:7:1:3:1867 :Y:0:ATTATGTT
AGAAGCATTCTCAGAAACTTATTTGTGATG
+
BB>81>BB?->?;07>4;B at BABB?:<@=:
- at HiMom:7:1:3:347
+ at machine1:HiMom:abcdeACXX:7:1:3:347 :N:0:ATTATGTT
NGTGGTGTGAGGTGTATCTGGGTCAGCAGG
+
##############################
- at HiMom:7:2:3:889
+ at machine1:HiMom:abcdeACXX:7:2:3:889 :N:0:ATTATGTT
NTTTTTATAACACCTCAGGCATCGTCAAAC
+
##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTT.barcode_1.fastq
index 7b04426..7086d40 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTT.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTT.barcode_1.fastq
@@ -1,12 +1,12 @@
- at HiMom:7:1:3:1867
+ at machine1:HiMom:abcdeACXX:7:1:3:1867 :Y:0:ATTATGTT
ATTATGTT
+
BBA at 79>B
- at HiMom:7:1:3:347
+ at machine1:HiMom:abcdeACXX:7:1:3:347 :N:0:ATTATGTT
ATTATGTT
+
4A>?@)6<
- at HiMom:7:2:3:889
+ at machine1:HiMom:abcdeACXX:7:2:3:889 :N:0:ATTATGTT
ATTATGTT
+
0A6=A<+A
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTTTCGGAATG.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTTTCGGAATG.1.fastq
index bd21d9c..c01ab5c 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTTTCGGAATG.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTTTCGGAATG.1.fastq
@@ -1,12 +1,12 @@
- at HiMom:9:1:3:1867
+ at machine1:HiMom:abcdeACXX:9:1:3:1867 :Y:0:ATTATGTTTCGGAATG
AGAAGCATTCTCAGAAACTTATTTGTGATG
+
BB>81>BB?->?;07>4;B at BABB?:<@=:
- at HiMom:9:1:3:347
+ at machine1:HiMom:abcdeACXX:9:1:3:347 :N:0:ATTATGTTTCGGAATG
NGTGGTGTGAGGTGTATCTGGGTCAGCAGG
+
##############################
- at HiMom:9:2:3:889
+ at machine1:HiMom:abcdeACXX:9:2:3:889 :N:0:ATTATGTTTCGGAATG
NTTTTTATAACACCTCAGGCATCGTCAAAC
+
##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTTTCGGAATG.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTTTCGGAATG.barcode_1.fastq
index 03fe4de..5d34be5 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTTTCGGAATG.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTTTCGGAATG.barcode_1.fastq
@@ -1,12 +1,12 @@
- at HiMom:9:1:3:1867
+ at machine1:HiMom:abcdeACXX:9:1:3:1867 :Y:0:ATTATGTTTCGGAATG
ATTATGTT
+
BBA at 79>B
- at HiMom:9:1:3:347
+ at machine1:HiMom:abcdeACXX:9:1:3:347 :N:0:ATTATGTTTCGGAATG
ATTATGTT
+
4A>?@)6<
- at HiMom:9:2:3:889
+ at machine1:HiMom:abcdeACXX:9:2:3:889 :N:0:ATTATGTTTCGGAATG
ATTATGTT
+
0A6=A<+A
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTTTCGGAATG.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTTTCGGAATG.barcode_2.fastq
index c44fa36..84ebff8 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTTTCGGAATG.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTTTCGGAATG.barcode_2.fastq
@@ -1,12 +1,12 @@
- at HiMom:9:1:3:1867
+ at machine1:HiMom:abcdeACXX:9:1:3:1867 :Y:0:ATTATGTTTCGGAATG
TCGGAATG
+
BBA at 79>B
- at HiMom:9:1:3:347
+ at machine1:HiMom:abcdeACXX:9:1:3:347 :N:0:ATTATGTTTCGGAATG
TCGGAATG
+
4A>?@)6<
- at HiMom:9:2:3:889
+ at machine1:HiMom:abcdeACXX:9:2:3:889 :N:0:ATTATGTTTCGGAATG
TCGGAATG
+
0A6=A<+A
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCT.1.fastq
index 4e2c306..739eb58 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCT.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCT.1.fastq
@@ -1,36 +1,36 @@
- at HiMom:7:1:2:1465
+ at machine1:HiMom:abcdeACXX:7:1:2:1465 :N:0:CACATCCT
NTTGTATTTCTGAAACCCCGAAGGGCATGG
+
##############################
- at HiMom:7:1:3:683
+ at machine1:HiMom:abcdeACXX:7:1:3:683 :Y:0:CACATCCT
NAAGTTTTTATTTATACGTAGAATTTATAC
+
%.611<<:;<98;<<<93993789<;<;9:
- at HiMom:7:1:3:751
+ at machine1:HiMom:abcdeACXX:7:1:3:751 :Y:0:CACATCCT
CACTTTTATTCTTAAGTACCACCTTCTGGA
+
6A=CCCCBCCCAAA??@CC8@@CCBC:>)@
- at HiMom:7:2:2:1012
+ at machine1:HiMom:abcdeACXX:7:2:2:1012 :Y:0:CACATCCT
NAGAAATACCATTTGACCCACCAATCCCAT
+
%066:::9636963567778::88895-58
- at HiMom:7:2:2:1402
+ at machine1:HiMom:abcdeACXX:7:2:2:1402 :N:0:CACATCCT
NGGATGGCTTCCAGTATGGGAACCTTTTCA
+
%.5484-/858865/78/(/62'/886555
- at HiMom:7:2:3:1094
+ at machine1:HiMom:abcdeACXX:7:2:3:1094 :Y:0:CACATCCT
CATATGGTATCACCACTCAGATACATAAAG
+
AABB<:=1CBBCBC@?AA@)>CCBBCCB?=
- at HiMom:7:2:3:16
+ at machine1:HiMom:abcdeACXX:7:2:3:16 :Y:0:CACATCCT
AGCTGGGCATGGTGATGCGCCCCTGTAATC
+
A;?;<<?@9?@@@@4=3)1 at 59??9<5.<2
- at HiMom:7:2:3:1712
+ at machine1:HiMom:abcdeACXX:7:2:3:1712 :Y:0:CACATCCT
AGTGCTGTGGCCTGGATGGATGTCAGGATT
+
>91:?5:=5:77>305>/;=>1:<B9694;
- at HiMom:7:2:3:328
+ at machine1:HiMom:abcdeACXX:7:2:3:328 :N:0:CACATCCT
AGCTTAATATAGCATAGCAGATAAGATTTG
+
(:*8>=,3:))<)?A<(8>###########
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCT.barcode_1.fastq
index 12d2016..209867c 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCT.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCT.barcode_1.fastq
@@ -1,36 +1,36 @@
- at HiMom:7:1:2:1465
+ at machine1:HiMom:abcdeACXX:7:1:2:1465 :N:0:CACATCCT
CACATCCT
+
<:@=BB@@
- at HiMom:7:1:3:683
+ at machine1:HiMom:abcdeACXX:7:1:3:683 :Y:0:CACATCCT
CACATCCT
+
B at 8@B?CB
- at HiMom:7:1:3:751
+ at machine1:HiMom:abcdeACXX:7:1:3:751 :Y:0:CACATCCT
CACATCCT
+
9 at CACCCC
- at HiMom:7:2:2:1012
+ at machine1:HiMom:abcdeACXX:7:2:2:1012 :Y:0:CACATCCT
CACATCCT
+
BB?BABBB
- at HiMom:7:2:2:1402
+ at machine1:HiMom:abcdeACXX:7:2:2:1402 :N:0:CACATCCT
CACATCCT
+
=@@BABCB
- at HiMom:7:2:3:1094
+ at machine1:HiMom:abcdeACXX:7:2:3:1094 :Y:0:CACATCCT
CACATCCT
+
ABCBC>:B
- at HiMom:7:2:3:16
+ at machine1:HiMom:abcdeACXX:7:2:3:16 :Y:0:CACATCCT
CACATCCT
+
<<4@@='@
- at HiMom:7:2:3:1712
+ at machine1:HiMom:abcdeACXX:7:2:3:1712 :Y:0:CACATCCT
CACATCCT
+
BB>@@?=>
- at HiMom:7:2:3:328
+ at machine1:HiMom:abcdeACXX:7:2:3:328 :N:0:CACATCCT
CAAATCCT
+
3<)):<(<
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCTTACTTAGC.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCTTACTTAGC.1.fastq
index a69b4a9..ba8f8d3 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCTTACTTAGC.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCTTACTTAGC.1.fastq
@@ -1,36 +1,36 @@
- at HiMom:9:1:2:1465
+ at machine1:HiMom:abcdeACXX:9:1:2:1465 :N:0:CACATCCTTACTTAGC
NTTGTATTTCTGAAACCCCGAAGGGCATGG
+
##############################
- at HiMom:9:1:3:683
+ at machine1:HiMom:abcdeACXX:9:1:3:683 :Y:0:CACATCCTTACTTAGC
NAAGTTTTTATTTATACGTAGAATTTATAC
+
%.611<<:;<98;<<<93993789<;<;9:
- at HiMom:9:1:3:751
+ at machine1:HiMom:abcdeACXX:9:1:3:751 :Y:0:CACATCCTTACTTAGC
CACTTTTATTCTTAAGTACCACCTTCTGGA
+
6A=CCCCBCCCAAA??@CC8@@CCBC:>)@
- at HiMom:9:2:2:1012
+ at machine1:HiMom:abcdeACXX:9:2:2:1012 :Y:0:CACATCCTTACTTAGC
NAGAAATACCATTTGACCCACCAATCCCAT
+
%066:::9636963567778::88895-58
- at HiMom:9:2:2:1402
+ at machine1:HiMom:abcdeACXX:9:2:2:1402 :N:0:CACATCCTTACTTAGC
NGGATGGCTTCCAGTATGGGAACCTTTTCA
+
%.5484-/858865/78/(/62'/886555
- at HiMom:9:2:3:1094
+ at machine1:HiMom:abcdeACXX:9:2:3:1094 :Y:0:CACATCCTTACTTAGC
CATATGGTATCACCACTCAGATACATAAAG
+
AABB<:=1CBBCBC@?AA@)>CCBBCCB?=
- at HiMom:9:2:3:16
+ at machine1:HiMom:abcdeACXX:9:2:3:16 :Y:0:CACATCCTTACTTAGC
AGCTGGGCATGGTGATGCGCCCCTGTAATC
+
A;?;<<?@9?@@@@4=3)1 at 59??9<5.<2
- at HiMom:9:2:3:1712
+ at machine1:HiMom:abcdeACXX:9:2:3:1712 :Y:0:CACATCCTTACTTAGC
AGTGCTGTGGCCTGGATGGATGTCAGGATT
+
>91:?5:=5:77>305>/;=>1:<B9694;
- at HiMom:9:2:3:328
+ at machine1:HiMom:abcdeACXX:9:2:3:328 :N:0:CACATCCTTACTTAGC
AGCTTAATATAGCATAGCAGATAAGATTTG
+
(:*8>=,3:))<)?A<(8>###########
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCTTACTTAGC.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCTTACTTAGC.barcode_1.fastq
index 417accc..1f3c848 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCTTACTTAGC.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCTTACTTAGC.barcode_1.fastq
@@ -1,36 +1,36 @@
- at HiMom:9:1:2:1465
+ at machine1:HiMom:abcdeACXX:9:1:2:1465 :N:0:CACATCCTTACTTAGC
CACATCCT
+
<:@=BB@@
- at HiMom:9:1:3:683
+ at machine1:HiMom:abcdeACXX:9:1:3:683 :Y:0:CACATCCTTACTTAGC
CACATCCT
+
B at 8@B?CB
- at HiMom:9:1:3:751
+ at machine1:HiMom:abcdeACXX:9:1:3:751 :Y:0:CACATCCTTACTTAGC
CACATCCT
+
9 at CACCCC
- at HiMom:9:2:2:1012
+ at machine1:HiMom:abcdeACXX:9:2:2:1012 :Y:0:CACATCCTTACTTAGC
CACATCCT
+
BB?BABBB
- at HiMom:9:2:2:1402
+ at machine1:HiMom:abcdeACXX:9:2:2:1402 :N:0:CACATCCTTACTTAGC
CACATCCT
+
=@@BABCB
- at HiMom:9:2:3:1094
+ at machine1:HiMom:abcdeACXX:9:2:3:1094 :Y:0:CACATCCTTACTTAGC
CACATCCT
+
ABCBC>:B
- at HiMom:9:2:3:16
+ at machine1:HiMom:abcdeACXX:9:2:3:16 :Y:0:CACATCCTTACTTAGC
CACATCCT
+
<<4@@='@
- at HiMom:9:2:3:1712
+ at machine1:HiMom:abcdeACXX:9:2:3:1712 :Y:0:CACATCCTTACTTAGC
CACATCCT
+
BB>@@?=>
- at HiMom:9:2:3:328
+ at machine1:HiMom:abcdeACXX:9:2:3:328 :N:0:CACATCCTTACTTAGC
CAAATCCT
+
3<)):<(<
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCTTACTTAGC.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCTTACTTAGC.barcode_2.fastq
index fc92bae..7d7b0f8 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCTTACTTAGC.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCTTACTTAGC.barcode_2.fastq
@@ -1,36 +1,36 @@
- at HiMom:9:1:2:1465
+ at machine1:HiMom:abcdeACXX:9:1:2:1465 :N:0:CACATCCTTACTTAGC
TACTTAGC
+
<:@=BB@@
- at HiMom:9:1:3:683
+ at machine1:HiMom:abcdeACXX:9:1:3:683 :Y:0:CACATCCTTACTTAGC
TACTTAGC
+
B at 8@B?CB
- at HiMom:9:1:3:751
+ at machine1:HiMom:abcdeACXX:9:1:3:751 :Y:0:CACATCCTTACTTAGC
TACTTAGC
+
9 at CACCCC
- at HiMom:9:2:2:1012
+ at machine1:HiMom:abcdeACXX:9:2:2:1012 :Y:0:CACATCCTTACTTAGC
TACTTAGC
+
BB?BABBB
- at HiMom:9:2:2:1402
+ at machine1:HiMom:abcdeACXX:9:2:2:1402 :N:0:CACATCCTTACTTAGC
TACTTAGC
+
=@@BABCB
- at HiMom:9:2:3:1094
+ at machine1:HiMom:abcdeACXX:9:2:3:1094 :Y:0:CACATCCTTACTTAGC
TACTTAGC
+
ABCBC>:B
- at HiMom:9:2:3:16
+ at machine1:HiMom:abcdeACXX:9:2:3:16 :Y:0:CACATCCTTACTTAGC
TACTTAGC
+
<<4@@='@
- at HiMom:9:2:3:1712
+ at machine1:HiMom:abcdeACXX:9:2:3:1712 :Y:0:CACATCCTTACTTAGC
TACTTAGC
+
BB>@@?=>
- at HiMom:9:2:3:328
+ at machine1:HiMom:abcdeACXX:9:2:3:328 :N:0:CACATCCTTACTTAGC
TACTTAGC
+
3<)):<(<
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCC.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCC.1.fastq
index 44d7567..e13284a 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCC.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCC.1.fastq
@@ -1,36 +1,36 @@
- at HiMom:7:1:2:1336
+ at machine1:HiMom:abcdeACXX:7:1:2:1336 :Y:0:CAGGAGCC
NAAGTCTAAAATTATCTTGAAGTAAAAAGT
+
%.75795:89<<<<4-7::58579<<<8.7
- at HiMom:7:1:2:1878
+ at machine1:HiMom:abcdeACXX:7:1:2:1878 :Y:0:CAGGAGCC
NAATACTGAGATGTATTTAAGGCTGACACT
+
%.9:957/3767079:::7:5/57::9999
- at HiMom:7:1:2:425
+ at machine1:HiMom:abcdeACXX:7:1:2:425 :Y:0:CAGGAGCC
NAATATATGCAAGACTCCTGTTATTAGAAA
+
%099:99055:726<<9<9977::9:::<<
- at HiMom:7:1:2:802
+ at machine1:HiMom:abcdeACXX:7:1:2:802 :Y:0:CAGGAGCC
NAAGTTAATTGTGTATTATTAACATCATTC
+
%/627<<<<444358<<::::989957972
- at HiMom:7:1:3:1927
+ at machine1:HiMom:abcdeACXX:7:1:3:1927 :N:0:CAGGAGCC
CACATCACCTTCTACTACATTTGAAATTCT
+
BCACA8B>C=BA?C8BC:'8=-5@)@=0=B
- at HiMom:7:2:2:303
+ at machine1:HiMom:abcdeACXX:7:2:2:303 :N:0:CAGGAGCC
NAGATCTTGTCTTTCAATCTTTTTAAATTC
+
##############################
- at HiMom:7:2:2:953
+ at machine1:HiMom:abcdeACXX:7:2:2:953 :N:0:CAGGAGCC
NGTTTAGTACATACTAGGTTTCACCAAATT
+
##############################
- at HiMom:7:2:3:151
+ at machine1:HiMom:abcdeACXX:7:2:3:151 :Y:0:CAGGAGCC
AGAGAACAGATAGGTCTGTCAGGGCTGACC
+
?>=99B>BA?B>)?;5AB;89;=6??<73>
- at HiMom:7:2:3:99
+ at machine1:HiMom:abcdeACXX:7:2:3:99 :N:0:CAGGAGCC
CATATCTGTGTTATTTTAGCATAAATTTGA
+
1 at +@31?('4(A;73>)?73))@))@C?##
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCC.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCC.barcode_1.fastq
index ef8167d..4779a34 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCC.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCC.barcode_1.fastq
@@ -1,36 +1,36 @@
- at HiMom:7:1:2:1336
+ at machine1:HiMom:abcdeACXX:7:1:2:1336 :Y:0:CAGGAGCC
CAGGAGCC
+
7 at 9=B=7@
- at HiMom:7:1:2:1878
+ at machine1:HiMom:abcdeACXX:7:1:2:1878 :Y:0:CAGGAGCC
CAGGAGCC
+
B<81<=7;
- at HiMom:7:1:2:425
+ at machine1:HiMom:abcdeACXX:7:1:2:425 :Y:0:CAGGAGCC
CAGGAGCC
+
AA@@=9;<
- at HiMom:7:1:2:802
+ at machine1:HiMom:abcdeACXX:7:1:2:802 :Y:0:CAGGAGCC
CAGGAGCC
+
=>0>?7>#
- at HiMom:7:1:3:1927
+ at machine1:HiMom:abcdeACXX:7:1:3:1927 :N:0:CAGGAGCC
CAGGAGCC
+
B@<@@=@?
- at HiMom:7:2:2:303
+ at machine1:HiMom:abcdeACXX:7:2:2:303 :N:0:CAGGAGCC
CAGGAGCC
+
A>*@@9##
- at HiMom:7:2:2:953
+ at machine1:HiMom:abcdeACXX:7:2:2:953 :N:0:CAGGAGCC
CAGGAACC
+
5(:9;';;
- at HiMom:7:2:3:151
+ at machine1:HiMom:abcdeACXX:7:2:3:151 :Y:0:CAGGAGCC
CAGGAGCC
+
@A8/;A==
- at HiMom:7:2:3:99
+ at machine1:HiMom:abcdeACXX:7:2:3:99 :N:0:CAGGAGCC
CAGGAGCG
+
(1;A;###
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCCGTATAACA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCCGTATAACA.1.fastq
index 7f00684..ec27872 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCCGTATAACA.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCCGTATAACA.1.fastq
@@ -1,36 +1,36 @@
- at HiMom:9:1:2:1336
+ at machine1:HiMom:abcdeACXX:9:1:2:1336 :Y:0:CAGGAGCCGTATAACA
NAAGTCTAAAATTATCTTGAAGTAAAAAGT
+
%.75795:89<<<<4-7::58579<<<8.7
- at HiMom:9:1:2:1878
+ at machine1:HiMom:abcdeACXX:9:1:2:1878 :Y:0:CAGGAGCCGTATAACA
NAATACTGAGATGTATTTAAGGCTGACACT
+
%.9:957/3767079:::7:5/57::9999
- at HiMom:9:1:2:425
+ at machine1:HiMom:abcdeACXX:9:1:2:425 :Y:0:CAGGAGCCGTATAACA
NAATATATGCAAGACTCCTGTTATTAGAAA
+
%099:99055:726<<9<9977::9:::<<
- at HiMom:9:1:2:802
+ at machine1:HiMom:abcdeACXX:9:1:2:802 :Y:0:CAGGAGCCGTATAACA
NAAGTTAATTGTGTATTATTAACATCATTC
+
%/627<<<<444358<<::::989957972
- at HiMom:9:1:3:1927
+ at machine1:HiMom:abcdeACXX:9:1:3:1927 :N:0:CAGGAGCCGTATAACA
CACATCACCTTCTACTACATTTGAAATTCT
+
BCACA8B>C=BA?C8BC:'8=-5@)@=0=B
- at HiMom:9:2:2:303
+ at machine1:HiMom:abcdeACXX:9:2:2:303 :N:0:CAGGAGCCGTATAACA
NAGATCTTGTCTTTCAATCTTTTTAAATTC
+
##############################
- at HiMom:9:2:2:953
+ at machine1:HiMom:abcdeACXX:9:2:2:953 :N:0:CAGGAGCCGTATAACA
NGTTTAGTACATACTAGGTTTCACCAAATT
+
##############################
- at HiMom:9:2:3:151
+ at machine1:HiMom:abcdeACXX:9:2:3:151 :Y:0:CAGGAGCCGTATAACA
AGAGAACAGATAGGTCTGTCAGGGCTGACC
+
?>=99B>BA?B>)?;5AB;89;=6??<73>
- at HiMom:9:2:3:99
+ at machine1:HiMom:abcdeACXX:9:2:3:99 :N:0:CAGGAGCCGTATAACA
CATATCTGTGTTATTTTAGCATAAATTTGA
+
1 at +@31?('4(A;73>)?73))@))@C?##
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCCGTATAACA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCCGTATAACA.barcode_1.fastq
index 9b0e584..5ad708c 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCCGTATAACA.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCCGTATAACA.barcode_1.fastq
@@ -1,36 +1,36 @@
- at HiMom:9:1:2:1336
+ at machine1:HiMom:abcdeACXX:9:1:2:1336 :Y:0:CAGGAGCCGTATAACA
CAGGAGCC
+
7 at 9=B=7@
- at HiMom:9:1:2:1878
+ at machine1:HiMom:abcdeACXX:9:1:2:1878 :Y:0:CAGGAGCCGTATAACA
CAGGAGCC
+
B<81<=7;
- at HiMom:9:1:2:425
+ at machine1:HiMom:abcdeACXX:9:1:2:425 :Y:0:CAGGAGCCGTATAACA
CAGGAGCC
+
AA@@=9;<
- at HiMom:9:1:2:802
+ at machine1:HiMom:abcdeACXX:9:1:2:802 :Y:0:CAGGAGCCGTATAACA
CAGGAGCC
+
=>0>?7>#
- at HiMom:9:1:3:1927
+ at machine1:HiMom:abcdeACXX:9:1:3:1927 :N:0:CAGGAGCCGTATAACA
CAGGAGCC
+
B@<@@=@?
- at HiMom:9:2:2:303
+ at machine1:HiMom:abcdeACXX:9:2:2:303 :N:0:CAGGAGCCGTATAACA
CAGGAGCC
+
A>*@@9##
- at HiMom:9:2:2:953
+ at machine1:HiMom:abcdeACXX:9:2:2:953 :N:0:CAGGAGCCGTATAACA
CAGGAACC
+
5(:9;';;
- at HiMom:9:2:3:151
+ at machine1:HiMom:abcdeACXX:9:2:3:151 :Y:0:CAGGAGCCGTATAACA
CAGGAGCC
+
@A8/;A==
- at HiMom:9:2:3:99
+ at machine1:HiMom:abcdeACXX:9:2:3:99 :N:0:CAGGAGCCGTATAACA
CAGGAGCG
+
(1;A;###
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCCGTATAACA.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCCGTATAACA.barcode_2.fastq
index 58a20e1..f2361f4 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCCGTATAACA.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCCGTATAACA.barcode_2.fastq
@@ -1,36 +1,36 @@
- at HiMom:9:1:2:1336
+ at machine1:HiMom:abcdeACXX:9:1:2:1336 :Y:0:CAGGAGCCGTATAACA
GTATAACA
+
7 at 9=B=7@
- at HiMom:9:1:2:1878
+ at machine1:HiMom:abcdeACXX:9:1:2:1878 :Y:0:CAGGAGCCGTATAACA
GTATAACA
+
B<81<=7;
- at HiMom:9:1:2:425
+ at machine1:HiMom:abcdeACXX:9:1:2:425 :Y:0:CAGGAGCCGTATAACA
GTATAACA
+
AA@@=9;<
- at HiMom:9:1:2:802
+ at machine1:HiMom:abcdeACXX:9:1:2:802 :Y:0:CAGGAGCCGTATAACA
GTATAACA
+
=>0>?7>#
- at HiMom:9:1:3:1927
+ at machine1:HiMom:abcdeACXX:9:1:3:1927 :N:0:CAGGAGCCGTATAACA
GTATAACA
+
B@<@@=@?
- at HiMom:9:2:2:303
+ at machine1:HiMom:abcdeACXX:9:2:2:303 :N:0:CAGGAGCCGTATAACA
GTATAACA
+
A>*@@9##
- at HiMom:9:2:2:953
+ at machine1:HiMom:abcdeACXX:9:2:2:953 :N:0:CAGGAGCCGTATAACA
GTATAACA
+
5(:9;';;
- at HiMom:9:2:3:151
+ at machine1:HiMom:abcdeACXX:9:2:3:151 :Y:0:CAGGAGCCGTATAACA
GTATAACA
+
@A8/;A==
- at HiMom:9:2:3:99
+ at machine1:HiMom:abcdeACXX:9:2:3:99 :N:0:CAGGAGCCGTATAACA
GTATAACA
+
(1;A;###
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGA.1.fastq
index 1ff81e0..27cd699 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGA.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGA.1.fastq
@@ -1,48 +1,48 @@
- at HiMom:7:1:2:119
+ at machine1:HiMom:abcdeACXX:7:1:2:119 :Y:0:CATAGCGA
NGATTGGAATCAACCCGAGTGGAATGGAAT
+
%06:75577786742-6-66///288517#
- at HiMom:7:1:2:1895
+ at machine1:HiMom:abcdeACXX:7:1:2:1895 :Y:0:CATAGCGA
NAAAACTTCTAAGTAATCATGAAGCTCTGC
+
%.7;9:::::<84:99989:<678<:6776
- at HiMom:7:1:2:190
+ at machine1:HiMom:abcdeACXX:7:1:2:190 :Y:0:CATAGCGA
NATAAGTGTATATTTATTTGTACCATGACA
+
%-;8694777:8;;9<:<<<<99998:996
- at HiMom:7:1:3:1513
+ at machine1:HiMom:abcdeACXX:7:1:3:1513 :Y:0:CATAGCGA
CACGCCACTGCGCCTGCAGCCTGGGCAATA
+
B=55 at AA6@=;>;>/;@@9@<>52<?@ABA
- at HiMom:7:1:3:277
+ at machine1:HiMom:abcdeACXX:7:1:3:277 :N:0:CATAGCGA
NGATGGGAAGGCCCCGGCCTGGGGAGGTGG
+
##############################
- at HiMom:7:2:2:463
+ at machine1:HiMom:abcdeACXX:7:2:2:463 :N:0:CATAGCGA
NGTGCTTGGGGGCGTCTGTGTTGATGCGTG
+
##############################
- at HiMom:7:2:2:611
+ at machine1:HiMom:abcdeACXX:7:2:2:611 :N:0:CATAGCGA
NGGAACCAGGCAGGGCCACACACAGGTAGC
+
##############################
- at HiMom:7:2:3:1016
+ at machine1:HiMom:abcdeACXX:7:2:3:1016 :Y:0:CATAGCGA
TGGCTCTGTCCTAATATCTTATTCTTACAA
+
<3=@BBA?@<=BBCC@>6>BBBBB at B?@AC
- at HiMom:7:2:3:1898
+ at machine1:HiMom:abcdeACXX:7:2:3:1898 :N:0:CATAGCGA
NTTGAATTGCTGGACTTCAATGTGTGTGGG
+
%08868:64680+0-5:8765255647522
- at HiMom:7:2:3:2013
+ at machine1:HiMom:abcdeACXX:7:2:3:2013 :N:0:CATAGCGA
AGCAGAAGCCTGCTGTGGGAACACTCAGTC
+
B?B###########################
- at HiMom:7:2:3:399
+ at machine1:HiMom:abcdeACXX:7:2:3:399 :Y:0:CATAGCGA
AGGGTATGTAAACCGAGTTTTGCGGGGGAT
+
A@@@>BBBBBAA>@;?B?BBAA>@:@:?AB
- at HiMom:7:2:3:983
+ at machine1:HiMom:abcdeACXX:7:2:3:983 :Y:0:CATAGCGA
TGTTTTTTATTTTAACAGATGAAGTACCAA
+
B=BCCCCCCCCCCCA>AACCBCC at AC@>BC
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGA.barcode_1.fastq
index c22c114..6ccf796 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGA.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGA.barcode_1.fastq
@@ -1,48 +1,48 @@
- at HiMom:7:1:2:119
+ at machine1:HiMom:abcdeACXX:7:1:2:119 :Y:0:CATAGCGA
CATAGCGA
+
?@>=;<CB
- at HiMom:7:1:2:1895
+ at machine1:HiMom:abcdeACXX:7:1:2:1895 :Y:0:CATAGCGA
CATAGCGA
+
?@CC@>BC
- at HiMom:7:1:2:190
+ at machine1:HiMom:abcdeACXX:7:1:2:190 :Y:0:CATAGCGA
CATAGCGA
+
AACC==@B
- at HiMom:7:1:3:1513
+ at machine1:HiMom:abcdeACXX:7:1:3:1513 :Y:0:CATAGCGA
CATAGCGA
+
5 at B=37 at B
- at HiMom:7:1:3:277
+ at machine1:HiMom:abcdeACXX:7:1:3:277 :N:0:CATAGCGA
CATAGCGA
+
BA?;3>B=
- at HiMom:7:2:2:463
+ at machine1:HiMom:abcdeACXX:7:2:2:463 :N:0:CATAGCGA
CNTAGCGA
+
:%98.(>9
- at HiMom:7:2:2:611
+ at machine1:HiMom:abcdeACXX:7:2:2:611 :N:0:CATAGCGA
CATAGCGA
+
8 at CCB=;@
- at HiMom:7:2:3:1016
+ at machine1:HiMom:abcdeACXX:7:2:3:1016 :Y:0:CATAGCGA
CATAGCGA
+
>@C@@1 at C
- at HiMom:7:2:3:1898
+ at machine1:HiMom:abcdeACXX:7:2:3:1898 :N:0:CATAGCGA
CATAGCGA
+
BBCB@=B@
- at HiMom:7:2:3:2013
+ at machine1:HiMom:abcdeACXX:7:2:3:2013 :N:0:CATAGCGA
CATAGCGA
+
7BCB<@?<
- at HiMom:7:2:3:399
+ at machine1:HiMom:abcdeACXX:7:2:3:399 :Y:0:CATAGCGA
CATAGCGA
+
=BB@==A@
- at HiMom:7:2:3:983
+ at machine1:HiMom:abcdeACXX:7:2:3:983 :Y:0:CATAGCGA
CATAGCGA
+
ACCC@?A?
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGAGGTCCAGA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGAGGTCCAGA.1.fastq
index e40d384..7b2474a 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGAGGTCCAGA.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGAGGTCCAGA.1.fastq
@@ -1,48 +1,48 @@
- at HiMom:9:1:2:119
+ at machine1:HiMom:abcdeACXX:9:1:2:119 :Y:0:CATAGCGAGGTCCAGA
NGATTGGAATCAACCCGAGTGGAATGGAAT
+
%06:75577786742-6-66///288517#
- at HiMom:9:1:2:1895
+ at machine1:HiMom:abcdeACXX:9:1:2:1895 :Y:0:CATAGCGAGGTCCAGA
NAAAACTTCTAAGTAATCATGAAGCTCTGC
+
%.7;9:::::<84:99989:<678<:6776
- at HiMom:9:1:2:190
+ at machine1:HiMom:abcdeACXX:9:1:2:190 :Y:0:CATAGCGAGGTCCAGA
NATAAGTGTATATTTATTTGTACCATGACA
+
%-;8694777:8;;9<:<<<<99998:996
- at HiMom:9:1:3:1513
+ at machine1:HiMom:abcdeACXX:9:1:3:1513 :Y:0:CATAGCGAGGTCCAGA
CACGCCACTGCGCCTGCAGCCTGGGCAATA
+
B=55 at AA6@=;>;>/;@@9@<>52<?@ABA
- at HiMom:9:1:3:277
+ at machine1:HiMom:abcdeACXX:9:1:3:277 :N:0:CATAGCGAGGTCCAGA
NGATGGGAAGGCCCCGGCCTGGGGAGGTGG
+
##############################
- at HiMom:9:2:2:463
+ at machine1:HiMom:abcdeACXX:9:2:2:463 :N:0:CATAGCGAGGTCCAGA
NGTGCTTGGGGGCGTCTGTGTTGATGCGTG
+
##############################
- at HiMom:9:2:2:611
+ at machine1:HiMom:abcdeACXX:9:2:2:611 :N:0:CATAGCGAGGTCCAGA
NGGAACCAGGCAGGGCCACACACAGGTAGC
+
##############################
- at HiMom:9:2:3:1016
+ at machine1:HiMom:abcdeACXX:9:2:3:1016 :Y:0:CATAGCGAGGTCCAGA
TGGCTCTGTCCTAATATCTTATTCTTACAA
+
<3=@BBA?@<=BBCC@>6>BBBBB at B?@AC
- at HiMom:9:2:3:1898
+ at machine1:HiMom:abcdeACXX:9:2:3:1898 :N:0:CATAGCGAGGTCCAGA
NTTGAATTGCTGGACTTCAATGTGTGTGGG
+
%08868:64680+0-5:8765255647522
- at HiMom:9:2:3:2013
+ at machine1:HiMom:abcdeACXX:9:2:3:2013 :N:0:CATAGCGAGGTCCAGA
AGCAGAAGCCTGCTGTGGGAACACTCAGTC
+
B?B###########################
- at HiMom:9:2:3:399
+ at machine1:HiMom:abcdeACXX:9:2:3:399 :Y:0:CATAGCGAGGTCCAGA
AGGGTATGTAAACCGAGTTTTGCGGGGGAT
+
A@@@>BBBBBAA>@;?B?BBAA>@:@:?AB
- at HiMom:9:2:3:983
+ at machine1:HiMom:abcdeACXX:9:2:3:983 :Y:0:CATAGCGAGGTCCAGA
TGTTTTTTATTTTAACAGATGAAGTACCAA
+
B=BCCCCCCCCCCCA>AACCBCC at AC@>BC
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGAGGTCCAGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGAGGTCCAGA.barcode_1.fastq
index 6852a17..a18a3f0 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGAGGTCCAGA.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGAGGTCCAGA.barcode_1.fastq
@@ -1,48 +1,48 @@
- at HiMom:9:1:2:119
+ at machine1:HiMom:abcdeACXX:9:1:2:119 :Y:0:CATAGCGAGGTCCAGA
CATAGCGA
+
?@>=;<CB
- at HiMom:9:1:2:1895
+ at machine1:HiMom:abcdeACXX:9:1:2:1895 :Y:0:CATAGCGAGGTCCAGA
CATAGCGA
+
?@CC@>BC
- at HiMom:9:1:2:190
+ at machine1:HiMom:abcdeACXX:9:1:2:190 :Y:0:CATAGCGAGGTCCAGA
CATAGCGA
+
AACC==@B
- at HiMom:9:1:3:1513
+ at machine1:HiMom:abcdeACXX:9:1:3:1513 :Y:0:CATAGCGAGGTCCAGA
CATAGCGA
+
5 at B=37 at B
- at HiMom:9:1:3:277
+ at machine1:HiMom:abcdeACXX:9:1:3:277 :N:0:CATAGCGAGGTCCAGA
CATAGCGA
+
BA?;3>B=
- at HiMom:9:2:2:463
+ at machine1:HiMom:abcdeACXX:9:2:2:463 :N:0:CATAGCGAGGTCCAGA
CNTAGCGA
+
:%98.(>9
- at HiMom:9:2:2:611
+ at machine1:HiMom:abcdeACXX:9:2:2:611 :N:0:CATAGCGAGGTCCAGA
CATAGCGA
+
8 at CCB=;@
- at HiMom:9:2:3:1016
+ at machine1:HiMom:abcdeACXX:9:2:3:1016 :Y:0:CATAGCGAGGTCCAGA
CATAGCGA
+
>@C@@1 at C
- at HiMom:9:2:3:1898
+ at machine1:HiMom:abcdeACXX:9:2:3:1898 :N:0:CATAGCGAGGTCCAGA
CATAGCGA
+
BBCB@=B@
- at HiMom:9:2:3:2013
+ at machine1:HiMom:abcdeACXX:9:2:3:2013 :N:0:CATAGCGAGGTCCAGA
CATAGCGA
+
7BCB<@?<
- at HiMom:9:2:3:399
+ at machine1:HiMom:abcdeACXX:9:2:3:399 :Y:0:CATAGCGAGGTCCAGA
CATAGCGA
+
=BB@==A@
- at HiMom:9:2:3:983
+ at machine1:HiMom:abcdeACXX:9:2:3:983 :Y:0:CATAGCGAGGTCCAGA
CATAGCGA
+
ACCC@?A?
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGAGGTCCAGA.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGAGGTCCAGA.barcode_2.fastq
index 4db2d75..4c51eff 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGAGGTCCAGA.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGAGGTCCAGA.barcode_2.fastq
@@ -1,48 +1,48 @@
- at HiMom:9:1:2:119
+ at machine1:HiMom:abcdeACXX:9:1:2:119 :Y:0:CATAGCGAGGTCCAGA
GGTCCAGA
+
?@>=;<CB
- at HiMom:9:1:2:1895
+ at machine1:HiMom:abcdeACXX:9:1:2:1895 :Y:0:CATAGCGAGGTCCAGA
GGTCCAGA
+
?@CC@>BC
- at HiMom:9:1:2:190
+ at machine1:HiMom:abcdeACXX:9:1:2:190 :Y:0:CATAGCGAGGTCCAGA
GGTCCAGA
+
AACC==@B
- at HiMom:9:1:3:1513
+ at machine1:HiMom:abcdeACXX:9:1:3:1513 :Y:0:CATAGCGAGGTCCAGA
GGTCCAGA
+
5 at B=37 at B
- at HiMom:9:1:3:277
+ at machine1:HiMom:abcdeACXX:9:1:3:277 :N:0:CATAGCGAGGTCCAGA
GGTCCAGA
+
BA?;3>B=
- at HiMom:9:2:2:463
+ at machine1:HiMom:abcdeACXX:9:2:2:463 :N:0:CATAGCGAGGTCCAGA
GGTCCAGA
+
:%98.(>9
- at HiMom:9:2:2:611
+ at machine1:HiMom:abcdeACXX:9:2:2:611 :N:0:CATAGCGAGGTCCAGA
GGTCCAGA
+
8 at CCB=;@
- at HiMom:9:2:3:1016
+ at machine1:HiMom:abcdeACXX:9:2:3:1016 :Y:0:CATAGCGAGGTCCAGA
GGTCCAGA
+
>@C@@1 at C
- at HiMom:9:2:3:1898
+ at machine1:HiMom:abcdeACXX:9:2:3:1898 :N:0:CATAGCGAGGTCCAGA
GGTCCAGA
+
BBCB@=B@
- at HiMom:9:2:3:2013
+ at machine1:HiMom:abcdeACXX:9:2:3:2013 :N:0:CATAGCGAGGTCCAGA
GGTCCAGA
+
7BCB<@?<
- at HiMom:9:2:3:399
+ at machine1:HiMom:abcdeACXX:9:2:3:399 :Y:0:CATAGCGAGGTCCAGA
GGTCCAGA
+
=BB@==A@
- at HiMom:9:2:3:983
+ at machine1:HiMom:abcdeACXX:9:2:3:983 :Y:0:CATAGCGAGGTCCAGA
GGTCCAGA
+
ACCC@?A?
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTA.1.fastq
index b12f767..fae42f1 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTA.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTA.1.fastq
@@ -1,20 +1,20 @@
- at HiMom:7:1:3:1525
+ at machine1:HiMom:abcdeACXX:7:1:3:1525 :Y:0:CATGCTTA
AGAAAATATCTGCATAGATGTGTTGAAGTC
+
BBBBBBAA@@?<3<:B=?B@@A at BAAA@=A
- at HiMom:7:2:2:679
+ at machine1:HiMom:abcdeACXX:7:2:2:679 :N:0:CATGCTTA
NCTCTGTCTCAAAAAATAAAAATAAAAATA
+
##############################
- at HiMom:7:2:3:1775
+ at machine1:HiMom:abcdeACXX:7:2:3:1775 :Y:0:CATGCTTA
NAATCCGACAATTATGTGTCTTGGAGTTGC
+
%.22301499988866456250*.424955
- at HiMom:7:2:3:584
+ at machine1:HiMom:abcdeACXX:7:2:3:584 :Y:0:CATGCTTA
AAAGTCCTGGGATTACAGGCATGAGCCACT
+
ABC2<@=>8;6=>?>3>-3<>B9@/=9A;<
- at HiMom:7:2:3:932
+ at machine1:HiMom:abcdeACXX:7:2:3:932 :Y:0:CATGCTTA
AGAAAGACAGACAGACAAACTGACTCTCAG
+
@>@C at 4A=?2 at B@.>ABABBBB>=A:;>@#
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTA.barcode_1.fastq
index 6b2a857..ebfad4f 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTA.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTA.barcode_1.fastq
@@ -1,20 +1,20 @@
- at HiMom:7:1:3:1525
+ at machine1:HiMom:abcdeACXX:7:1:3:1525 :Y:0:CATGCTTA
CATGCTTA
+
BBB;BBBB
- at HiMom:7:2:2:679
+ at machine1:HiMom:abcdeACXX:7:2:2:679 :N:0:CATGCTTA
CATGCTTA
+
5?@??8<@
- at HiMom:7:2:3:1775
+ at machine1:HiMom:abcdeACXX:7:2:3:1775 :Y:0:CATGCTTA
CATGCTTA
+
;<39<;@@
- at HiMom:7:2:3:584
+ at machine1:HiMom:abcdeACXX:7:2:3:584 :Y:0:CATGCTTA
CATGCTTA
+
>A??<CCC
- at HiMom:7:2:3:932
+ at machine1:HiMom:abcdeACXX:7:2:3:932 :Y:0:CATGCTTA
CATGCTTA
+
=C at AACCB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTAGCACATCT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTAGCACATCT.1.fastq
index 41b2e2d..eea26aa 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTAGCACATCT.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTAGCACATCT.1.fastq
@@ -1,20 +1,20 @@
- at HiMom:9:1:3:1525
+ at machine1:HiMom:abcdeACXX:9:1:3:1525 :Y:0:CATGCTTAGCACATCT
AGAAAATATCTGCATAGATGTGTTGAAGTC
+
BBBBBBAA@@?<3<:B=?B@@A at BAAA@=A
- at HiMom:9:2:2:679
+ at machine1:HiMom:abcdeACXX:9:2:2:679 :N:0:CATGCTTAGCACATCT
NCTCTGTCTCAAAAAATAAAAATAAAAATA
+
##############################
- at HiMom:9:2:3:1775
+ at machine1:HiMom:abcdeACXX:9:2:3:1775 :Y:0:CATGCTTAGCACATCT
NAATCCGACAATTATGTGTCTTGGAGTTGC
+
%.22301499988866456250*.424955
- at HiMom:9:2:3:584
+ at machine1:HiMom:abcdeACXX:9:2:3:584 :Y:0:CATGCTTAGCACATCT
AAAGTCCTGGGATTACAGGCATGAGCCACT
+
ABC2<@=>8;6=>?>3>-3<>B9@/=9A;<
- at HiMom:9:2:3:932
+ at machine1:HiMom:abcdeACXX:9:2:3:932 :Y:0:CATGCTTAGCACATCT
AGAAAGACAGACAGACAAACTGACTCTCAG
+
@>@C at 4A=?2 at B@.>ABABBBB>=A:;>@#
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTAGCACATCT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTAGCACATCT.barcode_1.fastq
index 78ddf07..c325e36 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTAGCACATCT.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTAGCACATCT.barcode_1.fastq
@@ -1,20 +1,20 @@
- at HiMom:9:1:3:1525
+ at machine1:HiMom:abcdeACXX:9:1:3:1525 :Y:0:CATGCTTAGCACATCT
CATGCTTA
+
BBB;BBBB
- at HiMom:9:2:2:679
+ at machine1:HiMom:abcdeACXX:9:2:2:679 :N:0:CATGCTTAGCACATCT
CATGCTTA
+
5?@??8<@
- at HiMom:9:2:3:1775
+ at machine1:HiMom:abcdeACXX:9:2:3:1775 :Y:0:CATGCTTAGCACATCT
CATGCTTA
+
;<39<;@@
- at HiMom:9:2:3:584
+ at machine1:HiMom:abcdeACXX:9:2:3:584 :Y:0:CATGCTTAGCACATCT
CATGCTTA
+
>A??<CCC
- at HiMom:9:2:3:932
+ at machine1:HiMom:abcdeACXX:9:2:3:932 :Y:0:CATGCTTAGCACATCT
CATGCTTA
+
=C at AACCB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTAGCACATCT.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTAGCACATCT.barcode_2.fastq
index 02a6c4e..b7db855 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTAGCACATCT.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTAGCACATCT.barcode_2.fastq
@@ -1,20 +1,20 @@
- at HiMom:9:1:3:1525
+ at machine1:HiMom:abcdeACXX:9:1:3:1525 :Y:0:CATGCTTAGCACATCT
GCACATCT
+
BBB;BBBB
- at HiMom:9:2:2:679
+ at machine1:HiMom:abcdeACXX:9:2:2:679 :N:0:CATGCTTAGCACATCT
GCACATCT
+
5?@??8<@
- at HiMom:9:2:3:1775
+ at machine1:HiMom:abcdeACXX:9:2:3:1775 :Y:0:CATGCTTAGCACATCT
GCACATCT
+
;<39<;@@
- at HiMom:9:2:3:584
+ at machine1:HiMom:abcdeACXX:9:2:3:584 :Y:0:CATGCTTAGCACATCT
GCACATCT
+
>A??<CCC
- at HiMom:9:2:3:932
+ at machine1:HiMom:abcdeACXX:9:2:3:932 :Y:0:CATGCTTAGCACATCT
GCACATCT
+
=C at AACCB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAG.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAG.1.fastq
index 800a1c6..36ae850 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAG.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAG.1.fastq
@@ -1,44 +1,44 @@
- at HiMom:7:1:3:1688
+ at machine1:HiMom:abcdeACXX:7:1:3:1688 :Y:0:CCAGTTAG
NCCTTCTTTACACACTGAGGAACTTAACCT
+
%..99999:9:7753564-357708:9777
- at HiMom:7:1:3:583
+ at machine1:HiMom:abcdeACXX:7:1:3:583 :Y:0:CCAGTTAG
GGCTTACACAGTCAAACTGGAGAGAAGTAG
+
(56=CCCC=B8BABBBC@:=BBAAA?, at A<
- at HiMom:7:1:3:996
+ at machine1:HiMom:abcdeACXX:7:1:3:996 :Y:0:CCAGTTAG
AAGGGAATTCTTGGACTTGATTAAATTGGT
+
=C9?6?BBB?6;6>;>A?BA?@2<@BB:##
- at HiMom:7:2:2:1671
+ at machine1:HiMom:abcdeACXX:7:2:2:1671 :N:0:CCAGTTAG
NGGGAATTACATGGAAAATGATCAAAGGAA
+
##############################
- at HiMom:7:2:2:1723
+ at machine1:HiMom:abcdeACXX:7:2:2:1723 :N:0:CCAGTTAG
NGAAGCTGACATTACAGGTTTCAGACACCA
+
##############################
- at HiMom:7:2:2:255
+ at machine1:HiMom:abcdeACXX:7:2:2:255 :Y:0:CCAGTTAG
NGGGTCCAAATAAGAGAAGGAGAAAAACAG
+
%00412036893057554167465;98977
- at HiMom:7:2:3:112
+ at machine1:HiMom:abcdeACXX:7:2:3:112 :Y:0:CCAGTTAG
NATGGAGTCTTGCTCTATTGCCCAGGCTGG
+
##############################
- at HiMom:7:2:3:1179
+ at machine1:HiMom:abcdeACXX:7:2:3:1179 :N:0:CCAGTTAG
ATTTAATAAATAAAGCAACCTGACAACTGA
+
@15;'88?A at 1/3='106/9A7.*:/08##
- at HiMom:7:2:3:1387
+ at machine1:HiMom:abcdeACXX:7:2:3:1387 :N:0:CCAGTTAG
NCGATTATGACTCTGAGAGAAAGTAGGGCA
+
##############################
- at HiMom:7:2:3:1484
+ at machine1:HiMom:abcdeACXX:7:2:3:1484 :Y:0:CCAGTTAG
CATCAACCTGTCACAAAATGACAAAACCTA
+
=A at 5@CB?B5@?B@@BBBB?ABCCBC at ABB
- at HiMom:7:2:3:1576
+ at machine1:HiMom:abcdeACXX:7:2:3:1576 :N:0:CCAGTTAG
NGAAACCACGTGCCCATTTTCAGTTCTGGT
+
%*/%.55663117868788787/765####
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAG.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAG.barcode_1.fastq
index e543f51..9de336b 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAG.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAG.barcode_1.fastq
@@ -1,44 +1,44 @@
- at HiMom:7:1:3:1688
+ at machine1:HiMom:abcdeACXX:7:1:3:1688 :Y:0:CCAGTTAG
CCAGTTAG
+
>@==;CA=
- at HiMom:7:1:3:583
+ at machine1:HiMom:abcdeACXX:7:1:3:583 :Y:0:CCAGTTAG
CCAGTTAG
+
=>93;CA>
- at HiMom:7:1:3:996
+ at machine1:HiMom:abcdeACXX:7:1:3:996 :Y:0:CCAGTTAG
CCAGTTAG
+
A at 5=>C<#
- at HiMom:7:2:2:1671
+ at machine1:HiMom:abcdeACXX:7:2:2:1671 :N:0:CCAGTTAG
CCAGTTAG
+
@>>B;BA9
- at HiMom:7:2:2:1723
+ at machine1:HiMom:abcdeACXX:7:2:2:1723 :N:0:CCAGTTAG
CCAATTAG
+
@A######
- at HiMom:7:2:2:255
+ at machine1:HiMom:abcdeACXX:7:2:2:255 :Y:0:CCAGTTAG
CCAGTTAG
+
A<?CAA@;
- at HiMom:7:2:3:112
+ at machine1:HiMom:abcdeACXX:7:2:3:112 :Y:0:CCAGTTAG
CCAGTTAG
+
B@<CAC at 6
- at HiMom:7:2:3:1179
+ at machine1:HiMom:abcdeACXX:7:2:3:1179 :N:0:CCAGTTAG
CCAGTTAG
+
);;9@@;#
- at HiMom:7:2:3:1387
+ at machine1:HiMom:abcdeACXX:7:2:3:1387 :N:0:CCAGTTAG
CCAGTTAG
+
;+B,232A
- at HiMom:7:2:3:1484
+ at machine1:HiMom:abcdeACXX:7:2:3:1484 :Y:0:CCAGTTAG
CCAGTTAG
+
>BAAAC@<
- at HiMom:7:2:3:1576
+ at machine1:HiMom:abcdeACXX:7:2:3:1576 :N:0:CCAGTTAG
CCAGTTAG
+
:B?=CACA
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAGGCACACGA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAGGCACACGA.1.fastq
index d9ab5d4..8bb1096 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAGGCACACGA.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAGGCACACGA.1.fastq
@@ -1,44 +1,44 @@
- at HiMom:9:1:3:1688
+ at machine1:HiMom:abcdeACXX:9:1:3:1688 :Y:0:CCAGTTAGGCACACGA
NCCTTCTTTACACACTGAGGAACTTAACCT
+
%..99999:9:7753564-357708:9777
- at HiMom:9:1:3:583
+ at machine1:HiMom:abcdeACXX:9:1:3:583 :Y:0:CCAGTTAGGCACACGA
GGCTTACACAGTCAAACTGGAGAGAAGTAG
+
(56=CCCC=B8BABBBC@:=BBAAA?, at A<
- at HiMom:9:1:3:996
+ at machine1:HiMom:abcdeACXX:9:1:3:996 :Y:0:CCAGTTAGGCACACGA
AAGGGAATTCTTGGACTTGATTAAATTGGT
+
=C9?6?BBB?6;6>;>A?BA?@2<@BB:##
- at HiMom:9:2:2:1671
+ at machine1:HiMom:abcdeACXX:9:2:2:1671 :N:0:CCAGTTAGGCACACGA
NGGGAATTACATGGAAAATGATCAAAGGAA
+
##############################
- at HiMom:9:2:2:1723
+ at machine1:HiMom:abcdeACXX:9:2:2:1723 :N:0:CCAGTTAGGCACACGA
NGAAGCTGACATTACAGGTTTCAGACACCA
+
##############################
- at HiMom:9:2:2:255
+ at machine1:HiMom:abcdeACXX:9:2:2:255 :Y:0:CCAGTTAGGCACACGA
NGGGTCCAAATAAGAGAAGGAGAAAAACAG
+
%00412036893057554167465;98977
- at HiMom:9:2:3:112
+ at machine1:HiMom:abcdeACXX:9:2:3:112 :Y:0:CCAGTTAGGCACACGA
NATGGAGTCTTGCTCTATTGCCCAGGCTGG
+
##############################
- at HiMom:9:2:3:1179
+ at machine1:HiMom:abcdeACXX:9:2:3:1179 :N:0:CCAGTTAGGCACACGA
ATTTAATAAATAAAGCAACCTGACAACTGA
+
@15;'88?A at 1/3='106/9A7.*:/08##
- at HiMom:9:2:3:1387
+ at machine1:HiMom:abcdeACXX:9:2:3:1387 :N:0:CCAGTTAGGCACACGA
NCGATTATGACTCTGAGAGAAAGTAGGGCA
+
##############################
- at HiMom:9:2:3:1484
+ at machine1:HiMom:abcdeACXX:9:2:3:1484 :Y:0:CCAGTTAGGCACACGA
CATCAACCTGTCACAAAATGACAAAACCTA
+
=A at 5@CB?B5@?B@@BBBB?ABCCBC at ABB
- at HiMom:9:2:3:1576
+ at machine1:HiMom:abcdeACXX:9:2:3:1576 :N:0:CCAGTTAGGCACACGA
NGAAACCACGTGCCCATTTTCAGTTCTGGT
+
%*/%.55663117868788787/765####
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAGGCACACGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAGGCACACGA.barcode_1.fastq
index 21cba4b..9891cd6 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAGGCACACGA.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAGGCACACGA.barcode_1.fastq
@@ -1,44 +1,44 @@
- at HiMom:9:1:3:1688
+ at machine1:HiMom:abcdeACXX:9:1:3:1688 :Y:0:CCAGTTAGGCACACGA
CCAGTTAG
+
>@==;CA=
- at HiMom:9:1:3:583
+ at machine1:HiMom:abcdeACXX:9:1:3:583 :Y:0:CCAGTTAGGCACACGA
CCAGTTAG
+
=>93;CA>
- at HiMom:9:1:3:996
+ at machine1:HiMom:abcdeACXX:9:1:3:996 :Y:0:CCAGTTAGGCACACGA
CCAGTTAG
+
A at 5=>C<#
- at HiMom:9:2:2:1671
+ at machine1:HiMom:abcdeACXX:9:2:2:1671 :N:0:CCAGTTAGGCACACGA
CCAGTTAG
+
@>>B;BA9
- at HiMom:9:2:2:1723
+ at machine1:HiMom:abcdeACXX:9:2:2:1723 :N:0:CCAGTTAGGCACACGA
CCAATTAG
+
@A######
- at HiMom:9:2:2:255
+ at machine1:HiMom:abcdeACXX:9:2:2:255 :Y:0:CCAGTTAGGCACACGA
CCAGTTAG
+
A<?CAA@;
- at HiMom:9:2:3:112
+ at machine1:HiMom:abcdeACXX:9:2:3:112 :Y:0:CCAGTTAGGCACACGA
CCAGTTAG
+
B@<CAC at 6
- at HiMom:9:2:3:1179
+ at machine1:HiMom:abcdeACXX:9:2:3:1179 :N:0:CCAGTTAGGCACACGA
CCAGTTAG
+
);;9@@;#
- at HiMom:9:2:3:1387
+ at machine1:HiMom:abcdeACXX:9:2:3:1387 :N:0:CCAGTTAGGCACACGA
CCAGTTAG
+
;+B,232A
- at HiMom:9:2:3:1484
+ at machine1:HiMom:abcdeACXX:9:2:3:1484 :Y:0:CCAGTTAGGCACACGA
CCAGTTAG
+
>BAAAC@<
- at HiMom:9:2:3:1576
+ at machine1:HiMom:abcdeACXX:9:2:3:1576 :N:0:CCAGTTAGGCACACGA
CCAGTTAG
+
:B?=CACA
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAGGCACACGA.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAGGCACACGA.barcode_2.fastq
index c416d9f..62a5fcb 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAGGCACACGA.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAGGCACACGA.barcode_2.fastq
@@ -1,44 +1,44 @@
- at HiMom:9:1:3:1688
+ at machine1:HiMom:abcdeACXX:9:1:3:1688 :Y:0:CCAGTTAGGCACACGA
GCACACGA
+
>@==;CA=
- at HiMom:9:1:3:583
+ at machine1:HiMom:abcdeACXX:9:1:3:583 :Y:0:CCAGTTAGGCACACGA
GCACACGA
+
=>93;CA>
- at HiMom:9:1:3:996
+ at machine1:HiMom:abcdeACXX:9:1:3:996 :Y:0:CCAGTTAGGCACACGA
GCACACGA
+
A at 5=>C<#
- at HiMom:9:2:2:1671
+ at machine1:HiMom:abcdeACXX:9:2:2:1671 :N:0:CCAGTTAGGCACACGA
GCACACGA
+
@>>B;BA9
- at HiMom:9:2:2:1723
+ at machine1:HiMom:abcdeACXX:9:2:2:1723 :N:0:CCAGTTAGGCACACGA
GCACACGA
+
@A######
- at HiMom:9:2:2:255
+ at machine1:HiMom:abcdeACXX:9:2:2:255 :Y:0:CCAGTTAGGCACACGA
GCACACGA
+
A<?CAA@;
- at HiMom:9:2:3:112
+ at machine1:HiMom:abcdeACXX:9:2:3:112 :Y:0:CCAGTTAGGCACACGA
GCACACGA
+
B@<CAC at 6
- at HiMom:9:2:3:1179
+ at machine1:HiMom:abcdeACXX:9:2:3:1179 :N:0:CCAGTTAGGCACACGA
GCACACGA
+
);;9@@;#
- at HiMom:9:2:3:1387
+ at machine1:HiMom:abcdeACXX:9:2:3:1387 :N:0:CCAGTTAGGCACACGA
GCACACGA
+
;+B,232A
- at HiMom:9:2:3:1484
+ at machine1:HiMom:abcdeACXX:9:2:3:1484 :Y:0:CCAGTTAGGCACACGA
GCACACGA
+
>BAAAC@<
- at HiMom:9:2:3:1576
+ at machine1:HiMom:abcdeACXX:9:2:3:1576 :N:0:CCAGTTAGGCACACGA
GCACACGA
+
:B?=CACA
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCAT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCAT.1.fastq
index 1c0467c..b2a2949 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCAT.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCAT.1.fastq
@@ -1,8 +1,8 @@
- at HiMom:7:1:2:636
+ at machine1:HiMom:abcdeACXX:7:1:2:636 :N:0:CCTACCAT
NGATCATTTACTGTTGTCAACTACCAAAAT
+
%/72'+769621513-1-563202356557
- at HiMom:7:2:3:875
+ at machine1:HiMom:abcdeACXX:7:2:3:875 :N:0:CCTACCAT
AGGCAGTAGTCTAATCCCGAGGATCCCAAG
+
:,73=@?<.=@;??@::3?8)5<=9%:?>7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCAT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCAT.barcode_1.fastq
index c95dfcc..194905a 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCAT.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCAT.barcode_1.fastq
@@ -1,8 +1,8 @@
- at HiMom:7:1:2:636
+ at machine1:HiMom:abcdeACXX:7:1:2:636 :N:0:CCTACCAT
CCTACCAT
+
63<@A?B=
- at HiMom:7:2:3:875
+ at machine1:HiMom:abcdeACXX:7:2:3:875 :N:0:CCTACCAT
CCTACCAT
+
;=@@@8 at B
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCATCTACCAGG.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCATCTACCAGG.1.fastq
index 0274ef2..96084b9 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCATCTACCAGG.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCATCTACCAGG.1.fastq
@@ -1,8 +1,8 @@
- at HiMom:9:1:2:636
+ at machine1:HiMom:abcdeACXX:9:1:2:636 :N:0:CCTACCATCTACCAGG
NGATCATTTACTGTTGTCAACTACCAAAAT
+
%/72'+769621513-1-563202356557
- at HiMom:9:2:3:875
+ at machine1:HiMom:abcdeACXX:9:2:3:875 :N:0:CCTACCATCTACCAGG
AGGCAGTAGTCTAATCCCGAGGATCCCAAG
+
:,73=@?<.=@;??@::3?8)5<=9%:?>7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCATCTACCAGG.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCATCTACCAGG.barcode_1.fastq
index 5f58846..b2ac984 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCATCTACCAGG.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCATCTACCAGG.barcode_1.fastq
@@ -1,8 +1,8 @@
- at HiMom:9:1:2:636
+ at machine1:HiMom:abcdeACXX:9:1:2:636 :N:0:CCTACCATCTACCAGG
CCTACCAT
+
63<@A?B=
- at HiMom:9:2:3:875
+ at machine1:HiMom:abcdeACXX:9:2:3:875 :N:0:CCTACCATCTACCAGG
CCTACCAT
+
;=@@@8 at B
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCATCTACCAGG.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCATCTACCAGG.barcode_2.fastq
index 424b9c2..626028b 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCATCTACCAGG.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCATCTACCAGG.barcode_2.fastq
@@ -1,8 +1,8 @@
- at HiMom:9:1:2:636
+ at machine1:HiMom:abcdeACXX:9:1:2:636 :N:0:CCTACCATCTACCAGG
CTACCAGG
+
63<@A?B=
- at HiMom:9:2:3:875
+ at machine1:HiMom:abcdeACXX:9:2:3:875 :N:0:CCTACCATCTACCAGG
CTACCAGG
+
;=@@@8 at B
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGG.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGG.1.fastq
index 399f535..b45415d 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGG.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGG.1.fastq
@@ -1,24 +1,24 @@
- at HiMom:7:1:2:1995
+ at machine1:HiMom:abcdeACXX:7:1:2:1995 :Y:0:CTACCAGG
NATTTCCTGAACACAGCACAGGGAAGAGGA
+
%/78777738777:8877786776858225
- at HiMom:7:1:3:1358
+ at machine1:HiMom:abcdeACXX:7:1:3:1358 :N:0:CTACCAGG
NTCCTTCCTCAAGGGGACCCCGCCTCCCCT
+
##############################
- at HiMom:7:1:3:176
+ at machine1:HiMom:abcdeACXX:7:1:3:176 :Y:0:CTACCAGG
ATATTTCATGAAAGACATAAATTTACAGTT
+
BBBCCB at BBBABBBB?ABBBBBBBBABB at B
- at HiMom:7:1:3:198
+ at machine1:HiMom:abcdeACXX:7:1:3:198 :Y:0:CTACCAGG
TATAATTTAATGGTTTTTATATATTCAGAG
+
BBC=BBCCA=@=8<BCBCBBABBCB=BB<9
- at HiMom:7:1:3:900
+ at machine1:HiMom:abcdeACXX:7:1:3:900 :N:0:CTACCAGG
TGAATCTTTGTTCAACACAGATTATTCCAG
+
)>@+5*<B1':(5,23A>5)@:)(/>:=##
- at HiMom:7:2:3:1970
+ at machine1:HiMom:abcdeACXX:7:2:3:1970 :Y:0:CTACCAGG
NTAATACTCTTTGAGAAAGGACTGAGGGAA
+
%.:77558:68862.3;8455:0057535;
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGG.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGG.barcode_1.fastq
index 075f3e3..95d94ae 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGG.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGG.barcode_1.fastq
@@ -1,24 +1,24 @@
- at HiMom:7:1:2:1995
+ at machine1:HiMom:abcdeACXX:7:1:2:1995 :Y:0:CTACCAGG
CTACCAGG
+
B=AA?BBA
- at HiMom:7:1:3:1358
+ at machine1:HiMom:abcdeACXX:7:1:3:1358 :N:0:CTACCAGG
CTACAAGG
+
62BB####
- at HiMom:7:1:3:176
+ at machine1:HiMom:abcdeACXX:7:1:3:176 :Y:0:CTACCAGG
CTACCAGG
+
ABBB?ABB
- at HiMom:7:1:3:198
+ at machine1:HiMom:abcdeACXX:7:1:3:198 :Y:0:CTACCAGG
CTACCAGG
+
ABBBAA?@
- at HiMom:7:1:3:900
+ at machine1:HiMom:abcdeACXX:7:1:3:900 :N:0:CTACCAGG
CTCCCAGG
+
(((.A at 85
- at HiMom:7:2:3:1970
+ at machine1:HiMom:abcdeACXX:7:2:3:1970 :Y:0:CTACCAGG
CTACCAGG
+
BABBBAB@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGGCCTACCAT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGGCCTACCAT.1.fastq
index d9cba2e..23d3451 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGGCCTACCAT.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGGCCTACCAT.1.fastq
@@ -1,24 +1,24 @@
- at HiMom:9:1:2:1995
+ at machine1:HiMom:abcdeACXX:9:1:2:1995 :Y:0:CTACCAGGCCTACCAT
NATTTCCTGAACACAGCACAGGGAAGAGGA
+
%/78777738777:8877786776858225
- at HiMom:9:1:3:1358
+ at machine1:HiMom:abcdeACXX:9:1:3:1358 :N:0:CTACCAGGCCTACCAT
NTCCTTCCTCAAGGGGACCCCGCCTCCCCT
+
##############################
- at HiMom:9:1:3:176
+ at machine1:HiMom:abcdeACXX:9:1:3:176 :Y:0:CTACCAGGCCTACCAT
ATATTTCATGAAAGACATAAATTTACAGTT
+
BBBCCB at BBBABBBB?ABBBBBBBBABB at B
- at HiMom:9:1:3:198
+ at machine1:HiMom:abcdeACXX:9:1:3:198 :Y:0:CTACCAGGCCTACCAT
TATAATTTAATGGTTTTTATATATTCAGAG
+
BBC=BBCCA=@=8<BCBCBBABBCB=BB<9
- at HiMom:9:1:3:900
+ at machine1:HiMom:abcdeACXX:9:1:3:900 :N:0:CTACCAGGCCTACCAT
TGAATCTTTGTTCAACACAGATTATTCCAG
+
)>@+5*<B1':(5,23A>5)@:)(/>:=##
- at HiMom:9:2:3:1970
+ at machine1:HiMom:abcdeACXX:9:2:3:1970 :Y:0:CTACCAGGCCTACCAT
NTAATACTCTTTGAGAAAGGACTGAGGGAA
+
%.:77558:68862.3;8455:0057535;
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGGCCTACCAT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGGCCTACCAT.barcode_1.fastq
index a0d64d5..fc9c0d0 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGGCCTACCAT.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGGCCTACCAT.barcode_1.fastq
@@ -1,24 +1,24 @@
- at HiMom:9:1:2:1995
+ at machine1:HiMom:abcdeACXX:9:1:2:1995 :Y:0:CTACCAGGCCTACCAT
CTACCAGG
+
B=AA?BBA
- at HiMom:9:1:3:1358
+ at machine1:HiMom:abcdeACXX:9:1:3:1358 :N:0:CTACCAGGCCTACCAT
CTACAAGG
+
62BB####
- at HiMom:9:1:3:176
+ at machine1:HiMom:abcdeACXX:9:1:3:176 :Y:0:CTACCAGGCCTACCAT
CTACCAGG
+
ABBB?ABB
- at HiMom:9:1:3:198
+ at machine1:HiMom:abcdeACXX:9:1:3:198 :Y:0:CTACCAGGCCTACCAT
CTACCAGG
+
ABBBAA?@
- at HiMom:9:1:3:900
+ at machine1:HiMom:abcdeACXX:9:1:3:900 :N:0:CTACCAGGCCTACCAT
CTCCCAGG
+
(((.A at 85
- at HiMom:9:2:3:1970
+ at machine1:HiMom:abcdeACXX:9:2:3:1970 :Y:0:CTACCAGGCCTACCAT
CTACCAGG
+
BABBBAB@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGGCCTACCAT.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGGCCTACCAT.barcode_2.fastq
index 715cf8c..20a2a23 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGGCCTACCAT.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGGCCTACCAT.barcode_2.fastq
@@ -1,24 +1,24 @@
- at HiMom:9:1:2:1995
+ at machine1:HiMom:abcdeACXX:9:1:2:1995 :Y:0:CTACCAGGCCTACCAT
CCTACCAT
+
B=AA?BBA
- at HiMom:9:1:3:1358
+ at machine1:HiMom:abcdeACXX:9:1:3:1358 :N:0:CTACCAGGCCTACCAT
CCTACCAT
+
62BB####
- at HiMom:9:1:3:176
+ at machine1:HiMom:abcdeACXX:9:1:3:176 :Y:0:CTACCAGGCCTACCAT
CCTACCAT
+
ABBB?ABB
- at HiMom:9:1:3:198
+ at machine1:HiMom:abcdeACXX:9:1:3:198 :Y:0:CTACCAGGCCTACCAT
CCTACCAT
+
ABBBAA?@
- at HiMom:9:1:3:900
+ at machine1:HiMom:abcdeACXX:9:1:3:900 :N:0:CTACCAGGCCTACCAT
CCTACCAT
+
(((.A at 85
- at HiMom:9:2:3:1970
+ at machine1:HiMom:abcdeACXX:9:2:3:1970 :Y:0:CTACCAGGCCTACCAT
CCTACCAT
+
BABBBAB@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGA.1.fastq
index 121cb84..591d507 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGA.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGA.1.fastq
@@ -1,36 +1,36 @@
- at HiMom:7:1:3:1311
+ at machine1:HiMom:abcdeACXX:7:1:3:1311 :Y:0:GCACACGA
AGACATAAAACCAGAGAGAAGATAGTGGGT
+
@@@BBBBCBA;>B>ABBBBBBBBA?;9:3>
- at HiMom:7:1:3:1544
+ at machine1:HiMom:abcdeACXX:7:1:3:1544 :N:0:GCACACGA
CGTGGATGGTTTTGATGAGTCCCACTGCAC
+
=@=<)*@22375A9@?36(768@:'897<#
- at HiMom:7:1:3:301
+ at machine1:HiMom:abcdeACXX:7:1:3:301 :N:0:GCACACGA
NTACGTGTGTGGCTGGATAGTCTGGACCAT
+
##############################
- at HiMom:7:1:3:959
+ at machine1:HiMom:abcdeACXX:7:1:3:959 :Y:0:GCACACGA
NAAAGTTTCCTGTGAGAAGGCGCATGGCAT
+
%.52-487848866757#############
- at HiMom:7:2:2:184
+ at machine1:HiMom:abcdeACXX:7:2:2:184 :N:0:GCACACGA
NGAAACGTTTTTCGGTTGAGGAAACTTTTT
+
##############################
- at HiMom:7:2:3:1025
+ at machine1:HiMom:abcdeACXX:7:2:3:1025 :Y:0:GCACACGA
NAATGGAAAGGAGTCCAATGGAAGGGAATC
+
%/4626885-+3-3777:532570313837
- at HiMom:7:2:3:1290
+ at machine1:HiMom:abcdeACXX:7:2:3:1290 :N:0:GCACACGA
NTCACCTGAATCCACGTTAGCTGGGGAAGA
+
##############################
- at HiMom:7:2:3:1917
+ at machine1:HiMom:abcdeACXX:7:2:3:1917 :N:0:GCACACGA
NTCCACAAAAAAAAAAAAAATTAGTTGGGT
+
%*6<737<4756##################
- at HiMom:7:2:3:495
+ at machine1:HiMom:abcdeACXX:7:2:3:495 :N:0:GCACACGA
NTCCGTTTTTATAACTGTAAATTTATCACT
+
##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGA.barcode_1.fastq
index 7b04eec..97f5863 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGA.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGA.barcode_1.fastq
@@ -1,36 +1,36 @@
- at HiMom:7:1:3:1311
+ at machine1:HiMom:abcdeACXX:7:1:3:1311 :Y:0:GCACACGA
GCACACGA
+
<?BAA at AB
- at HiMom:7:1:3:1544
+ at machine1:HiMom:abcdeACXX:7:1:3:1544 :N:0:GCACACGA
GCACACGA
+
((<.;;1;
- at HiMom:7:1:3:301
+ at machine1:HiMom:abcdeACXX:7:1:3:301 :N:0:GCACACGA
GCACACGA
+
########
- at HiMom:7:1:3:959
+ at machine1:HiMom:abcdeACXX:7:1:3:959 :Y:0:GCACACGA
GCACACGA
+
3?;AB?=<
- at HiMom:7:2:2:184
+ at machine1:HiMom:abcdeACXX:7:2:2:184 :N:0:GCACACGA
GCACACGA
+
>;<@A@@3
- at HiMom:7:2:3:1025
+ at machine1:HiMom:abcdeACXX:7:2:3:1025 :Y:0:GCACACGA
GCACACGA
+
@=ABA@@@
- at HiMom:7:2:3:1290
+ at machine1:HiMom:abcdeACXX:7:2:3:1290 :N:0:GCACACGA
GCACACGA
+
)5;=@<(;
- at HiMom:7:2:3:1917
+ at machine1:HiMom:abcdeACXX:7:2:3:1917 :N:0:GCACACGA
GCACACGA
+
/5;@=;B9
- at HiMom:7:2:3:495
+ at machine1:HiMom:abcdeACXX:7:2:3:495 :N:0:GCACACGA
GCACACGA
+
5;5<A@=;
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGACCAGTTAG.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGACCAGTTAG.1.fastq
index 41e7d43..967a3bb 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGACCAGTTAG.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGACCAGTTAG.1.fastq
@@ -1,36 +1,36 @@
- at HiMom:9:1:3:1311
+ at machine1:HiMom:abcdeACXX:9:1:3:1311 :Y:0:GCACACGACCAGTTAG
AGACATAAAACCAGAGAGAAGATAGTGGGT
+
@@@BBBBCBA;>B>ABBBBBBBBA?;9:3>
- at HiMom:9:1:3:1544
+ at machine1:HiMom:abcdeACXX:9:1:3:1544 :N:0:GCACACGACCAGTTAG
CGTGGATGGTTTTGATGAGTCCCACTGCAC
+
=@=<)*@22375A9@?36(768@:'897<#
- at HiMom:9:1:3:301
+ at machine1:HiMom:abcdeACXX:9:1:3:301 :N:0:GCACACGACCAGTTAG
NTACGTGTGTGGCTGGATAGTCTGGACCAT
+
##############################
- at HiMom:9:1:3:959
+ at machine1:HiMom:abcdeACXX:9:1:3:959 :Y:0:GCACACGACCAGTTAG
NAAAGTTTCCTGTGAGAAGGCGCATGGCAT
+
%.52-487848866757#############
- at HiMom:9:2:2:184
+ at machine1:HiMom:abcdeACXX:9:2:2:184 :N:0:GCACACGACCAGTTAG
NGAAACGTTTTTCGGTTGAGGAAACTTTTT
+
##############################
- at HiMom:9:2:3:1025
+ at machine1:HiMom:abcdeACXX:9:2:3:1025 :Y:0:GCACACGACCAGTTAG
NAATGGAAAGGAGTCCAATGGAAGGGAATC
+
%/4626885-+3-3777:532570313837
- at HiMom:9:2:3:1290
+ at machine1:HiMom:abcdeACXX:9:2:3:1290 :N:0:GCACACGACCAGTTAG
NTCACCTGAATCCACGTTAGCTGGGGAAGA
+
##############################
- at HiMom:9:2:3:1917
+ at machine1:HiMom:abcdeACXX:9:2:3:1917 :N:0:GCACACGACCAGTTAG
NTCCACAAAAAAAAAAAAAATTAGTTGGGT
+
%*6<737<4756##################
- at HiMom:9:2:3:495
+ at machine1:HiMom:abcdeACXX:9:2:3:495 :N:0:GCACACGACCAGTTAG
NTCCGTTTTTATAACTGTAAATTTATCACT
+
##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGACCAGTTAG.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGACCAGTTAG.barcode_1.fastq
index c999499..6c2aa56 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGACCAGTTAG.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGACCAGTTAG.barcode_1.fastq
@@ -1,36 +1,36 @@
- at HiMom:9:1:3:1311
+ at machine1:HiMom:abcdeACXX:9:1:3:1311 :Y:0:GCACACGACCAGTTAG
GCACACGA
+
<?BAA at AB
- at HiMom:9:1:3:1544
+ at machine1:HiMom:abcdeACXX:9:1:3:1544 :N:0:GCACACGACCAGTTAG
GCACACGA
+
((<.;;1;
- at HiMom:9:1:3:301
+ at machine1:HiMom:abcdeACXX:9:1:3:301 :N:0:GCACACGACCAGTTAG
GCACACGA
+
########
- at HiMom:9:1:3:959
+ at machine1:HiMom:abcdeACXX:9:1:3:959 :Y:0:GCACACGACCAGTTAG
GCACACGA
+
3?;AB?=<
- at HiMom:9:2:2:184
+ at machine1:HiMom:abcdeACXX:9:2:2:184 :N:0:GCACACGACCAGTTAG
GCACACGA
+
>;<@A@@3
- at HiMom:9:2:3:1025
+ at machine1:HiMom:abcdeACXX:9:2:3:1025 :Y:0:GCACACGACCAGTTAG
GCACACGA
+
@=ABA@@@
- at HiMom:9:2:3:1290
+ at machine1:HiMom:abcdeACXX:9:2:3:1290 :N:0:GCACACGACCAGTTAG
GCACACGA
+
)5;=@<(;
- at HiMom:9:2:3:1917
+ at machine1:HiMom:abcdeACXX:9:2:3:1917 :N:0:GCACACGACCAGTTAG
GCACACGA
+
/5;@=;B9
- at HiMom:9:2:3:495
+ at machine1:HiMom:abcdeACXX:9:2:3:495 :N:0:GCACACGACCAGTTAG
GCACACGA
+
5;5<A@=;
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGACCAGTTAG.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGACCAGTTAG.barcode_2.fastq
index f40a686..c77a493 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGACCAGTTAG.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGACCAGTTAG.barcode_2.fastq
@@ -1,36 +1,36 @@
- at HiMom:9:1:3:1311
+ at machine1:HiMom:abcdeACXX:9:1:3:1311 :Y:0:GCACACGACCAGTTAG
CCAGTTAG
+
<?BAA at AB
- at HiMom:9:1:3:1544
+ at machine1:HiMom:abcdeACXX:9:1:3:1544 :N:0:GCACACGACCAGTTAG
CCAGTTAG
+
((<.;;1;
- at HiMom:9:1:3:301
+ at machine1:HiMom:abcdeACXX:9:1:3:301 :N:0:GCACACGACCAGTTAG
CCAGTTAG
+
########
- at HiMom:9:1:3:959
+ at machine1:HiMom:abcdeACXX:9:1:3:959 :Y:0:GCACACGACCAGTTAG
CCAGTTAG
+
3?;AB?=<
- at HiMom:9:2:2:184
+ at machine1:HiMom:abcdeACXX:9:2:2:184 :N:0:GCACACGACCAGTTAG
CCAGTTAG
+
>;<@A@@3
- at HiMom:9:2:3:1025
+ at machine1:HiMom:abcdeACXX:9:2:3:1025 :Y:0:GCACACGACCAGTTAG
CCAGTTAG
+
@=ABA@@@
- at HiMom:9:2:3:1290
+ at machine1:HiMom:abcdeACXX:9:2:3:1290 :N:0:GCACACGACCAGTTAG
CCAGTTAG
+
)5;=@<(;
- at HiMom:9:2:3:1917
+ at machine1:HiMom:abcdeACXX:9:2:3:1917 :N:0:GCACACGACCAGTTAG
CCAGTTAG
+
/5;@=;B9
- at HiMom:9:2:3:495
+ at machine1:HiMom:abcdeACXX:9:2:3:495 :N:0:GCACACGACCAGTTAG
CCAGTTAG
+
5;5<A@=;
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCT.1.fastq
index 2fbc19f..3b95cbd 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCT.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCT.1.fastq
@@ -1,12 +1,12 @@
- at HiMom:7:1:3:389
+ at machine1:HiMom:abcdeACXX:7:1:3:389 :N:0:GCACATCT
NGATGTTCAAACATGCATAACTCTAAGTAT
+
##############################
- at HiMom:7:2:2:1567
+ at machine1:HiMom:abcdeACXX:7:2:2:1567 :Y:0:GCACATCT
NAGACAGCAGTAACCTCTGCAGACTTAAAC
+
%,67:720544;4667:62-5667::6877
- at HiMom:7:2:3:1053
+ at machine1:HiMom:abcdeACXX:7:2:3:1053 :N:0:GCACATCT
NTTTGATCATGATTCCATTCGAGACCATTC
+
%.;;##########################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCT.barcode_1.fastq
index b5fc06d..ac9d40b 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCT.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCT.barcode_1.fastq
@@ -1,12 +1,12 @@
- at HiMom:7:1:3:389
+ at machine1:HiMom:abcdeACXX:7:1:3:389 :N:0:GCACATCT
GCACATCT
+
<:@@@56;
- at HiMom:7:2:2:1567
+ at machine1:HiMom:abcdeACXX:7:2:2:1567 :Y:0:GCACATCT
GCACATCT
+
@B=;@B?@
- at HiMom:7:2:3:1053
+ at machine1:HiMom:abcdeACXX:7:2:3:1053 :N:0:GCACATCT
GCACATCT
+
6<?B?C at 4
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCTCATGCTTA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCTCATGCTTA.1.fastq
index 53dec96..1c0c245 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCTCATGCTTA.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCTCATGCTTA.1.fastq
@@ -1,12 +1,12 @@
- at HiMom:9:1:3:389
+ at machine1:HiMom:abcdeACXX:9:1:3:389 :N:0:GCACATCTCATGCTTA
NGATGTTCAAACATGCATAACTCTAAGTAT
+
##############################
- at HiMom:9:2:2:1567
+ at machine1:HiMom:abcdeACXX:9:2:2:1567 :Y:0:GCACATCTCATGCTTA
NAGACAGCAGTAACCTCTGCAGACTTAAAC
+
%,67:720544;4667:62-5667::6877
- at HiMom:9:2:3:1053
+ at machine1:HiMom:abcdeACXX:9:2:3:1053 :N:0:GCACATCTCATGCTTA
NTTTGATCATGATTCCATTCGAGACCATTC
+
%.;;##########################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCTCATGCTTA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCTCATGCTTA.barcode_1.fastq
index 64ab42f..8d9ec57 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCTCATGCTTA.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCTCATGCTTA.barcode_1.fastq
@@ -1,12 +1,12 @@
- at HiMom:9:1:3:389
+ at machine1:HiMom:abcdeACXX:9:1:3:389 :N:0:GCACATCTCATGCTTA
GCACATCT
+
<:@@@56;
- at HiMom:9:2:2:1567
+ at machine1:HiMom:abcdeACXX:9:2:2:1567 :Y:0:GCACATCTCATGCTTA
GCACATCT
+
@B=;@B?@
- at HiMom:9:2:3:1053
+ at machine1:HiMom:abcdeACXX:9:2:3:1053 :N:0:GCACATCTCATGCTTA
GCACATCT
+
6<?B?C at 4
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCTCATGCTTA.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCTCATGCTTA.barcode_2.fastq
index 36b26fb..cb34b4b 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCTCATGCTTA.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCTCATGCTTA.barcode_2.fastq
@@ -1,12 +1,12 @@
- at HiMom:9:1:3:389
+ at machine1:HiMom:abcdeACXX:9:1:3:389 :N:0:GCACATCTCATGCTTA
CATGCTTA
+
<:@@@56;
- at HiMom:9:2:2:1567
+ at machine1:HiMom:abcdeACXX:9:2:2:1567 :Y:0:GCACATCTCATGCTTA
CATGCTTA
+
@B=;@B?@
- at HiMom:9:2:3:1053
+ at machine1:HiMom:abcdeACXX:9:2:3:1053 :N:0:GCACATCTCATGCTTA
CATGCTTA
+
6<?B?C at 4
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGA.1.fastq
index 05dd585..edba24c 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGA.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGA.1.fastq
@@ -1,28 +1,28 @@
- at HiMom:7:1:3:33
+ at machine1:HiMom:abcdeACXX:7:1:3:33 :N:0:GGTCCAGA
CGGGCGCGGTGGATTCCGCCTTTAATCCTA
+
71@=>3?BA#####################
- at HiMom:7:1:3:471
+ at machine1:HiMom:abcdeACXX:7:1:3:471 :Y:0:GGTCCAGA
AGAAAAAGACAAGCAGGCCTCTCACAGAGC
+
@=B>CB@?8BBBA<B<@ABBAAA=<@>>3<
- at HiMom:7:1:3:676
+ at machine1:HiMom:abcdeACXX:7:1:3:676 :N:0:GGTCCAGA
ATAAGAAAATGCCAACCCATTTACAGTTTT
+
?':7%68>?<(.9A7(=:68>A=2>(9@??
- at HiMom:7:2:2:1038
+ at machine1:HiMom:abcdeACXX:7:2:2:1038 :N:0:GGTCCAGA
NATGGAATCAACCTGAGTGGAATGAAATGG
+
##############################
- at HiMom:7:2:3:1352
+ at machine1:HiMom:abcdeACXX:7:2:3:1352 :Y:0:GGTCCAGA
AAAGTGGCCCTTTCTGCATAATTCTTCTTG
+
@B@>2:@@:>B at AAA:AA>?B?>:=<1=<#
- at HiMom:7:2:3:1733
+ at machine1:HiMom:abcdeACXX:7:2:3:1733 :Y:0:GGTCCAGA
NTTAAATGAGTGTAAATATTCAATTATGCA
+
%,:6::2/5;393<<9:<;919<97#####
- at HiMom:7:2:3:386
+ at machine1:HiMom:abcdeACXX:7:2:3:386 :N:0:GGTCCAGA
NTGAATAAATAAATATCTGTATTATTCCTA
+
%156;99:999:5773,4-57973851.48
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGA.barcode_1.fastq
index 324ac2c..55d0c05 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGA.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGA.barcode_1.fastq
@@ -1,28 +1,28 @@
- at HiMom:7:1:3:33
+ at machine1:HiMom:abcdeACXX:7:1:3:33 :N:0:GGTCCAGA
GGTCCAGA
+
17=;,'@@
- at HiMom:7:1:3:471
+ at machine1:HiMom:abcdeACXX:7:1:3:471 :Y:0:GGTCCAGA
GGTCCAGA
+
<A=@B=?@
- at HiMom:7:1:3:676
+ at machine1:HiMom:abcdeACXX:7:1:3:676 :N:0:GGTCCAGA
GATCCAGA
+
:(.<((:@
- at HiMom:7:2:2:1038
+ at machine1:HiMom:abcdeACXX:7:2:2:1038 :N:0:GGTCCAGA
GGTCCAGA
+
=7=??B@@
- at HiMom:7:2:3:1352
+ at machine1:HiMom:abcdeACXX:7:2:3:1352 :Y:0:GGTCCAGA
GGTCCAGA
+
0)<0;@@@
- at HiMom:7:2:3:1733
+ at machine1:HiMom:abcdeACXX:7:2:3:1733 :Y:0:GGTCCAGA
GGTCCAGA
+
/>BBBAA=
- at HiMom:7:2:3:386
+ at machine1:HiMom:abcdeACXX:7:2:3:386 :N:0:GGTCCAGA
GGTCCAGA
+
9@@99@@9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGACATAGCGA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGACATAGCGA.1.fastq
index 6dde699..6223ca0 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGACATAGCGA.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGACATAGCGA.1.fastq
@@ -1,28 +1,28 @@
- at HiMom:9:1:3:33
+ at machine1:HiMom:abcdeACXX:9:1:3:33 :N:0:GGTCCAGACATAGCGA
CGGGCGCGGTGGATTCCGCCTTTAATCCTA
+
71@=>3?BA#####################
- at HiMom:9:1:3:471
+ at machine1:HiMom:abcdeACXX:9:1:3:471 :Y:0:GGTCCAGACATAGCGA
AGAAAAAGACAAGCAGGCCTCTCACAGAGC
+
@=B>CB@?8BBBA<B<@ABBAAA=<@>>3<
- at HiMom:9:1:3:676
+ at machine1:HiMom:abcdeACXX:9:1:3:676 :N:0:GGTCCAGACATAGCGA
ATAAGAAAATGCCAACCCATTTACAGTTTT
+
?':7%68>?<(.9A7(=:68>A=2>(9@??
- at HiMom:9:2:2:1038
+ at machine1:HiMom:abcdeACXX:9:2:2:1038 :N:0:GGTCCAGACATAGCGA
NATGGAATCAACCTGAGTGGAATGAAATGG
+
##############################
- at HiMom:9:2:3:1352
+ at machine1:HiMom:abcdeACXX:9:2:3:1352 :Y:0:GGTCCAGACATAGCGA
AAAGTGGCCCTTTCTGCATAATTCTTCTTG
+
@B@>2:@@:>B at AAA:AA>?B?>:=<1=<#
- at HiMom:9:2:3:1733
+ at machine1:HiMom:abcdeACXX:9:2:3:1733 :Y:0:GGTCCAGACATAGCGA
NTTAAATGAGTGTAAATATTCAATTATGCA
+
%,:6::2/5;393<<9:<;919<97#####
- at HiMom:9:2:3:386
+ at machine1:HiMom:abcdeACXX:9:2:3:386 :N:0:GGTCCAGACATAGCGA
NTGAATAAATAAATATCTGTATTATTCCTA
+
%156;99:999:5773,4-57973851.48
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGACATAGCGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGACATAGCGA.barcode_1.fastq
index 8b62c2b..4a21eb6 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGACATAGCGA.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGACATAGCGA.barcode_1.fastq
@@ -1,28 +1,28 @@
- at HiMom:9:1:3:33
+ at machine1:HiMom:abcdeACXX:9:1:3:33 :N:0:GGTCCAGACATAGCGA
GGTCCAGA
+
17=;,'@@
- at HiMom:9:1:3:471
+ at machine1:HiMom:abcdeACXX:9:1:3:471 :Y:0:GGTCCAGACATAGCGA
GGTCCAGA
+
<A=@B=?@
- at HiMom:9:1:3:676
+ at machine1:HiMom:abcdeACXX:9:1:3:676 :N:0:GGTCCAGACATAGCGA
GATCCAGA
+
:(.<((:@
- at HiMom:9:2:2:1038
+ at machine1:HiMom:abcdeACXX:9:2:2:1038 :N:0:GGTCCAGACATAGCGA
GGTCCAGA
+
=7=??B@@
- at HiMom:9:2:3:1352
+ at machine1:HiMom:abcdeACXX:9:2:3:1352 :Y:0:GGTCCAGACATAGCGA
GGTCCAGA
+
0)<0;@@@
- at HiMom:9:2:3:1733
+ at machine1:HiMom:abcdeACXX:9:2:3:1733 :Y:0:GGTCCAGACATAGCGA
GGTCCAGA
+
/>BBBAA=
- at HiMom:9:2:3:386
+ at machine1:HiMom:abcdeACXX:9:2:3:386 :N:0:GGTCCAGACATAGCGA
GGTCCAGA
+
9@@99@@9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGACATAGCGA.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGACATAGCGA.barcode_2.fastq
index 9b84f0e..c6b3f2d 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGACATAGCGA.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGACATAGCGA.barcode_2.fastq
@@ -1,28 +1,28 @@
- at HiMom:9:1:3:33
+ at machine1:HiMom:abcdeACXX:9:1:3:33 :N:0:GGTCCAGACATAGCGA
CATAGCGA
+
17=;,'@@
- at HiMom:9:1:3:471
+ at machine1:HiMom:abcdeACXX:9:1:3:471 :Y:0:GGTCCAGACATAGCGA
CATAGCGA
+
<A=@B=?@
- at HiMom:9:1:3:676
+ at machine1:HiMom:abcdeACXX:9:1:3:676 :N:0:GGTCCAGACATAGCGA
CATAGCGA
+
:(.<((:@
- at HiMom:9:2:2:1038
+ at machine1:HiMom:abcdeACXX:9:2:2:1038 :N:0:GGTCCAGACATAGCGA
CATAGCGA
+
=7=??B@@
- at HiMom:9:2:3:1352
+ at machine1:HiMom:abcdeACXX:9:2:3:1352 :Y:0:GGTCCAGACATAGCGA
CATAGCGA
+
0)<0;@@@
- at HiMom:9:2:3:1733
+ at machine1:HiMom:abcdeACXX:9:2:3:1733 :Y:0:GGTCCAGACATAGCGA
CATAGCGA
+
/>BBBAA=
- at HiMom:9:2:3:386
+ at machine1:HiMom:abcdeACXX:9:2:3:386 :N:0:GGTCCAGACATAGCGA
CATAGCGA
+
9@@99@@9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACA.1.fastq
index a435a39..c1ae9f8 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACA.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACA.1.fastq
@@ -1,40 +1,40 @@
- at HiMom:7:1:2:11
+ at machine1:HiMom:abcdeACXX:7:1:2:11 :N:0:GTATAACA
NAAATGAAAAAAGAAATGCATTGTCAGGTG
+
##############################
- at HiMom:7:1:2:455
+ at machine1:HiMom:abcdeACXX:7:1:2:455 :N:0:GTATAACA
NGCTTGAACTCAGGATTCACAATTTCAACC
+
##############################
- at HiMom:7:1:3:1188
+ at machine1:HiMom:abcdeACXX:7:1:3:1188 :Y:0:GTATAACA
GCGAATGCCATTATTTCATTCCTTTTCATG
+
=@CACA?AABCCCCCCCCAB??CBCBCCBB
- at HiMom:7:1:3:131
+ at machine1:HiMom:abcdeACXX:7:1:3:131 :Y:0:GTATAACA
TAAAATAAAGTAAAAAGAAAGCAAGGTCCT
+
BBBBCCCBBA<CCCCA<<CBC>BBC=AC=C
- at HiMom:7:1:3:1488
+ at machine1:HiMom:abcdeACXX:7:1:3:1488 :Y:0:GTATAACA
NATTCTGAGTAGCATGCTGGATCCCACCCC
+
%-445014,42/1666423###########
- at HiMom:7:1:3:1973
+ at machine1:HiMom:abcdeACXX:7:1:3:1973 :Y:0:GTATAACA
NCTTTTATTGAATTAGCTTCTGTGGAAACC
+
%.<774<<145;105<<:6<7<:88;####
- at HiMom:7:1:3:289
+ at machine1:HiMom:abcdeACXX:7:1:3:289 :Y:0:GTATAACA
ATAGTGCTACAATAAACATGGGAGTGCAGA
+
BB=;>AABB at BBBBBB@ACBA>>BA;9@?A
- at HiMom:7:2:2:1662
+ at machine1:HiMom:abcdeACXX:7:2:2:1662 :N:0:GTATAACA
NACTAAAGACCTTATTCATGTAGCCAAATA
+
%.2556331)%079799::9:71855<88:
- at HiMom:7:2:2:61
+ at machine1:HiMom:abcdeACXX:7:2:2:61 :Y:0:GTATAACA
NTTTCGATGGTGTTTCCATTTGATTCATTC
+
%0;:9:;799:8:97779:<679<977;::
- at HiMom:7:2:3:1581
+ at machine1:HiMom:abcdeACXX:7:2:3:1581 :N:0:GTATAACA
NATAGGCAGGGAGCAAACCTCAATAAAAAG
+
##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACA.barcode_1.fastq
index 5b03a50..250d81c 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACA.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACA.barcode_1.fastq
@@ -1,40 +1,40 @@
- at HiMom:7:1:2:11
+ at machine1:HiMom:abcdeACXX:7:1:2:11 :N:0:GTATAACA
GTATAAGA
+
@7==@7##
- at HiMom:7:1:2:455
+ at machine1:HiMom:abcdeACXX:7:1:2:455 :N:0:GTATAACA
GTATAACT
+
,@######
- at HiMom:7:1:3:1188
+ at machine1:HiMom:abcdeACXX:7:1:3:1188 :Y:0:GTATAACA
GTATAACA
+
BBBCBCCB
- at HiMom:7:1:3:131
+ at machine1:HiMom:abcdeACXX:7:1:3:131 :Y:0:GTATAACA
GTATAACA
+
48CCACAC
- at HiMom:7:1:3:1488
+ at machine1:HiMom:abcdeACXX:7:1:3:1488 :Y:0:GTATAACA
GTATAACA
+
)7<9BBBB
- at HiMom:7:1:3:1973
+ at machine1:HiMom:abcdeACXX:7:1:3:1973 :Y:0:GTATAACA
GTATAACA
+
7;CACCBC
- at HiMom:7:1:3:289
+ at machine1:HiMom:abcdeACXX:7:1:3:289 :Y:0:GTATAACA
GTATAACA
+
>BCCCCB>
- at HiMom:7:2:2:1662
+ at machine1:HiMom:abcdeACXX:7:2:2:1662 :N:0:GTATAACA
GTATAACA
+
82BA at AAB
- at HiMom:7:2:2:61
+ at machine1:HiMom:abcdeACXX:7:2:2:61 :Y:0:GTATAACA
GTATAACA
+
<ABCBB9B
- at HiMom:7:2:3:1581
+ at machine1:HiMom:abcdeACXX:7:2:3:1581 :N:0:GTATAACA
GTATAACA
+
:4<BAAAC
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACACAGGAGCC.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACACAGGAGCC.1.fastq
index 3353c03..c3a3023 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACACAGGAGCC.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACACAGGAGCC.1.fastq
@@ -1,40 +1,40 @@
- at HiMom:9:1:2:11
+ at machine1:HiMom:abcdeACXX:9:1:2:11 :N:0:GTATAACACAGGAGCC
NAAATGAAAAAAGAAATGCATTGTCAGGTG
+
##############################
- at HiMom:9:1:2:455
+ at machine1:HiMom:abcdeACXX:9:1:2:455 :N:0:GTATAACACAGGAGCC
NGCTTGAACTCAGGATTCACAATTTCAACC
+
##############################
- at HiMom:9:1:3:1188
+ at machine1:HiMom:abcdeACXX:9:1:3:1188 :Y:0:GTATAACACAGGAGCC
GCGAATGCCATTATTTCATTCCTTTTCATG
+
=@CACA?AABCCCCCCCCAB??CBCBCCBB
- at HiMom:9:1:3:131
+ at machine1:HiMom:abcdeACXX:9:1:3:131 :Y:0:GTATAACACAGGAGCC
TAAAATAAAGTAAAAAGAAAGCAAGGTCCT
+
BBBBCCCBBA<CCCCA<<CBC>BBC=AC=C
- at HiMom:9:1:3:1488
+ at machine1:HiMom:abcdeACXX:9:1:3:1488 :Y:0:GTATAACACAGGAGCC
NATTCTGAGTAGCATGCTGGATCCCACCCC
+
%-445014,42/1666423###########
- at HiMom:9:1:3:1973
+ at machine1:HiMom:abcdeACXX:9:1:3:1973 :Y:0:GTATAACACAGGAGCC
NCTTTTATTGAATTAGCTTCTGTGGAAACC
+
%.<774<<145;105<<:6<7<:88;####
- at HiMom:9:1:3:289
+ at machine1:HiMom:abcdeACXX:9:1:3:289 :Y:0:GTATAACACAGGAGCC
ATAGTGCTACAATAAACATGGGAGTGCAGA
+
BB=;>AABB at BBBBBB@ACBA>>BA;9@?A
- at HiMom:9:2:2:1662
+ at machine1:HiMom:abcdeACXX:9:2:2:1662 :N:0:GTATAACACAGGAGCC
NACTAAAGACCTTATTCATGTAGCCAAATA
+
%.2556331)%079799::9:71855<88:
- at HiMom:9:2:2:61
+ at machine1:HiMom:abcdeACXX:9:2:2:61 :Y:0:GTATAACACAGGAGCC
NTTTCGATGGTGTTTCCATTTGATTCATTC
+
%0;:9:;799:8:97779:<679<977;::
- at HiMom:9:2:3:1581
+ at machine1:HiMom:abcdeACXX:9:2:3:1581 :N:0:GTATAACACAGGAGCC
NATAGGCAGGGAGCAAACCTCAATAAAAAG
+
##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACACAGGAGCC.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACACAGGAGCC.barcode_1.fastq
index ab807c8..9ab10a3 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACACAGGAGCC.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACACAGGAGCC.barcode_1.fastq
@@ -1,40 +1,40 @@
- at HiMom:9:1:2:11
+ at machine1:HiMom:abcdeACXX:9:1:2:11 :N:0:GTATAACACAGGAGCC
GTATAAGA
+
@7==@7##
- at HiMom:9:1:2:455
+ at machine1:HiMom:abcdeACXX:9:1:2:455 :N:0:GTATAACACAGGAGCC
GTATAACT
+
,@######
- at HiMom:9:1:3:1188
+ at machine1:HiMom:abcdeACXX:9:1:3:1188 :Y:0:GTATAACACAGGAGCC
GTATAACA
+
BBBCBCCB
- at HiMom:9:1:3:131
+ at machine1:HiMom:abcdeACXX:9:1:3:131 :Y:0:GTATAACACAGGAGCC
GTATAACA
+
48CCACAC
- at HiMom:9:1:3:1488
+ at machine1:HiMom:abcdeACXX:9:1:3:1488 :Y:0:GTATAACACAGGAGCC
GTATAACA
+
)7<9BBBB
- at HiMom:9:1:3:1973
+ at machine1:HiMom:abcdeACXX:9:1:3:1973 :Y:0:GTATAACACAGGAGCC
GTATAACA
+
7;CACCBC
- at HiMom:9:1:3:289
+ at machine1:HiMom:abcdeACXX:9:1:3:289 :Y:0:GTATAACACAGGAGCC
GTATAACA
+
>BCCCCB>
- at HiMom:9:2:2:1662
+ at machine1:HiMom:abcdeACXX:9:2:2:1662 :N:0:GTATAACACAGGAGCC
GTATAACA
+
82BA at AAB
- at HiMom:9:2:2:61
+ at machine1:HiMom:abcdeACXX:9:2:2:61 :Y:0:GTATAACACAGGAGCC
GTATAACA
+
<ABCBB9B
- at HiMom:9:2:3:1581
+ at machine1:HiMom:abcdeACXX:9:2:3:1581 :N:0:GTATAACACAGGAGCC
GTATAACA
+
:4<BAAAC
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACACAGGAGCC.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACACAGGAGCC.barcode_2.fastq
index 07a5b88..ade5931 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACACAGGAGCC.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACACAGGAGCC.barcode_2.fastq
@@ -1,40 +1,40 @@
- at HiMom:9:1:2:11
+ at machine1:HiMom:abcdeACXX:9:1:2:11 :N:0:GTATAACACAGGAGCC
CAGGAGCC
+
@7==@7##
- at HiMom:9:1:2:455
+ at machine1:HiMom:abcdeACXX:9:1:2:455 :N:0:GTATAACACAGGAGCC
CAGGAGCC
+
,@######
- at HiMom:9:1:3:1188
+ at machine1:HiMom:abcdeACXX:9:1:3:1188 :Y:0:GTATAACACAGGAGCC
CAGGAGCC
+
BBBCBCCB
- at HiMom:9:1:3:131
+ at machine1:HiMom:abcdeACXX:9:1:3:131 :Y:0:GTATAACACAGGAGCC
CAGGAGCC
+
48CCACAC
- at HiMom:9:1:3:1488
+ at machine1:HiMom:abcdeACXX:9:1:3:1488 :Y:0:GTATAACACAGGAGCC
CAGGAGCC
+
)7<9BBBB
- at HiMom:9:1:3:1973
+ at machine1:HiMom:abcdeACXX:9:1:3:1973 :Y:0:GTATAACACAGGAGCC
CAGGAGCC
+
7;CACCBC
- at HiMom:9:1:3:289
+ at machine1:HiMom:abcdeACXX:9:1:3:289 :Y:0:GTATAACACAGGAGCC
CAGGAGCC
+
>BCCCCB>
- at HiMom:9:2:2:1662
+ at machine1:HiMom:abcdeACXX:9:2:2:1662 :N:0:GTATAACACAGGAGCC
CAGGAGCC
+
82BA at AAB
- at HiMom:9:2:2:61
+ at machine1:HiMom:abcdeACXX:9:2:2:61 :Y:0:GTATAACACAGGAGCC
CAGGAGCC
+
<ABCBB9B
- at HiMom:9:2:3:1581
+ at machine1:HiMom:abcdeACXX:9:2:3:1581 :N:0:GTATAACACAGGAGCC
CAGGAGCC
+
:4<BAAAC
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/N.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/N.1.fastq
index a107b32..0d031e7 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/N.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/N.1.fastq
@@ -1,892 +1,892 @@
- at HiMom:7:1:0:1038
+ at machine1:HiMom:abcdeACXX:7:1:0:1038 :N:0:
NNNNNCNNCANNNCNNNCNCCNNNCNNNNN
+
##############################
- at HiMom:7:1:0:1093
+ at machine1:HiMom:abcdeACXX:7:1:0:1093 :N:0:
NNNNNCNNGTNNNANNNGNAANNNANNNNN
+
##############################
- at HiMom:7:1:0:113
+ at machine1:HiMom:abcdeACXX:7:1:0:113 :N:0:
NNNNNNNNGNNNNNNNNNNNANNNNNNNNN
+
##############################
- at HiMom:7:1:0:1193
+ at machine1:HiMom:abcdeACXX:7:1:0:1193 :N:0:
NNNNNNNNTNNNNTNNNTNNTNNNCNNNNN
+
##############################
- at HiMom:7:1:0:1291
+ at machine1:HiMom:abcdeACXX:7:1:0:1291 :N:0:
NNNNNNNNANNNNNNNNANNTNNNNNNNNN
+
##############################
- at HiMom:7:1:0:1307
+ at machine1:HiMom:abcdeACXX:7:1:0:1307 :N:0:
NNNNNNNNCNNNNANNNTNNTNNNCNNNNN
+
##############################
- at HiMom:7:1:0:1434
+ at machine1:HiMom:abcdeACXX:7:1:0:1434 :N:0:
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
##############################
- at HiMom:7:1:0:1475
+ at machine1:HiMom:abcdeACXX:7:1:0:1475 :N:0:
NNNNNGNNANNNNANNNANNANNNANNNNN
+
##############################
- at HiMom:7:1:0:1690
+ at machine1:HiMom:abcdeACXX:7:1:0:1690 :N:0:
NNNNNNNNANNNNNNNNGNNCNNNCNNNNN
+
##############################
- at HiMom:7:1:0:1703
+ at machine1:HiMom:abcdeACXX:7:1:0:1703 :N:0:
NNNNNNNNANNNNNNNNNNNANNNNNNNNN
+
##############################
- at HiMom:7:1:0:1940
+ at machine1:HiMom:abcdeACXX:7:1:0:1940 :N:0:
NNNNNNNNCNNNNNNNNTNNTNNNNNNNNN
+
##############################
- at HiMom:7:1:0:2001
+ at machine1:HiMom:abcdeACXX:7:1:0:2001 :N:0:
NNNNNANNTGNNNGNNNANGCNNNANNNNN
+
##############################
- at HiMom:7:1:0:205
+ at machine1:HiMom:abcdeACXX:7:1:0:205 :N:0:
NNNNNNNNANNNNNNNNANNTNNNANNNNN
+
##############################
- at HiMom:7:1:0:275
+ at machine1:HiMom:abcdeACXX:7:1:0:275 :N:0:
NNNNNANNCANNNTNNNGNCCNNNANNNNN
+
##############################
- at HiMom:7:1:0:324
+ at machine1:HiMom:abcdeACXX:7:1:0:324 :N:0:
NNNNNNNNTNNNNNNNNTNNANNNANNNNN
+
##############################
- at HiMom:7:1:0:37
+ at machine1:HiMom:abcdeACXX:7:1:0:37 :N:0:
NNNNNNNNANNNNNNNNCNNTNNNCNNNNN
+
##############################
- at HiMom:7:1:0:464
+ at machine1:HiMom:abcdeACXX:7:1:0:464 :N:0:
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
##############################
- at HiMom:7:1:0:586
+ at machine1:HiMom:abcdeACXX:7:1:0:586 :N:0:
NNNNNNNNCNNNNNNNNCNNCNNNANNNNN
+
##############################
- at HiMom:7:1:0:841
+ at machine1:HiMom:abcdeACXX:7:1:0:841 :N:0:
NNNNNNNNCNNNNNNNNNNNTNNNNNNNNN
+
##############################
- at HiMom:7:1:0:879
+ at machine1:HiMom:abcdeACXX:7:1:0:879 :N:0:
NNNNNNNNTNNNNNNNNNNNTNNNNNNNNN
+
##############################
- at HiMom:7:1:1:1013
+ at machine1:HiMom:abcdeACXX:7:1:1:1013 :N:0:
NNCNNTNCAGNNNCNNNANGTNNNGNNNNN
+
##############################
- at HiMom:7:1:1:111
+ at machine1:HiMom:abcdeACXX:7:1:1:111 :N:0:
NNCNNTNGCGNNNTNNNANCTNNNTNNNNN
+
##############################
- at HiMom:7:1:1:1153
+ at machine1:HiMom:abcdeACXX:7:1:1:1153 :N:0:
NNTNNTNTGGNNNTNNNCNTCNNNTNNNNN
+
##############################
- at HiMom:7:1:1:1184
+ at machine1:HiMom:abcdeACXX:7:1:1:1184 :N:0:
NNANNGNTCGNNNANNNTNCANNNTNNNNN
+
##############################
- at HiMom:7:1:1:1241
+ at machine1:HiMom:abcdeACXX:7:1:1:1241 :N:0:
NNANNGNTGGNNNTNNNCNTGNNNANNNNN
+
##############################
- at HiMom:7:1:1:1243
+ at machine1:HiMom:abcdeACXX:7:1:1:1243 :N:0:
NNANNANGGANNNANNNCNTANNNTNNNNN
+
##############################
- at HiMom:7:1:1:1247
+ at machine1:HiMom:abcdeACXX:7:1:1:1247 :N:0:
NCCAGCNTTTNNNTNNNTNCTNNNGNNNNN
+
##############################
- at HiMom:7:1:1:1282
+ at machine1:HiMom:abcdeACXX:7:1:1:1282 :N:0:
NNANNANGGGNNNTNNNGNAGNNNCNNNNN
+
##############################
- at HiMom:7:1:1:132
+ at machine1:HiMom:abcdeACXX:7:1:1:132 :N:0:
NNANNGNGGGNNNGNNNGNGGNNNGNNNNN
+
##############################
- at HiMom:7:1:1:1320
+ at machine1:HiMom:abcdeACXX:7:1:1:1320 :N:0:
NNANNTNAGTNNNGNNNGNTANNNCNNNNN
+
##############################
- at HiMom:7:1:1:1372
+ at machine1:HiMom:abcdeACXX:7:1:1:1372 :N:0:
NACATTTTTTAGNTNANTTGTTNACNANNN
+
##############################
- at HiMom:7:1:1:1379
+ at machine1:HiMom:abcdeACXX:7:1:1:1379 :N:0:
NAATATAATTNNNTNNNTTAGANTTNNNNN
+
##############################
- at HiMom:7:1:1:1391
+ at machine1:HiMom:abcdeACXX:7:1:1:1391 :N:0:
NNGNNTNTAANNNANNNTNATNNNTNNNNN
+
##############################
- at HiMom:7:1:1:140
+ at machine1:HiMom:abcdeACXX:7:1:1:140 :N:0:
NNANNTNTAANNNGNNNCNTTNNNTNNNNN
+
##############################
- at HiMom:7:1:1:1513
+ at machine1:HiMom:abcdeACXX:7:1:1:1513 :N:0:
NNNNNANNTTNNNANNNANAANNNCNNNNN
+
##############################
- at HiMom:7:1:1:1521
+ at machine1:HiMom:abcdeACXX:7:1:1:1521 :N:0:
NAACAANATTNNNTNNNANTANNTANNNNN
+
##############################
- at HiMom:7:1:1:155
+ at machine1:HiMom:abcdeACXX:7:1:1:155 :N:0:
NNGNNCNAGTNNNCNNNANTTNNNGNNNNN
+
##############################
- at HiMom:7:1:1:1555
+ at machine1:HiMom:abcdeACXX:7:1:1:1555 :N:0:
NNTNNGNAGANNNANNNCNTANNNANNNNN
+
##############################
- at HiMom:7:1:1:164
+ at machine1:HiMom:abcdeACXX:7:1:1:164 :N:0:
NNANNANTAANNNTNNNTNATNNNTNNNNN
+
##############################
- at HiMom:7:1:1:1684
+ at machine1:HiMom:abcdeACXX:7:1:1:1684 :N:0:
NNGNNANGGTNNNGNNNTNTCNNNTNNNNN
+
##############################
- at HiMom:7:1:1:1696
+ at machine1:HiMom:abcdeACXX:7:1:1:1696 :N:0:
NNANNGNNGCNNNGNNNANACNNNTNNNNN
+
##############################
- at HiMom:7:1:1:170
+ at machine1:HiMom:abcdeACXX:7:1:1:170 :N:0:
NNTNNCNCACNNNGNNNGNTCNNNGNNNNN
+
##############################
- at HiMom:7:1:1:173
+ at machine1:HiMom:abcdeACXX:7:1:1:173 :N:0:
NNNNNANNATNNNTNNNCNTTNNNTNNNNN
+
##############################
- at HiMom:7:1:1:1733
+ at machine1:HiMom:abcdeACXX:7:1:1:1733 :N:0:
NNANNGNGTCNNNTNNNTNAGNNNANNNNN
+
##############################
- at HiMom:7:1:1:1770
+ at machine1:HiMom:abcdeACXX:7:1:1:1770 :N:0:
NNCNNTNCTGNNNGNNNGNCANNNANNNNN
+
##############################
- at HiMom:7:1:1:18
+ at machine1:HiMom:abcdeACXX:7:1:1:18 :N:0:
NATCAGNCTGNNNANNNTNGTNNAANNNNN
+
##############################
- at HiMom:7:1:1:1815
+ at machine1:HiMom:abcdeACXX:7:1:1:1815 :N:0:
NATGAAAATANNNTNNNTAAATNATNNNNN
+
##############################
- at HiMom:7:1:1:1836
+ at machine1:HiMom:abcdeACXX:7:1:1:1836 :N:0:
NNNNNGNNTANNNGNNNTNCTNNNCNNNNN
+
##############################
- at HiMom:7:1:1:184
+ at machine1:HiMom:abcdeACXX:7:1:1:184 :N:0:
NNCNNTNTAANNNANNNTNATNNNGNNNNN
+
##############################
- at HiMom:7:1:1:1886
+ at machine1:HiMom:abcdeACXX:7:1:1:1886 :Y:0:
NACATATGCATACATATATAATAGATANNN
+
%.9:;<217;:999;<;;<<<;;#######
- at HiMom:7:1:1:1906
+ at machine1:HiMom:abcdeACXX:7:1:1:1906 :N:0:
NNTNNCNATANNNCNNNTNCTNNNGNNNNN
+
##############################
- at HiMom:7:1:1:1917
+ at machine1:HiMom:abcdeACXX:7:1:1:1917 :N:0:
NNNNNTNNGANNNCNNNANAANNNANNNNN
+
##############################
- at HiMom:7:1:1:195
+ at machine1:HiMom:abcdeACXX:7:1:1:195 :N:0:
NNANNGNGTGNNNGNNNCNATNNNANNNNN
+
##############################
- at HiMom:7:1:1:1954
+ at machine1:HiMom:abcdeACXX:7:1:1:1954 :N:0:
NAGANTNCTTNNNGNNNGNAGNNNCNNNNN
+
##############################
- at HiMom:7:1:1:2
+ at machine1:HiMom:abcdeACXX:7:1:1:2 :N:0:
NNANNGNGAANNNCNNNNNNNNNNNNNNNN
+
##############################
- at HiMom:7:1:1:2011
+ at machine1:HiMom:abcdeACXX:7:1:1:2011 :N:0:
NACAGCTGGCANNTNNNAGAGCNAGNANNN
+
##############################
- at HiMom:7:1:1:240
+ at machine1:HiMom:abcdeACXX:7:1:1:240 :N:0:
NNGNNANGTANNNTNNNTNCCNNNCNNNNN
+
##############################
- at HiMom:7:1:1:262
+ at machine1:HiMom:abcdeACXX:7:1:1:262 :N:0:
NNCNNGNCATNNNANNNCNTGNNNCNNNNN
+
##############################
- at HiMom:7:1:1:264
+ at machine1:HiMom:abcdeACXX:7:1:1:264 :N:0:
NAACTGNAATNNNCNNNANCANNCTNNNNN
+
##############################
- at HiMom:7:1:1:299
+ at machine1:HiMom:abcdeACXX:7:1:1:299 :N:0:
NNCNNTNGCANNNANNNCNAANNNTNNNNN
+
##############################
- at HiMom:7:1:1:30
+ at machine1:HiMom:abcdeACXX:7:1:1:30 :N:0:
NNANNANTTTNNNTNNNGNTCNNNTNNNNN
+
##############################
- at HiMom:7:1:1:353
+ at machine1:HiMom:abcdeACXX:7:1:1:353 :N:0:
NNANNTNTAGNNNANNNTNATNNNANNNNN
+
##############################
- at HiMom:7:1:1:367
+ at machine1:HiMom:abcdeACXX:7:1:1:367 :N:0:
NNANNTNAGCNNNGNNNANGTNNNCNNNNN
+
##############################
- at HiMom:7:1:1:41
+ at machine1:HiMom:abcdeACXX:7:1:1:41 :N:0:
NNANNCNAAANNNGNNNTNCANNNCNNNNN
+
##############################
- at HiMom:7:1:1:416
+ at machine1:HiMom:abcdeACXX:7:1:1:416 :N:0:
NNANNCNAATNNNGNNNGNACNNNCNNNNN
+
##############################
- at HiMom:7:1:1:483
+ at machine1:HiMom:abcdeACXX:7:1:1:483 :N:0:
NNGNNGNGGGNNNGNNNGNTTNNNTNNNNN
+
##############################
- at HiMom:7:1:1:486
+ at machine1:HiMom:abcdeACXX:7:1:1:486 :N:0:
NNANNANTTTNNNANNNANAGNNNTNNNNN
+
##############################
- at HiMom:7:1:1:495
+ at machine1:HiMom:abcdeACXX:7:1:1:495 :N:0:
NNCNNANCGTNNNTNNNTNAANNNCNNNNN
+
##############################
- at HiMom:7:1:1:508
+ at machine1:HiMom:abcdeACXX:7:1:1:508 :N:0:
NNGNNCNCAGNNNTNNNCNCTNNNCNNNNN
+
##############################
- at HiMom:7:1:1:517
+ at machine1:HiMom:abcdeACXX:7:1:1:517 :N:0:
NTCATAAAACATCANTATTGGAAAGGANNN
+
%.75:<999578##################
- at HiMom:7:1:1:535
+ at machine1:HiMom:abcdeACXX:7:1:1:535 :N:0:
NGCCCAAGTATTGANTATGTGCTCTAANNN
+
%.599:7187:940%0::52599#######
- at HiMom:7:1:1:55
+ at machine1:HiMom:abcdeACXX:7:1:1:55 :N:0:
NTTTATGTCCTTNANAACTTAGNAGTTNNN
+
%/9<<83599####################
- at HiMom:7:1:1:554
+ at machine1:HiMom:abcdeACXX:7:1:1:554 :N:0:
NNANNGNAGANNNGNNNTNTCNNNANNNNN
+
##############################
- at HiMom:7:1:1:567
+ at machine1:HiMom:abcdeACXX:7:1:1:567 :N:0:
NNCNNCNGTTNNNCNNNGNACNNNCNNNNN
+
##############################
- at HiMom:7:1:1:59
+ at machine1:HiMom:abcdeACXX:7:1:1:59 :N:0:
NNANNGNTGCNNNTNNNTNACNNNANNNNN
+
##############################
- at HiMom:7:1:1:613
+ at machine1:HiMom:abcdeACXX:7:1:1:613 :N:0:
NNGNNANTATNNNCNNNGNATNNNANNNNN
+
##############################
- at HiMom:7:1:1:622
+ at machine1:HiMom:abcdeACXX:7:1:1:622 :N:0:
NNTNNCNAGTNNNCNNNANCTNNNTNNNNN
+
##############################
- at HiMom:7:1:1:627
+ at machine1:HiMom:abcdeACXX:7:1:1:627 :N:0:
NNANNTNGACNNNTNNNANGCNNNCNNNNN
+
##############################
- at HiMom:7:1:1:684
+ at machine1:HiMom:abcdeACXX:7:1:1:684 :N:0:
NNTNNTNAGANNNCNNNANAGNNNANNNNN
+
##############################
- at HiMom:7:1:1:72
+ at machine1:HiMom:abcdeACXX:7:1:1:72 :N:0:
NACACACATATCACNCACATCATACACNNN
+
%..48696;5:6;.%)49;;;9########
- at HiMom:7:1:1:812
+ at machine1:HiMom:abcdeACXX:7:1:1:812 :N:0:
NNANNCNAAGNNNTNNNANTCNNNANNNNN
+
##############################
- at HiMom:7:1:1:874
+ at machine1:HiMom:abcdeACXX:7:1:1:874 :N:0:
NNANNANGCCNNNGNNNTNTANNNTNNNNN
+
##############################
- at HiMom:7:1:1:931
+ at machine1:HiMom:abcdeACXX:7:1:1:931 :N:0:
NNTNNGNGATNNNGNNNCNTTNNNCNNNNN
+
##############################
- at HiMom:7:1:1:965
+ at machine1:HiMom:abcdeACXX:7:1:1:965 :N:0:
NACTAATCTTCCGCNCATATCCCCAAANNN
+
##############################
- at HiMom:7:1:1:994
+ at machine1:HiMom:abcdeACXX:7:1:1:994 :N:0:
NNANNTNGATNNNTNNNGNTTNNNCNNNNN
+
##############################
- at HiMom:7:1:2:1158
+ at machine1:HiMom:abcdeACXX:7:1:2:1158 :Y:0:
NGGGTCCTTCATAGTTTTTTTCTACTTTCC
+
%0777646;099:::95;;;688::99###
- at HiMom:7:1:2:1238
+ at machine1:HiMom:abcdeACXX:7:1:2:1238 :N:0:
NTCCTTATATTCAATTATTAATATTTTTAC
+
##############################
- at HiMom:7:1:2:1275
+ at machine1:HiMom:abcdeACXX:7:1:2:1275 :Y:0:
NAGTGAAATAAGCCAGACACAGAAAGACAN
+
%/5204:99971773,44755-39717###
- at HiMom:7:1:2:1301
+ at machine1:HiMom:abcdeACXX:7:1:2:1301 :N:0:
NAGTAGACTGCATTAATTAATTGGAAGAGN
+
%0370)024263144:48;;##########
- at HiMom:7:1:2:1453
+ at machine1:HiMom:abcdeACXX:7:1:2:1453 :Y:0:
NATATCTTATTTTCTTTTCTTTCAGGCTCT
+
%.:7,,395255##################
- at HiMom:7:1:2:150
+ at machine1:HiMom:abcdeACXX:7:1:2:150 :N:0:
NAAGACTTGATTATATCCCTTGTATGANNN
+
##############################
- at HiMom:7:1:2:1592
+ at machine1:HiMom:abcdeACXX:7:1:2:1592 :Y:0:
NGAAAACTGGCACAAGACAAGGATGCCCTC
+
%,67786861,3466(8485868648583#
- at HiMom:7:1:2:1706
+ at machine1:HiMom:abcdeACXX:7:1:2:1706 :Y:0:
NGATATGTGGATACAGCTCACAAAGAGNNN
+
%,99:6/566999/7###############
- at HiMom:7:1:2:1722
+ at machine1:HiMom:abcdeACXX:7:1:2:1722 :N:0:
NAAAGAAAATTAAAGAAAAATATACACGTN
+
##############################
- at HiMom:7:1:2:1727
+ at machine1:HiMom:abcdeACXX:7:1:2:1727 :N:0:
NTATTGAAGGACTTTTGTATCCTCCTTATN
+
##############################
- at HiMom:7:1:2:1753
+ at machine1:HiMom:abcdeACXX:7:1:2:1753 :N:0:
NGTTCACACAAGGATAATATTTTTGATTAT
+
##############################
- at HiMom:7:1:2:1782
+ at machine1:HiMom:abcdeACXX:7:1:2:1782 :Y:0:
NACCAAGTGTTTGGAGTATGCTGCCTANNN
+
%0:::668885-5335/85###########
- at HiMom:7:1:2:1827
+ at machine1:HiMom:abcdeACXX:7:1:2:1827 :Y:0:
NAACCGAGGATGTACACTGTCCCTGTGAAA
+
##############################
- at HiMom:7:1:2:1932
+ at machine1:HiMom:abcdeACXX:7:1:2:1932 :Y:0:
NAGCGATCCTCCCGCCTCTGCCTCCCANNN
+
%,1545541455##################
- at HiMom:7:1:2:1946
+ at machine1:HiMom:abcdeACXX:7:1:2:1946 :N:0:
NATCTTCTGGAATTTCTAACAGCTTGGAAN
+
%0515.,.35<997################
- at HiMom:7:1:2:209
+ at machine1:HiMom:abcdeACXX:7:1:2:209 :N:0:
NGACTCAACTCCTGGGCTCCCTACGACCAT
+
##############################
- at HiMom:7:1:2:246
+ at machine1:HiMom:abcdeACXX:7:1:2:246 :N:0:
NGGAGGTTTCATTTAGCCGATATTGTGNNN
+
##############################
- at HiMom:7:1:2:25
+ at machine1:HiMom:abcdeACXX:7:1:2:25 :N:0:
NGCTTTGGCAAGACAAATCTCCCGTCTGGN
+
##############################
- at HiMom:7:1:2:307
+ at machine1:HiMom:abcdeACXX:7:1:2:307 :N:0:
NGGATGAACAGAAACTAAAATAACACANNN
+
##############################
- at HiMom:7:1:2:363
+ at machine1:HiMom:abcdeACXX:7:1:2:363 :N:0:
NATATTCTTTTTTTTTATTTATCAGATNNN
+
##############################
- at HiMom:7:1:2:449
+ at machine1:HiMom:abcdeACXX:7:1:2:449 :N:0:
NATTCTAATTCTAGGAAATTAACAATCNNN
+
%.9315<936970%0###############
- at HiMom:7:1:2:546
+ at machine1:HiMom:abcdeACXX:7:1:2:546 :N:0:
NGGTTGTGTCTCTCTCAGCCTTTGGGATCN
+
%,46888444685-35##############
- at HiMom:7:1:2:605
+ at machine1:HiMom:abcdeACXX:7:1:2:605 :Y:0:
NGCATTGAGCAGACGTGGCATCCAGATNNN
+
%)085222/55453################
- at HiMom:7:1:2:69
+ at machine1:HiMom:abcdeACXX:7:1:2:69 :N:0:
NTCAGTCTGCTGTTTTAAAAAAATACTGTG
+
##############################
- at HiMom:7:1:2:747
+ at machine1:HiMom:abcdeACXX:7:1:2:747 :N:0:
NAACAACAGCGGAAAATAATAAAAAAAAAN
+
##############################
- at HiMom:7:1:2:786
+ at machine1:HiMom:abcdeACXX:7:1:2:786 :Y:0:
NTAAACAATAATCTGATGATTTATAATCCN
+
%09<<<<;<;<8<9;<9<;<::<<::####
- at HiMom:7:1:2:858
+ at machine1:HiMom:abcdeACXX:7:1:2:858 :Y:0:
NAAACGTTGCTGATCTTCTGTTTTAAACTA
+
%/;7-222265366-6977035:::;626;
- at HiMom:7:1:2:943
+ at machine1:HiMom:abcdeACXX:7:1:2:943 :Y:0:
NAATACCAATAAACCTAGAATGTCTCATAC
+
%08<9646<6378744774:1005799<4#
- at HiMom:7:1:2:974
+ at machine1:HiMom:abcdeACXX:7:1:2:974 :Y:0:
NGATCAATGATCACATCTTTGGATATGTAT
+
%/9979<99:999::9;;:7511<<<77<<
- at HiMom:7:1:2:988
+ at machine1:HiMom:abcdeACXX:7:1:2:988 :Y:0:
NAAAGGAATGTTCAGCTCTGTGAGTTGAAC
+
%/92/04:2-2785-3875/404362-162
- at HiMom:7:1:3:1233
+ at machine1:HiMom:abcdeACXX:7:1:3:1233 :N:0:
NAACCAATTTCTTTACATACCAAATACGCC
+
##############################
- at HiMom:7:1:3:1294
+ at machine1:HiMom:abcdeACXX:7:1:3:1294 :N:0:
TGTAACTTTACTTTAGTTGCTTATTTGTAG
+
BA############################
- at HiMom:7:1:3:405
+ at machine1:HiMom:abcdeACXX:7:1:3:405 :N:0:
AAAAAACATAGAACGGGGTCAATATTTTAT
+
(?A>8(7B?<(:')?@)8(:(*:<8:0>'>
- at HiMom:7:1:3:579
+ at machine1:HiMom:abcdeACXX:7:1:3:579 :N:0:
NGAAAAATGACCACACTTGCCTCCTGAGAA
+
##############################
- at HiMom:7:1:3:673
+ at machine1:HiMom:abcdeACXX:7:1:3:673 :N:0:
TCCTCAAAAACAAGATAAAACGGTTGAAAT
+
>()>)''85BBC?#################
- at HiMom:7:1:3:890
+ at machine1:HiMom:abcdeACXX:7:1:3:890 :N:0:
TGCTTCTGTTTCCGTTAGCTAGATAAAGTT
+
##############################
- at HiMom:7:1:3:905
+ at machine1:HiMom:abcdeACXX:7:1:3:905 :N:0:
TGTTATGTTTAATTTTCTTTAGCACCCTTC
+
>7>?A:-<BA at 0>@:@8=A;5%7;9?=:9@
- at HiMom:7:1:3:918
+ at machine1:HiMom:abcdeACXX:7:1:3:918 :N:0:
TTTTCATTCCTAGTCATCCACCCCATCAGA
+
0()@A=:2>3:>(/((<22A>:0(20:@)@
- at HiMom:7:2:0:1073
+ at machine1:HiMom:abcdeACXX:7:2:0:1073 :N:0:
NNNNNANCACNNNCNNNCNCANNNCNNNNN
+
##############################
- at HiMom:7:2:0:1135
+ at machine1:HiMom:abcdeACXX:7:2:0:1135 :N:0:
NNNNNGNNGTNNNANNNTNTANNNGNNNNN
+
##############################
- at HiMom:7:2:0:1198
+ at machine1:HiMom:abcdeACXX:7:2:0:1198 :N:0:
NNNNNTNCTANNNTNNNCNCANNNANNNNN
+
##############################
- at HiMom:7:2:0:1278
+ at machine1:HiMom:abcdeACXX:7:2:0:1278 :N:0:
NNNNNNNNTANNNTNNNCNNANNNGNNNNN
+
##############################
- at HiMom:7:2:0:135
+ at machine1:HiMom:abcdeACXX:7:2:0:135 :N:0:
NNNNNNNNANNNNNNNNNNNGNNNNNNNNN
+
##############################
- at HiMom:7:2:0:1547
+ at machine1:HiMom:abcdeACXX:7:2:0:1547 :N:0:
NNNNNNNNCNNNNNNNNNNNGNNNANNNNN
+
##############################
- at HiMom:7:2:0:1598
+ at machine1:HiMom:abcdeACXX:7:2:0:1598 :N:0:
NNNNNNNNATNNNTNNNANNGNNNCNNNNN
+
##############################
- at HiMom:7:2:0:1620
+ at machine1:HiMom:abcdeACXX:7:2:0:1620 :N:0:
NNNNNNNNCANNNNNNNANNCNNNCNNNNN
+
##############################
- at HiMom:7:2:0:1668
+ at machine1:HiMom:abcdeACXX:7:2:0:1668 :N:0:
NNNNNANATANNNANNNGNTGNNNTNNNNN
+
##############################
- at HiMom:7:2:0:186
+ at machine1:HiMom:abcdeACXX:7:2:0:186 :N:0:
NNNNNNNNCCNNNANNNTNNTNNNTNNNNN
+
##############################
- at HiMom:7:2:0:205
+ at machine1:HiMom:abcdeACXX:7:2:0:205 :N:0:
NNNNNNNNANNNNNNNNTNNCNNNTNNNNN
+
##############################
- at HiMom:7:2:0:287
+ at machine1:HiMom:abcdeACXX:7:2:0:287 :N:0:
NNNNNNNNCCNNNCNNNTNNANNNANNNNN
+
##############################
- at HiMom:7:2:0:382
+ at machine1:HiMom:abcdeACXX:7:2:0:382 :N:0:
NNNNNNNNCANNNTNNNTNNANNNANNNNN
+
##############################
- at HiMom:7:2:0:441
+ at machine1:HiMom:abcdeACXX:7:2:0:441 :N:0:
NNNNNNNNTTNNNANNNANNTNNNTNNNNN
+
##############################
- at HiMom:7:2:0:50
+ at machine1:HiMom:abcdeACXX:7:2:0:50 :N:0:
NNNNNNNNTNNNNNNNNTNNGNNNGNNNNN
+
##############################
- at HiMom:7:2:0:501
+ at machine1:HiMom:abcdeACXX:7:2:0:501 :N:0:
NNNNNGNNAGNNNANNNCNCTNNNCNNNNN
+
##############################
- at HiMom:7:2:0:73
+ at machine1:HiMom:abcdeACXX:7:2:0:73 :N:0:
NNNNNANCATNNNGNNNANACNNNGNNNNN
+
##############################
- at HiMom:7:2:0:740
+ at machine1:HiMom:abcdeACXX:7:2:0:740 :N:0:
NNNNNNNNTTNNNANNNTNNANNNANNNNN
+
##############################
- at HiMom:7:2:0:766
+ at machine1:HiMom:abcdeACXX:7:2:0:766 :N:0:
NNNNNNNNTGNNNANNNANNTNNNTNNNNN
+
##############################
- at HiMom:7:2:0:87
+ at machine1:HiMom:abcdeACXX:7:2:0:87 :N:0:
NNNNNNNNGNNNNNNNNANNTNNNTNNNNN
+
##############################
- at HiMom:7:2:1:1004
+ at machine1:HiMom:abcdeACXX:7:2:1:1004 :N:0:
NATTTATCACTANANATCCGCAAACCCTCC
+
##############################
- at HiMom:7:2:1:1034
+ at machine1:HiMom:abcdeACXX:7:2:1:1034 :N:0:
NATCATTTTCATNCNTTTCACTGATACATT
+
%.737:887471%-%1:8555545;696::
- at HiMom:7:2:1:1159
+ at machine1:HiMom:abcdeACXX:7:2:1:1159 :N:0:
NNACTTNTAGNNNGNNNAAATNNCCNANNN
+
##############################
- at HiMom:7:2:1:1168
+ at machine1:HiMom:abcdeACXX:7:2:1:1168 :N:0:
NNTCTANCTTNNNTNNNATTGNNTTNTNNN
+
##############################
- at HiMom:7:2:1:1180
+ at machine1:HiMom:abcdeACXX:7:2:1:1180 :N:0:
NNATGGNCTTNNNCNNNAGAANNTCNANNN
+
##############################
- at HiMom:7:2:1:1214
+ at machine1:HiMom:abcdeACXX:7:2:1:1214 :N:0:
NAAAAAAAAAAANANTATAAGAAAGAATCA
+
%035:#########################
- at HiMom:7:2:1:1221
+ at machine1:HiMom:abcdeACXX:7:2:1:1221 :N:0:
NGGTCACACTCACATAGTGTTCAGAGCACT
+
##############################
- at HiMom:7:2:1:1306
+ at machine1:HiMom:abcdeACXX:7:2:1:1306 :N:0:
NNACATNAAANNNTNNNAACANNGTNANNN
+
##############################
- at HiMom:7:2:1:1351
+ at machine1:HiMom:abcdeACXX:7:2:1:1351 :N:0:
NNNNNCNATANNNTNNNANAANNNTNNNNN
+
##############################
- at HiMom:7:2:1:1424
+ at machine1:HiMom:abcdeACXX:7:2:1:1424 :N:0:
NNTCATNTAGNNNCNNNATGGNNGTNCNNN
+
##############################
- at HiMom:7:2:1:1452
+ at machine1:HiMom:abcdeACXX:7:2:1:1452 :N:0:
NGAAATTTGTAAAANCACCTGCAGAATACT
+
##############################
- at HiMom:7:2:1:1515
+ at machine1:HiMom:abcdeACXX:7:2:1:1515 :N:0:
NATTAAATATNANANNGTAATAATAATANN
+
%/9###########################
- at HiMom:7:2:1:1521
+ at machine1:HiMom:abcdeACXX:7:2:1:1521 :N:0:
NNACACNAAANNNGNNNATCTNNTTNCNNN
+
##############################
- at HiMom:7:2:1:1536
+ at machine1:HiMom:abcdeACXX:7:2:1:1536 :N:0:
NAGCAAAGACTTNGNACCAACCCAAATGTT
+
##############################
- at HiMom:7:2:1:1543
+ at machine1:HiMom:abcdeACXX:7:2:1:1543 :N:0:
NNTTGANATCNNNANNNAATANNTANCNNN
+
##############################
- at HiMom:7:2:1:1617
+ at machine1:HiMom:abcdeACXX:7:2:1:1617 :N:0:
NNCCATNATCNNNGNNNCCAGNNGTNTNNN
+
##############################
- at HiMom:7:2:1:1627
+ at machine1:HiMom:abcdeACXX:7:2:1:1627 :N:0:
NNTGGTNAGANNNCNNNAAAANNCANTNNN
+
##############################
- at HiMom:7:2:1:1646
+ at machine1:HiMom:abcdeACXX:7:2:1:1646 :N:0:
NTTAATTATANNNANNTAAACATTCTAANN
+
##############################
- at HiMom:7:2:1:1653
+ at machine1:HiMom:abcdeACXX:7:2:1:1653 :N:0:
NNAATTNAAANNNTNNNATCTNNAGNANNN
+
##############################
- at HiMom:7:2:1:1682
+ at machine1:HiMom:abcdeACXX:7:2:1:1682 :N:0:
NNTCTTNTTTNNNGNNNAAAANNAANTNNN
+
##############################
- at HiMom:7:2:1:170
+ at machine1:HiMom:abcdeACXX:7:2:1:170 :Y:0:
NAGAAGAAATGGGATCCTGCTGTGGCCAGT
+
%/888865284168866767663(6874/5
- at HiMom:7:2:1:1731
+ at machine1:HiMom:abcdeACXX:7:2:1:1731 :N:0:
NNTATANGAANNNTNNNTGCTNNAGNTNNN
+
##############################
- at HiMom:7:2:1:1755
+ at machine1:HiMom:abcdeACXX:7:2:1:1755 :N:0:
NNGTNANTCTNNNCNNNCNTGNNNGNANNN
+
##############################
- at HiMom:7:2:1:1812
+ at machine1:HiMom:abcdeACXX:7:2:1:1812 :N:0:
NNTTGCNCACNNNCNNNCCATNNAANGNNN
+
##############################
- at HiMom:7:2:1:1853
+ at machine1:HiMom:abcdeACXX:7:2:1:1853 :N:0:
NNATCTNTTCNNNANNNAGTGNNATNCNNN
+
##############################
- at HiMom:7:2:1:1919
+ at machine1:HiMom:abcdeACXX:7:2:1:1919 :N:0:
NNAATTNAAANNNANNNAGAANNAGNANNN
+
##############################
- at HiMom:7:2:1:1924
+ at machine1:HiMom:abcdeACXX:7:2:1:1924 :N:0:
NATATTCTGAAGNANNCCAATGAACCAAAN
+
%116<9579<7###################
- at HiMom:7:2:1:1933
+ at machine1:HiMom:abcdeACXX:7:2:1:1933 :N:0:
NAGGGTACATNTNCNNAATGTGCGGGTTNN
+
##############################
- at HiMom:7:2:1:1938
+ at machine1:HiMom:abcdeACXX:7:2:1:1938 :Y:0:
NAGTCCAGTGTCTCTGCTTCCGCAGGGACA
+
%/818865/058858644866457646668
- at HiMom:7:2:1:1950
+ at machine1:HiMom:abcdeACXX:7:2:1:1950 :N:0:
NNTTNANAAANNNCNNNTNCANNNTNCNNN
+
##############################
- at HiMom:7:2:1:1959
+ at machine1:HiMom:abcdeACXX:7:2:1:1959 :N:0:
NGACACATTCCTACNACAGAGAAAAATTTA
+
%*77;;<;<<:<;,%.::;:6:9::<4488
- at HiMom:7:2:1:1987
+ at machine1:HiMom:abcdeACXX:7:2:1:1987 :N:0:
NNATNGNACANNNCNNNTNGTNNNTNNNNN
+
##############################
- at HiMom:7:2:1:2006
+ at machine1:HiMom:abcdeACXX:7:2:1:2006 :N:0:
NNGTATNTGANNNGNNNCCTTNNAGNANNN
+
##############################
- at HiMom:7:2:1:211
+ at machine1:HiMom:abcdeACXX:7:2:1:211 :N:0:
NNCTGANACANNNGNNNTGCANNACNCNNN
+
##############################
- at HiMom:7:2:1:234
+ at machine1:HiMom:abcdeACXX:7:2:1:234 :N:0:
NAAGCCTGTGGGNANNCCCAGTGGGAGCGN
+
##############################
- at HiMom:7:2:1:242
+ at machine1:HiMom:abcdeACXX:7:2:1:242 :N:0:
NNGCTCNAGCNNNANNNATATNNTTNGNNN
+
##############################
- at HiMom:7:2:1:262
+ at machine1:HiMom:abcdeACXX:7:2:1:262 :N:0:
NNATTGNAATNNNCNNNTTCCNNATNTNNN
+
##############################
- at HiMom:7:2:1:298
+ at machine1:HiMom:abcdeACXX:7:2:1:298 :N:0:
NNTCAANTTGNNNTNNNCTGCNNTTNTNNN
+
##############################
- at HiMom:7:2:1:312
+ at machine1:HiMom:abcdeACXX:7:2:1:312 :N:0:
NNTTGCNAGANNNANNNAACTNNTGNANNN
+
##############################
- at HiMom:7:2:1:363
+ at machine1:HiMom:abcdeACXX:7:2:1:363 :Y:0:
NGAAAGGTTTTGCAGCATGTGCAAACTCAC
+
%-5565678:8177656503512/377856
- at HiMom:7:2:1:37
+ at machine1:HiMom:abcdeACXX:7:2:1:37 :N:0:
NTGTAAACGANNNCNNTTCCTGTTCAGCNN
+
##############################
- at HiMom:7:2:1:370
+ at machine1:HiMom:abcdeACXX:7:2:1:370 :N:0:
NNCTGGNAGCNNNTNNNCATANNAANCNNN
+
##############################
- at HiMom:7:2:1:377
+ at machine1:HiMom:abcdeACXX:7:2:1:377 :N:0:
NNAGAANGTGNNNTNNNAAATNNAANANNN
+
##############################
- at HiMom:7:2:1:414
+ at machine1:HiMom:abcdeACXX:7:2:1:414 :N:0:
NNTAGANAGCNNNANNNTCAGNNACNGNNN
+
##############################
- at HiMom:7:2:1:421
+ at machine1:HiMom:abcdeACXX:7:2:1:421 :N:0:
NNGTTANTTCNNNANNNCGTGNNATNCNNN
+
##############################
- at HiMom:7:2:1:428
+ at machine1:HiMom:abcdeACXX:7:2:1:428 :N:0:
NATGTGAATANTNANNTAGTTGGGATTCAN
+
##############################
- at HiMom:7:2:1:44
+ at machine1:HiMom:abcdeACXX:7:2:1:44 :N:0:
NACTACCTCANGNANNAAGCAGGTTCTAAN
+
##############################
- at HiMom:7:2:1:466
+ at machine1:HiMom:abcdeACXX:7:2:1:466 :N:0:
NACACTCACANCNANNTGTTTGGAATGANN
+
##############################
- at HiMom:7:2:1:555
+ at machine1:HiMom:abcdeACXX:7:2:1:555 :N:0:
NNCAATNTCTNNNGNNNTACANNCTNCNNN
+
##############################
- at HiMom:7:2:1:558
+ at machine1:HiMom:abcdeACXX:7:2:1:558 :N:0:
NAAAATATCANTNANNAATAAATAATCANN
+
##############################
- at HiMom:7:2:1:56
+ at machine1:HiMom:abcdeACXX:7:2:1:56 :N:0:
NNGCCANGGTNNNANNNTCACNNGGNCNNN
+
##############################
- at HiMom:7:2:1:569
+ at machine1:HiMom:abcdeACXX:7:2:1:569 :N:0:
NNAGGCNAGTNNNGNNNGTCCNNGTNANNN
+
##############################
- at HiMom:7:2:1:604
+ at machine1:HiMom:abcdeACXX:7:2:1:604 :N:0:
NATGATGAAACTCTNTCTCTACTAAAAATA
+
##############################
- at HiMom:7:2:1:628
+ at machine1:HiMom:abcdeACXX:7:2:1:628 :N:0:
NAGTATGCCCNCNCNNACCACTCCTATTNN
+
##############################
- at HiMom:7:2:1:64
+ at machine1:HiMom:abcdeACXX:7:2:1:64 :N:0:
NATTAATCTTNNNTNNGCACAATTCATTNN
+
##############################
- at HiMom:7:2:1:684
+ at machine1:HiMom:abcdeACXX:7:2:1:684 :N:0:
NAAAAATCAAATGANCATAATTTTATAAAA
+
##############################
- at HiMom:7:2:1:699
+ at machine1:HiMom:abcdeACXX:7:2:1:699 :N:0:
NNAATTNTTGNNNTNNNATTTNNGANTNNN
+
##############################
- at HiMom:7:2:1:714
+ at machine1:HiMom:abcdeACXX:7:2:1:714 :N:0:
NATTAACTTANANTNNACCACAACCTAANN
+
%.:###########################
- at HiMom:7:2:1:722
+ at machine1:HiMom:abcdeACXX:7:2:1:722 :N:0:
NNCCTCNCTGNNNCNNNCTGTNNTGNCNNN
+
##############################
- at HiMom:7:2:1:749
+ at machine1:HiMom:abcdeACXX:7:2:1:749 :N:0:
NNAGTGNTACNNNTNNNCTTGNNCTNTNNN
+
##############################
- at HiMom:7:2:1:760
+ at machine1:HiMom:abcdeACXX:7:2:1:760 :N:0:
NGTCTGTTTTATGTNAAATATTTTGTTTAA
+
##############################
- at HiMom:7:2:1:8
+ at machine1:HiMom:abcdeACXX:7:2:1:8 :N:0:
NNTGCGNTGGNNNCNNNAGGCNNTTNTNNN
+
##############################
- at HiMom:7:2:1:833
+ at machine1:HiMom:abcdeACXX:7:2:1:833 :N:0:
NNGAGCNCCTNNNANNNCTCCNNGANGNNN
+
##############################
- at HiMom:7:2:1:848
+ at machine1:HiMom:abcdeACXX:7:2:1:848 :N:0:
NNTACTNAGTNNNGNNNTGTTNNGCNTNNN
+
##############################
- at HiMom:7:2:1:893
+ at machine1:HiMom:abcdeACXX:7:2:1:893 :N:0:
NGAGACAGAGTCTCNCTCTGTTCCCTAGCC
+
##############################
- at HiMom:7:2:1:998
+ at machine1:HiMom:abcdeACXX:7:2:1:998 :N:0:
NNATGTNTGCNNNANNNTATANNGGNANNN
+
##############################
- at HiMom:7:2:2:0
+ at machine1:HiMom:abcdeACXX:7:2:2:0 :N:0:
NATTCCTTNANNNNNNNNNNNNNNNNNNNN
+
##############################
- at HiMom:7:2:2:131
+ at machine1:HiMom:abcdeACXX:7:2:2:131 :Y:0:
NATATATTGACAGCAGTCATGTTGTTGAAG
+
%0<<<:<959874492:96999969:7784
- at HiMom:7:2:2:1636
+ at machine1:HiMom:abcdeACXX:7:2:2:1636 :N:0:
NGTGTAAAAGTAGGGAAATACTATAGCAAG
+
##############################
- at HiMom:7:2:2:1974
+ at machine1:HiMom:abcdeACXX:7:2:2:1974 :N:0:
NACGCCAATACAAAAATGTTGAAGCTAGCT
+
##############################
- at HiMom:7:2:2:351
+ at machine1:HiMom:abcdeACXX:7:2:2:351 :N:0:
NGGGGTTGAGGTGTAAATAGAACATTTGTA
+
##############################
- at HiMom:7:2:2:646
+ at machine1:HiMom:abcdeACXX:7:2:2:646 :N:0:
NGAATCTAAGAAGACACAAAACTAAGGAAA
+
##############################
- at HiMom:7:2:2:828
+ at machine1:HiMom:abcdeACXX:7:2:2:828 :N:0:
NTCAAGTCAATTTGGGACTTGAAACAGCTC
+
##############################
- at HiMom:7:2:3:1529
+ at machine1:HiMom:abcdeACXX:7:2:3:1529 :N:0:
NTTATATGAATAGATAAATAAATAATCAAT
+
##############################
- at HiMom:7:2:3:179
+ at machine1:HiMom:abcdeACXX:7:2:3:179 :N:0:
CATTATTGTTAGACTGATTTTTTATAATCT
+
B@)104..*0-A(@@(<A9A<(+9)-=6(B
- at HiMom:7:2:3:198
+ at machine1:HiMom:abcdeACXX:7:2:3:198 :N:0:
TGTCATTTTCTTTGCCTTAATTGTTCTTCT
+
5 at CBB7-*<=####################
- at HiMom:7:2:3:2030
+ at machine1:HiMom:abcdeACXX:7:2:3:2030 :N:0:
CGAGATAATTTTTTAAAAAAAGTCCAAAAA
+
((@;()@==*7<(5A@<C>###########
- at HiMom:7:2:3:247
+ at machine1:HiMom:abcdeACXX:7:2:3:247 :N:0:
TGTACATGACCAGGTAATTTGGTTATGTGA
+
<@596353;)>@A7=:,A0'6>########
- at HiMom:7:2:3:4
+ at machine1:HiMom:abcdeACXX:7:2:3:4 :N:0:
AGAGGCAATAAGTTTTAANNNNNNNNNNNN
+
A>BA at 9BAB3AA##################
- at HiMom:7:2:3:862
+ at machine1:HiMom:abcdeACXX:7:2:3:862 :N:0:
NCTTTAAGAAATCATTCATTCTGCAAACAC
+
##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/N.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/N.barcode_1.fastq
index f6e41a7..37130a3 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/N.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/N.barcode_1.fastq
@@ -1,892 +1,892 @@
- at HiMom:7:1:0:1038
+ at machine1:HiMom:abcdeACXX:7:1:0:1038 :N:0:
NNNNNGTN
+
########
- at HiMom:7:1:0:1093
+ at machine1:HiMom:abcdeACXX:7:1:0:1093 :N:0:
NNNNNTGN
+
########
- at HiMom:7:1:0:113
+ at machine1:HiMom:abcdeACXX:7:1:0:113 :N:0:
NNNNNNNN
+
########
- at HiMom:7:1:0:1193
+ at machine1:HiMom:abcdeACXX:7:1:0:1193 :N:0:
NNNNNGTN
+
########
- at HiMom:7:1:0:1291
+ at machine1:HiMom:abcdeACXX:7:1:0:1291 :N:0:
NNNNNGNN
+
########
- at HiMom:7:1:0:1307
+ at machine1:HiMom:abcdeACXX:7:1:0:1307 :N:0:
NNNNNTAN
+
########
- at HiMom:7:1:0:1434
+ at machine1:HiMom:abcdeACXX:7:1:0:1434 :N:0:
NNNNNNNN
+
########
- at HiMom:7:1:0:1475
+ at machine1:HiMom:abcdeACXX:7:1:0:1475 :N:0:
NNNNNCCN
+
########
- at HiMom:7:1:0:1690
+ at machine1:HiMom:abcdeACXX:7:1:0:1690 :N:0:
NNNNNANN
+
########
- at HiMom:7:1:0:1703
+ at machine1:HiMom:abcdeACXX:7:1:0:1703 :N:0:
NNNNNNNN
+
########
- at HiMom:7:1:0:1940
+ at machine1:HiMom:abcdeACXX:7:1:0:1940 :N:0:
NNNNNCNN
+
########
- at HiMom:7:1:0:2001
+ at machine1:HiMom:abcdeACXX:7:1:0:2001 :N:0:
NNNNNGAN
+
########
- at HiMom:7:1:0:205
+ at machine1:HiMom:abcdeACXX:7:1:0:205 :N:0:
NNNNNCGN
+
########
- at HiMom:7:1:0:275
+ at machine1:HiMom:abcdeACXX:7:1:0:275 :N:0:
NNNNNATN
+
########
- at HiMom:7:1:0:324
+ at machine1:HiMom:abcdeACXX:7:1:0:324 :N:0:
NNNNNGTN
+
########
- at HiMom:7:1:0:37
+ at machine1:HiMom:abcdeACXX:7:1:0:37 :N:0:
NNNNNGNN
+
########
- at HiMom:7:1:0:464
+ at machine1:HiMom:abcdeACXX:7:1:0:464 :N:0:
NNNNNNNN
+
########
- at HiMom:7:1:0:586
+ at machine1:HiMom:abcdeACXX:7:1:0:586 :N:0:
NNNNNCNN
+
########
- at HiMom:7:1:0:841
+ at machine1:HiMom:abcdeACXX:7:1:0:841 :N:0:
NNNNNNNN
+
########
- at HiMom:7:1:0:879
+ at machine1:HiMom:abcdeACXX:7:1:0:879 :N:0:
NNNNNNNN
+
########
- at HiMom:7:1:1:1013
+ at machine1:HiMom:abcdeACXX:7:1:1:1013 :N:0:
NNNNNGAN
+
########
- at HiMom:7:1:1:111
+ at machine1:HiMom:abcdeACXX:7:1:1:111 :N:0:
NNNNNCGN
+
########
- at HiMom:7:1:1:1153
+ at machine1:HiMom:abcdeACXX:7:1:1:1153 :N:0:
NNNNNCTN
+
########
- at HiMom:7:1:1:1184
+ at machine1:HiMom:abcdeACXX:7:1:1:1184 :N:0:
NNNNNAGN
+
########
- at HiMom:7:1:1:1241
+ at machine1:HiMom:abcdeACXX:7:1:1:1241 :N:0:
NNNNNCTN
+
########
- at HiMom:7:1:1:1243
+ at machine1:HiMom:abcdeACXX:7:1:1:1243 :N:0:
NNNNNTGN
+
########
- at HiMom:7:1:1:1247
+ at machine1:HiMom:abcdeACXX:7:1:1:1247 :N:0:
NNNNNACN
+
########
- at HiMom:7:1:1:1282
+ at machine1:HiMom:abcdeACXX:7:1:1:1282 :N:0:
NNNNNCCN
+
########
- at HiMom:7:1:1:132
+ at machine1:HiMom:abcdeACXX:7:1:1:132 :N:0:
NNNNNTGN
+
########
- at HiMom:7:1:1:1320
+ at machine1:HiMom:abcdeACXX:7:1:1:1320 :N:0:
NNNNNCGN
+
########
- at HiMom:7:1:1:1372
+ at machine1:HiMom:abcdeACXX:7:1:1:1372 :N:0:
NNNGNTTA
+
########
- at HiMom:7:1:1:1379
+ at machine1:HiMom:abcdeACXX:7:1:1:1379 :N:0:
NNNCNGAT
+
########
- at HiMom:7:1:1:1391
+ at machine1:HiMom:abcdeACXX:7:1:1:1391 :N:0:
NNNNNAGN
+
########
- at HiMom:7:1:1:140
+ at machine1:HiMom:abcdeACXX:7:1:1:140 :N:0:
NNNNNCAN
+
########
- at HiMom:7:1:1:1513
+ at machine1:HiMom:abcdeACXX:7:1:1:1513 :N:0:
NNNNNCTN
+
########
- at HiMom:7:1:1:1521
+ at machine1:HiMom:abcdeACXX:7:1:1:1521 :N:0:
NNNNNCCN
+
########
- at HiMom:7:1:1:155
+ at machine1:HiMom:abcdeACXX:7:1:1:155 :N:0:
NNNNNCAN
+
########
- at HiMom:7:1:1:1555
+ at machine1:HiMom:abcdeACXX:7:1:1:1555 :N:0:
NNNNNCAN
+
########
- at HiMom:7:1:1:164
+ at machine1:HiMom:abcdeACXX:7:1:1:164 :N:0:
NNNNNTTN
+
########
- at HiMom:7:1:1:1684
+ at machine1:HiMom:abcdeACXX:7:1:1:1684 :N:0:
NNNNNCGN
+
########
- at HiMom:7:1:1:1696
+ at machine1:HiMom:abcdeACXX:7:1:1:1696 :N:0:
NNNNNCTN
+
########
- at HiMom:7:1:1:170
+ at machine1:HiMom:abcdeACXX:7:1:1:170 :N:0:
NNNNNACN
+
########
- at HiMom:7:1:1:173
+ at machine1:HiMom:abcdeACXX:7:1:1:173 :N:0:
NNNNNCCN
+
########
- at HiMom:7:1:1:1733
+ at machine1:HiMom:abcdeACXX:7:1:1:1733 :N:0:
NNNNNGAN
+
########
- at HiMom:7:1:1:1770
+ at machine1:HiMom:abcdeACXX:7:1:1:1770 :N:0:
NNNNNTCN
+
########
- at HiMom:7:1:1:18
+ at machine1:HiMom:abcdeACXX:7:1:1:18 :N:0:
NNNNNCGN
+
########
- at HiMom:7:1:1:1815
+ at machine1:HiMom:abcdeACXX:7:1:1:1815 :N:0:
NNNTNGAC
+
########
- at HiMom:7:1:1:1836
+ at machine1:HiMom:abcdeACXX:7:1:1:1836 :N:0:
NNNNNGTN
+
########
- at HiMom:7:1:1:184
+ at machine1:HiMom:abcdeACXX:7:1:1:184 :N:0:
NNNNNGTN
+
########
- at HiMom:7:1:1:1886
+ at machine1:HiMom:abcdeACXX:7:1:1:1886 :Y:0:
NNNGNGCC
+
########
- at HiMom:7:1:1:1906
+ at machine1:HiMom:abcdeACXX:7:1:1:1906 :N:0:
NNNNNCGN
+
########
- at HiMom:7:1:1:1917
+ at machine1:HiMom:abcdeACXX:7:1:1:1917 :N:0:
NNNNNACN
+
########
- at HiMom:7:1:1:195
+ at machine1:HiMom:abcdeACXX:7:1:1:195 :N:0:
NNNNNCGN
+
########
- at HiMom:7:1:1:1954
+ at machine1:HiMom:abcdeACXX:7:1:1:1954 :N:0:
NNNNNCCN
+
########
- at HiMom:7:1:1:2
+ at machine1:HiMom:abcdeACXX:7:1:1:2 :N:0:
NNNNNNNN
+
########
- at HiMom:7:1:1:2011
+ at machine1:HiMom:abcdeACXX:7:1:1:2011 :N:0:
NNNGNTAG
+
########
- at HiMom:7:1:1:240
+ at machine1:HiMom:abcdeACXX:7:1:1:240 :N:0:
NNNNNGAN
+
########
- at HiMom:7:1:1:262
+ at machine1:HiMom:abcdeACXX:7:1:1:262 :N:0:
NNNNNCAN
+
########
- at HiMom:7:1:1:264
+ at machine1:HiMom:abcdeACXX:7:1:1:264 :N:0:
NNNNNCGA
+
########
- at HiMom:7:1:1:299
+ at machine1:HiMom:abcdeACXX:7:1:1:299 :N:0:
NNNNNCGN
+
########
- at HiMom:7:1:1:30
+ at machine1:HiMom:abcdeACXX:7:1:1:30 :N:0:
NNNNNACN
+
########
- at HiMom:7:1:1:353
+ at machine1:HiMom:abcdeACXX:7:1:1:353 :N:0:
NNNNNCGN
+
########
- at HiMom:7:1:1:367
+ at machine1:HiMom:abcdeACXX:7:1:1:367 :N:0:
NNNNNAGN
+
########
- at HiMom:7:1:1:41
+ at machine1:HiMom:abcdeACXX:7:1:1:41 :N:0:
NNNNNGAN
+
########
- at HiMom:7:1:1:416
+ at machine1:HiMom:abcdeACXX:7:1:1:416 :N:0:
NNNNNGAN
+
########
- at HiMom:7:1:1:483
+ at machine1:HiMom:abcdeACXX:7:1:1:483 :N:0:
NNNNNTAN
+
########
- at HiMom:7:1:1:486
+ at machine1:HiMom:abcdeACXX:7:1:1:486 :N:0:
NNNNNTGN
+
########
- at HiMom:7:1:1:495
+ at machine1:HiMom:abcdeACXX:7:1:1:495 :N:0:
NNNNNGAN
+
########
- at HiMom:7:1:1:508
+ at machine1:HiMom:abcdeACXX:7:1:1:508 :N:0:
NNNNNCTN
+
########
- at HiMom:7:1:1:517
+ at machine1:HiMom:abcdeACXX:7:1:1:517 :N:0:
NNNCNAGA
+
########
- at HiMom:7:1:1:535
+ at machine1:HiMom:abcdeACXX:7:1:1:535 :N:0:
NNNCNCGA
+
########
- at HiMom:7:1:1:55
+ at machine1:HiMom:abcdeACXX:7:1:1:55 :N:0:
NNNGNTTA
+
########
- at HiMom:7:1:1:554
+ at machine1:HiMom:abcdeACXX:7:1:1:554 :N:0:
NNNNNTAN
+
########
- at HiMom:7:1:1:567
+ at machine1:HiMom:abcdeACXX:7:1:1:567 :N:0:
NNNNNCCN
+
########
- at HiMom:7:1:1:59
+ at machine1:HiMom:abcdeACXX:7:1:1:59 :N:0:
NNNNNACN
+
########
- at HiMom:7:1:1:613
+ at machine1:HiMom:abcdeACXX:7:1:1:613 :N:0:
NNNNNAGN
+
########
- at HiMom:7:1:1:622
+ at machine1:HiMom:abcdeACXX:7:1:1:622 :N:0:
NNNNNAGN
+
########
- at HiMom:7:1:1:627
+ at machine1:HiMom:abcdeACXX:7:1:1:627 :N:0:
NNNNNGAN
+
########
- at HiMom:7:1:1:684
+ at machine1:HiMom:abcdeACXX:7:1:1:684 :N:0:
NNNNNGAN
+
########
- at HiMom:7:1:1:72
+ at machine1:HiMom:abcdeACXX:7:1:1:72 :N:0:
NNNTNGAC
+
########
- at HiMom:7:1:1:812
+ at machine1:HiMom:abcdeACXX:7:1:1:812 :N:0:
NNNNNGAN
+
########
- at HiMom:7:1:1:874
+ at machine1:HiMom:abcdeACXX:7:1:1:874 :N:0:
NNNNNGTN
+
########
- at HiMom:7:1:1:931
+ at machine1:HiMom:abcdeACXX:7:1:1:931 :N:0:
NNNNNCAN
+
########
- at HiMom:7:1:1:965
+ at machine1:HiMom:abcdeACXX:7:1:1:965 :N:0:
NNNTNTAA
+
########
- at HiMom:7:1:1:994
+ at machine1:HiMom:abcdeACXX:7:1:1:994 :N:0:
NNNNNCGN
+
########
- at HiMom:7:1:2:1158
+ at machine1:HiMom:abcdeACXX:7:1:2:1158 :Y:0:
NNCTTAGC
+
########
- at HiMom:7:1:2:1238
+ at machine1:HiMom:abcdeACXX:7:1:2:1238 :N:0:
NNCTAAGC
+
########
- at HiMom:7:1:2:1275
+ at machine1:HiMom:abcdeACXX:7:1:2:1275 :Y:0:
NNNANCTG
+
########
- at HiMom:7:1:2:1301
+ at machine1:HiMom:abcdeACXX:7:1:2:1301 :N:0:
NNNTAACA
+
########
- at HiMom:7:1:2:1453
+ at machine1:HiMom:abcdeACXX:7:1:2:1453 :Y:0:
NNACCAGG
+
########
- at HiMom:7:1:2:150
+ at machine1:HiMom:abcdeACXX:7:1:2:150 :N:0:
NNNANCCT
+
########
- at HiMom:7:1:2:1592
+ at machine1:HiMom:abcdeACXX:7:1:2:1592 :Y:0:
NNNGAGCC
+
########
- at HiMom:7:1:2:1706
+ at machine1:HiMom:abcdeACXX:7:1:2:1706 :Y:0:
NNNCNGAT
+
########
- at HiMom:7:1:2:1722
+ at machine1:HiMom:abcdeACXX:7:1:2:1722 :N:0:
NNNTCGAC
+
########
- at HiMom:7:1:2:1727
+ at machine1:HiMom:abcdeACXX:7:1:2:1727 :N:0:
NNNTNCTT
+
########
- at HiMom:7:1:2:1753
+ at machine1:HiMom:abcdeACXX:7:1:2:1753 :N:0:
NNTGCTTA
+
########
- at HiMom:7:1:2:1782
+ at machine1:HiMom:abcdeACXX:7:1:2:1782 :Y:0:
NNNTNAGC
+
########
- at HiMom:7:1:2:1827
+ at machine1:HiMom:abcdeACXX:7:1:2:1827 :Y:0:
NNCAACTG
+
########
- at HiMom:7:1:2:1932
+ at machine1:HiMom:abcdeACXX:7:1:2:1932 :Y:0:
NNNCNAGA
+
########
- at HiMom:7:1:2:1946
+ at machine1:HiMom:abcdeACXX:7:1:2:1946 :N:0:
NNNTNGAC
+
########
- at HiMom:7:1:2:209
+ at machine1:HiMom:abcdeACXX:7:1:2:209 :N:0:
NNCATTTC
+
########
- at HiMom:7:1:2:246
+ at machine1:HiMom:abcdeACXX:7:1:2:246 :N:0:
NNNANTTC
+
########
- at HiMom:7:1:2:25
+ at machine1:HiMom:abcdeACXX:7:1:2:25 :N:0:
NNNGATGA
+
########
- at HiMom:7:1:2:307
+ at machine1:HiMom:abcdeACXX:7:1:2:307 :N:0:
NNNTNGAC
+
########
- at HiMom:7:1:2:363
+ at machine1:HiMom:abcdeACXX:7:1:2:363 :N:0:
NNNTNCTT
+
########
- at HiMom:7:1:2:449
+ at machine1:HiMom:abcdeACXX:7:1:2:449 :N:0:
NNNGNTGT
+
########
- at HiMom:7:1:2:546
+ at machine1:HiMom:abcdeACXX:7:1:2:546 :N:0:
NNNANGTT
+
########
- at HiMom:7:1:2:605
+ at machine1:HiMom:abcdeACXX:7:1:2:605 :Y:0:
NNNTNGAC
+
########
- at HiMom:7:1:2:69
+ at machine1:HiMom:abcdeACXX:7:1:2:69 :N:0:
NNGGAGCC
+
########
- at HiMom:7:1:2:747
+ at machine1:HiMom:abcdeACXX:7:1:2:747 :N:0:
NNNCCAGG
+
########
- at HiMom:7:1:2:786
+ at machine1:HiMom:abcdeACXX:7:1:2:786 :Y:0:
NNNGATGT
+
########
- at HiMom:7:1:2:858
+ at machine1:HiMom:abcdeACXX:7:1:2:858 :Y:0:
NNACATCT
+
%%/57799
- at HiMom:7:1:2:943
+ at machine1:HiMom:abcdeACXX:7:1:2:943 :Y:0:
NNACCAGG
+
########
- at HiMom:7:1:2:974
+ at machine1:HiMom:abcdeACXX:7:1:2:974 :Y:0:
NNTATGTT
+
%%0::::<
- at HiMom:7:1:2:988
+ at machine1:HiMom:abcdeACXX:7:1:2:988 :Y:0:
NNTGGCGA
+
########
- at HiMom:7:1:3:1233
+ at machine1:HiMom:abcdeACXX:7:1:3:1233 :N:0:
CCAACAGG
+
########
- at HiMom:7:1:3:1294
+ at machine1:HiMom:abcdeACXX:7:1:3:1294 :N:0:
TCACAATG
+
*37<<@5<
- at HiMom:7:1:3:405
+ at machine1:HiMom:abcdeACXX:7:1:3:405 :N:0:
ACACAAGA
+
0(><=###
- at HiMom:7:1:3:579
+ at machine1:HiMom:abcdeACXX:7:1:3:579 :N:0:
AATCATGT
+
73######
- at HiMom:7:1:3:673
+ at machine1:HiMom:abcdeACXX:7:1:3:673 :N:0:
TGCCCAAA
+
(<######
- at HiMom:7:1:3:890
+ at machine1:HiMom:abcdeACXX:7:1:3:890 :N:0:
GTCACCAT
+
########
- at HiMom:7:1:3:905
+ at machine1:HiMom:abcdeACXX:7:1:3:905 :N:0:
ACATCCTA
+
AA78/<:#
- at HiMom:7:1:3:918
+ at machine1:HiMom:abcdeACXX:7:1:3:918 :N:0:
ACTACCTT
+
)?4B>###
- at HiMom:7:2:0:1073
+ at machine1:HiMom:abcdeACXX:7:2:0:1073 :N:0:
NNNNNCAN
+
########
- at HiMom:7:2:0:1135
+ at machine1:HiMom:abcdeACXX:7:2:0:1135 :N:0:
NNNNNAGN
+
########
- at HiMom:7:2:0:1198
+ at machine1:HiMom:abcdeACXX:7:2:0:1198 :N:0:
NNNNNCCN
+
########
- at HiMom:7:2:0:1278
+ at machine1:HiMom:abcdeACXX:7:2:0:1278 :N:0:
NNNNNTAN
+
########
- at HiMom:7:2:0:135
+ at machine1:HiMom:abcdeACXX:7:2:0:135 :N:0:
NNNNNCGN
+
########
- at HiMom:7:2:0:1547
+ at machine1:HiMom:abcdeACXX:7:2:0:1547 :N:0:
NNNNNCAN
+
########
- at HiMom:7:2:0:1598
+ at machine1:HiMom:abcdeACXX:7:2:0:1598 :N:0:
NNNNNAGN
+
########
- at HiMom:7:2:0:1620
+ at machine1:HiMom:abcdeACXX:7:2:0:1620 :N:0:
NNNNNTGN
+
########
- at HiMom:7:2:0:1668
+ at machine1:HiMom:abcdeACXX:7:2:0:1668 :N:0:
NNNNNCTN
+
########
- at HiMom:7:2:0:186
+ at machine1:HiMom:abcdeACXX:7:2:0:186 :N:0:
NNNNNCCN
+
########
- at HiMom:7:2:0:205
+ at machine1:HiMom:abcdeACXX:7:2:0:205 :N:0:
NNNNNAGN
+
########
- at HiMom:7:2:0:287
+ at machine1:HiMom:abcdeACXX:7:2:0:287 :N:0:
NNNNNGAN
+
########
- at HiMom:7:2:0:382
+ at machine1:HiMom:abcdeACXX:7:2:0:382 :N:0:
NNNNNTAN
+
########
- at HiMom:7:2:0:441
+ at machine1:HiMom:abcdeACXX:7:2:0:441 :N:0:
NNNNNAGN
+
########
- at HiMom:7:2:0:50
+ at machine1:HiMom:abcdeACXX:7:2:0:50 :N:0:
NNNNNGAN
+
########
- at HiMom:7:2:0:501
+ at machine1:HiMom:abcdeACXX:7:2:0:501 :N:0:
NNNNNTAN
+
########
- at HiMom:7:2:0:73
+ at machine1:HiMom:abcdeACXX:7:2:0:73 :N:0:
NNNNNCGN
+
########
- at HiMom:7:2:0:740
+ at machine1:HiMom:abcdeACXX:7:2:0:740 :N:0:
NNNNNGGN
+
########
- at HiMom:7:2:0:766
+ at machine1:HiMom:abcdeACXX:7:2:0:766 :N:0:
NNNNNCCN
+
########
- at HiMom:7:2:0:87
+ at machine1:HiMom:abcdeACXX:7:2:0:87 :N:0:
NNNNNCGN
+
########
- at HiMom:7:2:1:1004
+ at machine1:HiMom:abcdeACXX:7:2:1:1004 :N:0:
NNNGCCGA
+
########
- at HiMom:7:2:1:1034
+ at machine1:HiMom:abcdeACXX:7:2:1:1034 :N:0:
NNNAGCCT
+
########
- at HiMom:7:2:1:1159
+ at machine1:HiMom:abcdeACXX:7:2:1:1159 :N:0:
NNNTNGAC
+
########
- at HiMom:7:2:1:1168
+ at machine1:HiMom:abcdeACXX:7:2:1:1168 :N:0:
NNNGNTAG
+
########
- at HiMom:7:2:1:1180
+ at machine1:HiMom:abcdeACXX:7:2:1:1180 :N:0:
NNNTNAGC
+
########
- at HiMom:7:2:1:1214
+ at machine1:HiMom:abcdeACXX:7:2:1:1214 :N:0:
NNNCATGA
+
########
- at HiMom:7:2:1:1221
+ at machine1:HiMom:abcdeACXX:7:2:1:1221 :N:0:
NNGGATGT
+
########
- at HiMom:7:2:1:1306
+ at machine1:HiMom:abcdeACXX:7:2:1:1306 :N:0:
NNNANCTG
+
########
- at HiMom:7:2:1:1351
+ at machine1:HiMom:abcdeACXX:7:2:1:1351 :N:0:
NNNNNTTN
+
########
- at HiMom:7:2:1:1424
+ at machine1:HiMom:abcdeACXX:7:2:1:1424 :N:0:
NNNCNTCT
+
########
- at HiMom:7:2:1:1452
+ at machine1:HiMom:abcdeACXX:7:2:1:1452 :N:0:
NNAGATCC
+
########
- at HiMom:7:2:1:1515
+ at machine1:HiMom:abcdeACXX:7:2:1:1515 :N:0:
NNNGNATG
+
########
- at HiMom:7:2:1:1521
+ at machine1:HiMom:abcdeACXX:7:2:1:1521 :N:0:
NNNCNAGG
+
########
- at HiMom:7:2:1:1536
+ at machine1:HiMom:abcdeACXX:7:2:1:1536 :N:0:
NNACATCT
+
########
- at HiMom:7:2:1:1543
+ at machine1:HiMom:abcdeACXX:7:2:1:1543 :N:0:
NNNANTTC
+
########
- at HiMom:7:2:1:1617
+ at machine1:HiMom:abcdeACXX:7:2:1:1617 :N:0:
NNNCNAGG
+
########
- at HiMom:7:2:1:1627
+ at machine1:HiMom:abcdeACXX:7:2:1:1627 :N:0:
NNNANCTG
+
########
- at HiMom:7:2:1:1646
+ at machine1:HiMom:abcdeACXX:7:2:1:1646 :N:0:
NNNTNGAC
+
########
- at HiMom:7:2:1:1653
+ at machine1:HiMom:abcdeACXX:7:2:1:1653 :N:0:
NNNGNTGT
+
########
- at HiMom:7:2:1:1682
+ at machine1:HiMom:abcdeACXX:7:2:1:1682 :N:0:
NNNGNGCC
+
########
- at HiMom:7:2:1:170
+ at machine1:HiMom:abcdeACXX:7:2:1:170 :Y:0:
NNGAGCCT
+
########
- at HiMom:7:2:1:1731
+ at machine1:HiMom:abcdeACXX:7:2:1:1731 :N:0:
NNNTNAGC
+
########
- at HiMom:7:2:1:1755
+ at machine1:HiMom:abcdeACXX:7:2:1:1755 :N:0:
NNNNNCAN
+
########
- at HiMom:7:2:1:1812
+ at machine1:HiMom:abcdeACXX:7:2:1:1812 :N:0:
NNNCNTAT
+
########
- at HiMom:7:2:1:1853
+ at machine1:HiMom:abcdeACXX:7:2:1:1853 :N:0:
NNNCNCGA
+
########
- at HiMom:7:2:1:1919
+ at machine1:HiMom:abcdeACXX:7:2:1:1919 :N:0:
NNNANCTG
+
########
- at HiMom:7:2:1:1924
+ at machine1:HiMom:abcdeACXX:7:2:1:1924 :N:0:
NNNAACTG
+
########
- at HiMom:7:2:1:1933
+ at machine1:HiMom:abcdeACXX:7:2:1:1933 :N:0:
NNNTTAGC
+
########
- at HiMom:7:2:1:1938
+ at machine1:HiMom:abcdeACXX:7:2:1:1938 :Y:0:
NNCTCGAC
+
########
- at HiMom:7:2:1:1950
+ at machine1:HiMom:abcdeACXX:7:2:1:1950 :N:0:
NNNNNGTN
+
########
- at HiMom:7:2:1:1959
+ at machine1:HiMom:abcdeACXX:7:2:1:1959 :N:0:
NNTGCTTA
+
########
- at HiMom:7:2:1:1987
+ at machine1:HiMom:abcdeACXX:7:2:1:1987 :N:0:
NNNNNTAN
+
########
- at HiMom:7:2:1:2006
+ at machine1:HiMom:abcdeACXX:7:2:1:2006 :N:0:
NNNGNGCC
+
########
- at HiMom:7:2:1:211
+ at machine1:HiMom:abcdeACXX:7:2:1:211 :N:0:
NNNGNTGT
+
########
- at HiMom:7:2:1:234
+ at machine1:HiMom:abcdeACXX:7:2:1:234 :N:0:
NNNGCTTA
+
########
- at HiMom:7:2:1:242
+ at machine1:HiMom:abcdeACXX:7:2:1:242 :N:0:
NNNCNCGC
+
########
- at HiMom:7:2:1:262
+ at machine1:HiMom:abcdeACXX:7:2:1:262 :N:0:
NNNCNAGG
+
########
- at HiMom:7:2:1:298
+ at machine1:HiMom:abcdeACXX:7:2:1:298 :N:0:
NNNGNTAG
+
########
- at HiMom:7:2:1:312
+ at machine1:HiMom:abcdeACXX:7:2:1:312 :N:0:
NNNANGTT
+
########
- at HiMom:7:2:1:363
+ at machine1:HiMom:abcdeACXX:7:2:1:363 :Y:0:
NNTATGTT
+
%%.99999
- at HiMom:7:2:1:37
+ at machine1:HiMom:abcdeACXX:7:2:1:37 :N:0:
NNNGNCGA
+
########
- at HiMom:7:2:1:370
+ at machine1:HiMom:abcdeACXX:7:2:1:370 :N:0:
NNNANCAT
+
########
- at HiMom:7:2:1:377
+ at machine1:HiMom:abcdeACXX:7:2:1:377 :N:0:
NNNCNTCT
+
########
- at HiMom:7:2:1:414
+ at machine1:HiMom:abcdeACXX:7:2:1:414 :N:0:
NNNGNTTA
+
########
- at HiMom:7:2:1:421
+ at machine1:HiMom:abcdeACXX:7:2:1:421 :N:0:
NNNANCCT
+
########
- at HiMom:7:2:1:428
+ at machine1:HiMom:abcdeACXX:7:2:1:428 :N:0:
NNNATGTT
+
########
- at HiMom:7:2:1:44
+ at machine1:HiMom:abcdeACXX:7:2:1:44 :N:0:
NNNAGCGA
+
########
- at HiMom:7:2:1:466
+ at machine1:HiMom:abcdeACXX:7:2:1:466 :N:0:
NNNTNACA
+
########
- at HiMom:7:2:1:555
+ at machine1:HiMom:abcdeACXX:7:2:1:555 :N:0:
NNNCNGAT
+
########
- at HiMom:7:2:1:558
+ at machine1:HiMom:abcdeACXX:7:2:1:558 :N:0:
NNNANCGA
+
########
- at HiMom:7:2:1:56
+ at machine1:HiMom:abcdeACXX:7:2:1:56 :N:0:
NNNTNAGC
+
########
- at HiMom:7:2:1:569
+ at machine1:HiMom:abcdeACXX:7:2:1:569 :N:0:
NNNANCTG
+
########
- at HiMom:7:2:1:604
+ at machine1:HiMom:abcdeACXX:7:2:1:604 :N:0:
NNCAACTG
+
########
- at HiMom:7:2:1:628
+ at machine1:HiMom:abcdeACXX:7:2:1:628 :N:0:
NNNTAACA
+
########
- at HiMom:7:2:1:64
+ at machine1:HiMom:abcdeACXX:7:2:1:64 :N:0:
NNNANGTT
+
########
- at HiMom:7:2:1:684
+ at machine1:HiMom:abcdeACXX:7:2:1:684 :N:0:
NNAAACGA
+
########
- at HiMom:7:2:1:699
+ at machine1:HiMom:abcdeACXX:7:2:1:699 :N:0:
NNNCNCGA
+
########
- at HiMom:7:2:1:714
+ at machine1:HiMom:abcdeACXX:7:2:1:714 :N:0:
NNNAGCGA
+
########
- at HiMom:7:2:1:722
+ at machine1:HiMom:abcdeACXX:7:2:1:722 :N:0:
NNNCNAGG
+
########
- at HiMom:7:2:1:749
+ at machine1:HiMom:abcdeACXX:7:2:1:749 :N:0:
NNNTNGAC
+
########
- at HiMom:7:2:1:760
+ at machine1:HiMom:abcdeACXX:7:2:1:760 :N:0:
NNACAACA
+
########
- at HiMom:7:2:1:8
+ at machine1:HiMom:abcdeACXX:7:2:1:8 :N:0:
NNNANNNN
+
########
- at HiMom:7:2:1:833
+ at machine1:HiMom:abcdeACXX:7:2:1:833 :N:0:
NNNANCCT
+
########
- at HiMom:7:2:1:848
+ at machine1:HiMom:abcdeACXX:7:2:1:848 :N:0:
NNNANCGA
+
########
- at HiMom:7:2:1:893
+ at machine1:HiMom:abcdeACXX:7:2:1:893 :N:0:
NNCAATTC
+
########
- at HiMom:7:2:1:998
+ at machine1:HiMom:abcdeACXX:7:2:1:998 :N:0:
NNNANGTT
+
########
- at HiMom:7:2:2:0
+ at machine1:HiMom:abcdeACXX:7:2:2:0 :N:0:
NNNNNNNN
+
########
- at HiMom:7:2:2:131
+ at machine1:HiMom:abcdeACXX:7:2:2:131 :Y:0:
CACAATCC
+
AACCBCA@
- at HiMom:7:2:2:1636
+ at machine1:HiMom:abcdeACXX:7:2:2:1636 :N:0:
ATCAACCC
+
368?####
- at HiMom:7:2:2:1974
+ at machine1:HiMom:abcdeACXX:7:2:2:1974 :N:0:
AGCAATCT
+
>#######
- at HiMom:7:2:2:351
+ at machine1:HiMom:abcdeACXX:7:2:2:351 :N:0:
TGATAGAA
+
########
- at HiMom:7:2:2:646
+ at machine1:HiMom:abcdeACXX:7:2:2:646 :N:0:
ATCAATTA
+
((>4/406
- at HiMom:7:2:2:828
+ at machine1:HiMom:abcdeACXX:7:2:2:828 :N:0:
TATATCGA
+
########
- at HiMom:7:2:3:1529
+ at machine1:HiMom:abcdeACXX:7:2:3:1529 :N:0:
TAGAACCT
+
9)@73?B=
- at HiMom:7:2:3:179
+ at machine1:HiMom:abcdeACXX:7:2:3:179 :N:0:
GTTTATTA
+
########
- at HiMom:7:2:3:198
+ at machine1:HiMom:abcdeACXX:7:2:3:198 :N:0:
CAGGATCT
+
5)0*@782
- at HiMom:7:2:3:2030
+ at machine1:HiMom:abcdeACXX:7:2:3:2030 :N:0:
GATCAAGA
+
(((>(<@<
- at HiMom:7:2:3:247
+ at machine1:HiMom:abcdeACXX:7:2:3:247 :N:0:
CGGTAGCT
+
########
- at HiMom:7:2:3:4
+ at machine1:HiMom:abcdeACXX:7:2:3:4 :N:0:
NNNNNNNN
+
########
- at HiMom:7:2:3:862
+ at machine1:HiMom:abcdeACXX:7:2:3:862 :N:0:
TAACAAGA
+
4)=69)=@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/NN.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/NN.1.fastq
index b602901..9603643 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/NN.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/NN.1.fastq
@@ -1,892 +1,892 @@
- at HiMom:9:1:0:1038
+ at machine1:HiMom:abcdeACXX:9:1:0:1038 :N:0:
NNNNNCNNCANNNCNNNCNCCNNNCNNNNN
+
##############################
- at HiMom:9:1:0:1093
+ at machine1:HiMom:abcdeACXX:9:1:0:1093 :N:0:
NNNNNCNNGTNNNANNNGNAANNNANNNNN
+
##############################
- at HiMom:9:1:0:113
+ at machine1:HiMom:abcdeACXX:9:1:0:113 :N:0:
NNNNNNNNGNNNNNNNNNNNANNNNNNNNN
+
##############################
- at HiMom:9:1:0:1193
+ at machine1:HiMom:abcdeACXX:9:1:0:1193 :N:0:
NNNNNNNNTNNNNTNNNTNNTNNNCNNNNN
+
##############################
- at HiMom:9:1:0:1291
+ at machine1:HiMom:abcdeACXX:9:1:0:1291 :N:0:
NNNNNNNNANNNNNNNNANNTNNNNNNNNN
+
##############################
- at HiMom:9:1:0:1307
+ at machine1:HiMom:abcdeACXX:9:1:0:1307 :N:0:
NNNNNNNNCNNNNANNNTNNTNNNCNNNNN
+
##############################
- at HiMom:9:1:0:1434
+ at machine1:HiMom:abcdeACXX:9:1:0:1434 :N:0:
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
##############################
- at HiMom:9:1:0:1475
+ at machine1:HiMom:abcdeACXX:9:1:0:1475 :N:0:
NNNNNGNNANNNNANNNANNANNNANNNNN
+
##############################
- at HiMom:9:1:0:1690
+ at machine1:HiMom:abcdeACXX:9:1:0:1690 :N:0:
NNNNNNNNANNNNNNNNGNNCNNNCNNNNN
+
##############################
- at HiMom:9:1:0:1703
+ at machine1:HiMom:abcdeACXX:9:1:0:1703 :N:0:
NNNNNNNNANNNNNNNNNNNANNNNNNNNN
+
##############################
- at HiMom:9:1:0:1940
+ at machine1:HiMom:abcdeACXX:9:1:0:1940 :N:0:
NNNNNNNNCNNNNNNNNTNNTNNNNNNNNN
+
##############################
- at HiMom:9:1:0:2001
+ at machine1:HiMom:abcdeACXX:9:1:0:2001 :N:0:
NNNNNANNTGNNNGNNNANGCNNNANNNNN
+
##############################
- at HiMom:9:1:0:205
+ at machine1:HiMom:abcdeACXX:9:1:0:205 :N:0:
NNNNNNNNANNNNNNNNANNTNNNANNNNN
+
##############################
- at HiMom:9:1:0:275
+ at machine1:HiMom:abcdeACXX:9:1:0:275 :N:0:
NNNNNANNCANNNTNNNGNCCNNNANNNNN
+
##############################
- at HiMom:9:1:0:324
+ at machine1:HiMom:abcdeACXX:9:1:0:324 :N:0:
NNNNNNNNTNNNNNNNNTNNANNNANNNNN
+
##############################
- at HiMom:9:1:0:37
+ at machine1:HiMom:abcdeACXX:9:1:0:37 :N:0:
NNNNNNNNANNNNNNNNCNNTNNNCNNNNN
+
##############################
- at HiMom:9:1:0:464
+ at machine1:HiMom:abcdeACXX:9:1:0:464 :N:0:
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
##############################
- at HiMom:9:1:0:586
+ at machine1:HiMom:abcdeACXX:9:1:0:586 :N:0:
NNNNNNNNCNNNNNNNNCNNCNNNANNNNN
+
##############################
- at HiMom:9:1:0:841
+ at machine1:HiMom:abcdeACXX:9:1:0:841 :N:0:
NNNNNNNNCNNNNNNNNNNNTNNNNNNNNN
+
##############################
- at HiMom:9:1:0:879
+ at machine1:HiMom:abcdeACXX:9:1:0:879 :N:0:
NNNNNNNNTNNNNNNNNNNNTNNNNNNNNN
+
##############################
- at HiMom:9:1:1:1013
+ at machine1:HiMom:abcdeACXX:9:1:1:1013 :N:0:
NNCNNTNCAGNNNCNNNANGTNNNGNNNNN
+
##############################
- at HiMom:9:1:1:111
+ at machine1:HiMom:abcdeACXX:9:1:1:111 :N:0:
NNCNNTNGCGNNNTNNNANCTNNNTNNNNN
+
##############################
- at HiMom:9:1:1:1153
+ at machine1:HiMom:abcdeACXX:9:1:1:1153 :N:0:
NNTNNTNTGGNNNTNNNCNTCNNNTNNNNN
+
##############################
- at HiMom:9:1:1:1184
+ at machine1:HiMom:abcdeACXX:9:1:1:1184 :N:0:
NNANNGNTCGNNNANNNTNCANNNTNNNNN
+
##############################
- at HiMom:9:1:1:1241
+ at machine1:HiMom:abcdeACXX:9:1:1:1241 :N:0:
NNANNGNTGGNNNTNNNCNTGNNNANNNNN
+
##############################
- at HiMom:9:1:1:1243
+ at machine1:HiMom:abcdeACXX:9:1:1:1243 :N:0:
NNANNANGGANNNANNNCNTANNNTNNNNN
+
##############################
- at HiMom:9:1:1:1247
+ at machine1:HiMom:abcdeACXX:9:1:1:1247 :N:0:
NCCAGCNTTTNNNTNNNTNCTNNNGNNNNN
+
##############################
- at HiMom:9:1:1:1282
+ at machine1:HiMom:abcdeACXX:9:1:1:1282 :N:0:
NNANNANGGGNNNTNNNGNAGNNNCNNNNN
+
##############################
- at HiMom:9:1:1:132
+ at machine1:HiMom:abcdeACXX:9:1:1:132 :N:0:
NNANNGNGGGNNNGNNNGNGGNNNGNNNNN
+
##############################
- at HiMom:9:1:1:1320
+ at machine1:HiMom:abcdeACXX:9:1:1:1320 :N:0:
NNANNTNAGTNNNGNNNGNTANNNCNNNNN
+
##############################
- at HiMom:9:1:1:1372
+ at machine1:HiMom:abcdeACXX:9:1:1:1372 :N:0:
NACATTTTTTAGNTNANTTGTTNACNANNN
+
##############################
- at HiMom:9:1:1:1379
+ at machine1:HiMom:abcdeACXX:9:1:1:1379 :N:0:
NAATATAATTNNNTNNNTTAGANTTNNNNN
+
##############################
- at HiMom:9:1:1:1391
+ at machine1:HiMom:abcdeACXX:9:1:1:1391 :N:0:
NNGNNTNTAANNNANNNTNATNNNTNNNNN
+
##############################
- at HiMom:9:1:1:140
+ at machine1:HiMom:abcdeACXX:9:1:1:140 :N:0:
NNANNTNTAANNNGNNNCNTTNNNTNNNNN
+
##############################
- at HiMom:9:1:1:1513
+ at machine1:HiMom:abcdeACXX:9:1:1:1513 :N:0:
NNNNNANNTTNNNANNNANAANNNCNNNNN
+
##############################
- at HiMom:9:1:1:1521
+ at machine1:HiMom:abcdeACXX:9:1:1:1521 :N:0:
NAACAANATTNNNTNNNANTANNTANNNNN
+
##############################
- at HiMom:9:1:1:155
+ at machine1:HiMom:abcdeACXX:9:1:1:155 :N:0:
NNGNNCNAGTNNNCNNNANTTNNNGNNNNN
+
##############################
- at HiMom:9:1:1:1555
+ at machine1:HiMom:abcdeACXX:9:1:1:1555 :N:0:
NNTNNGNAGANNNANNNCNTANNNANNNNN
+
##############################
- at HiMom:9:1:1:164
+ at machine1:HiMom:abcdeACXX:9:1:1:164 :N:0:
NNANNANTAANNNTNNNTNATNNNTNNNNN
+
##############################
- at HiMom:9:1:1:1684
+ at machine1:HiMom:abcdeACXX:9:1:1:1684 :N:0:
NNGNNANGGTNNNGNNNTNTCNNNTNNNNN
+
##############################
- at HiMom:9:1:1:1696
+ at machine1:HiMom:abcdeACXX:9:1:1:1696 :N:0:
NNANNGNNGCNNNGNNNANACNNNTNNNNN
+
##############################
- at HiMom:9:1:1:170
+ at machine1:HiMom:abcdeACXX:9:1:1:170 :N:0:
NNTNNCNCACNNNGNNNGNTCNNNGNNNNN
+
##############################
- at HiMom:9:1:1:173
+ at machine1:HiMom:abcdeACXX:9:1:1:173 :N:0:
NNNNNANNATNNNTNNNCNTTNNNTNNNNN
+
##############################
- at HiMom:9:1:1:1733
+ at machine1:HiMom:abcdeACXX:9:1:1:1733 :N:0:
NNANNGNGTCNNNTNNNTNAGNNNANNNNN
+
##############################
- at HiMom:9:1:1:1770
+ at machine1:HiMom:abcdeACXX:9:1:1:1770 :N:0:
NNCNNTNCTGNNNGNNNGNCANNNANNNNN
+
##############################
- at HiMom:9:1:1:18
+ at machine1:HiMom:abcdeACXX:9:1:1:18 :N:0:
NATCAGNCTGNNNANNNTNGTNNAANNNNN
+
##############################
- at HiMom:9:1:1:1815
+ at machine1:HiMom:abcdeACXX:9:1:1:1815 :N:0:
NATGAAAATANNNTNNNTAAATNATNNNNN
+
##############################
- at HiMom:9:1:1:1836
+ at machine1:HiMom:abcdeACXX:9:1:1:1836 :N:0:
NNNNNGNNTANNNGNNNTNCTNNNCNNNNN
+
##############################
- at HiMom:9:1:1:184
+ at machine1:HiMom:abcdeACXX:9:1:1:184 :N:0:
NNCNNTNTAANNNANNNTNATNNNGNNNNN
+
##############################
- at HiMom:9:1:1:1886
+ at machine1:HiMom:abcdeACXX:9:1:1:1886 :Y:0:
NACATATGCATACATATATAATAGATANNN
+
%.9:;<217;:999;<;;<<<;;#######
- at HiMom:9:1:1:1906
+ at machine1:HiMom:abcdeACXX:9:1:1:1906 :N:0:
NNTNNCNATANNNCNNNTNCTNNNGNNNNN
+
##############################
- at HiMom:9:1:1:1917
+ at machine1:HiMom:abcdeACXX:9:1:1:1917 :N:0:
NNNNNTNNGANNNCNNNANAANNNANNNNN
+
##############################
- at HiMom:9:1:1:195
+ at machine1:HiMom:abcdeACXX:9:1:1:195 :N:0:
NNANNGNGTGNNNGNNNCNATNNNANNNNN
+
##############################
- at HiMom:9:1:1:1954
+ at machine1:HiMom:abcdeACXX:9:1:1:1954 :N:0:
NAGANTNCTTNNNGNNNGNAGNNNCNNNNN
+
##############################
- at HiMom:9:1:1:2
+ at machine1:HiMom:abcdeACXX:9:1:1:2 :N:0:
NNANNGNGAANNNCNNNNNNNNNNNNNNNN
+
##############################
- at HiMom:9:1:1:2011
+ at machine1:HiMom:abcdeACXX:9:1:1:2011 :N:0:
NACAGCTGGCANNTNNNAGAGCNAGNANNN
+
##############################
- at HiMom:9:1:1:240
+ at machine1:HiMom:abcdeACXX:9:1:1:240 :N:0:
NNGNNANGTANNNTNNNTNCCNNNCNNNNN
+
##############################
- at HiMom:9:1:1:262
+ at machine1:HiMom:abcdeACXX:9:1:1:262 :N:0:
NNCNNGNCATNNNANNNCNTGNNNCNNNNN
+
##############################
- at HiMom:9:1:1:264
+ at machine1:HiMom:abcdeACXX:9:1:1:264 :N:0:
NAACTGNAATNNNCNNNANCANNCTNNNNN
+
##############################
- at HiMom:9:1:1:299
+ at machine1:HiMom:abcdeACXX:9:1:1:299 :N:0:
NNCNNTNGCANNNANNNCNAANNNTNNNNN
+
##############################
- at HiMom:9:1:1:30
+ at machine1:HiMom:abcdeACXX:9:1:1:30 :N:0:
NNANNANTTTNNNTNNNGNTCNNNTNNNNN
+
##############################
- at HiMom:9:1:1:353
+ at machine1:HiMom:abcdeACXX:9:1:1:353 :N:0:
NNANNTNTAGNNNANNNTNATNNNANNNNN
+
##############################
- at HiMom:9:1:1:367
+ at machine1:HiMom:abcdeACXX:9:1:1:367 :N:0:
NNANNTNAGCNNNGNNNANGTNNNCNNNNN
+
##############################
- at HiMom:9:1:1:41
+ at machine1:HiMom:abcdeACXX:9:1:1:41 :N:0:
NNANNCNAAANNNGNNNTNCANNNCNNNNN
+
##############################
- at HiMom:9:1:1:416
+ at machine1:HiMom:abcdeACXX:9:1:1:416 :N:0:
NNANNCNAATNNNGNNNGNACNNNCNNNNN
+
##############################
- at HiMom:9:1:1:483
+ at machine1:HiMom:abcdeACXX:9:1:1:483 :N:0:
NNGNNGNGGGNNNGNNNGNTTNNNTNNNNN
+
##############################
- at HiMom:9:1:1:486
+ at machine1:HiMom:abcdeACXX:9:1:1:486 :N:0:
NNANNANTTTNNNANNNANAGNNNTNNNNN
+
##############################
- at HiMom:9:1:1:495
+ at machine1:HiMom:abcdeACXX:9:1:1:495 :N:0:
NNCNNANCGTNNNTNNNTNAANNNCNNNNN
+
##############################
- at HiMom:9:1:1:508
+ at machine1:HiMom:abcdeACXX:9:1:1:508 :N:0:
NNGNNCNCAGNNNTNNNCNCTNNNCNNNNN
+
##############################
- at HiMom:9:1:1:517
+ at machine1:HiMom:abcdeACXX:9:1:1:517 :N:0:
NTCATAAAACATCANTATTGGAAAGGANNN
+
%.75:<999578##################
- at HiMom:9:1:1:535
+ at machine1:HiMom:abcdeACXX:9:1:1:535 :N:0:
NGCCCAAGTATTGANTATGTGCTCTAANNN
+
%.599:7187:940%0::52599#######
- at HiMom:9:1:1:55
+ at machine1:HiMom:abcdeACXX:9:1:1:55 :N:0:
NTTTATGTCCTTNANAACTTAGNAGTTNNN
+
%/9<<83599####################
- at HiMom:9:1:1:554
+ at machine1:HiMom:abcdeACXX:9:1:1:554 :N:0:
NNANNGNAGANNNGNNNTNTCNNNANNNNN
+
##############################
- at HiMom:9:1:1:567
+ at machine1:HiMom:abcdeACXX:9:1:1:567 :N:0:
NNCNNCNGTTNNNCNNNGNACNNNCNNNNN
+
##############################
- at HiMom:9:1:1:59
+ at machine1:HiMom:abcdeACXX:9:1:1:59 :N:0:
NNANNGNTGCNNNTNNNTNACNNNANNNNN
+
##############################
- at HiMom:9:1:1:613
+ at machine1:HiMom:abcdeACXX:9:1:1:613 :N:0:
NNGNNANTATNNNCNNNGNATNNNANNNNN
+
##############################
- at HiMom:9:1:1:622
+ at machine1:HiMom:abcdeACXX:9:1:1:622 :N:0:
NNTNNCNAGTNNNCNNNANCTNNNTNNNNN
+
##############################
- at HiMom:9:1:1:627
+ at machine1:HiMom:abcdeACXX:9:1:1:627 :N:0:
NNANNTNGACNNNTNNNANGCNNNCNNNNN
+
##############################
- at HiMom:9:1:1:684
+ at machine1:HiMom:abcdeACXX:9:1:1:684 :N:0:
NNTNNTNAGANNNCNNNANAGNNNANNNNN
+
##############################
- at HiMom:9:1:1:72
+ at machine1:HiMom:abcdeACXX:9:1:1:72 :N:0:
NACACACATATCACNCACATCATACACNNN
+
%..48696;5:6;.%)49;;;9########
- at HiMom:9:1:1:812
+ at machine1:HiMom:abcdeACXX:9:1:1:812 :N:0:
NNANNCNAAGNNNTNNNANTCNNNANNNNN
+
##############################
- at HiMom:9:1:1:874
+ at machine1:HiMom:abcdeACXX:9:1:1:874 :N:0:
NNANNANGCCNNNGNNNTNTANNNTNNNNN
+
##############################
- at HiMom:9:1:1:931
+ at machine1:HiMom:abcdeACXX:9:1:1:931 :N:0:
NNTNNGNGATNNNGNNNCNTTNNNCNNNNN
+
##############################
- at HiMom:9:1:1:965
+ at machine1:HiMom:abcdeACXX:9:1:1:965 :N:0:
NACTAATCTTCCGCNCATATCCCCAAANNN
+
##############################
- at HiMom:9:1:1:994
+ at machine1:HiMom:abcdeACXX:9:1:1:994 :N:0:
NNANNTNGATNNNTNNNGNTTNNNCNNNNN
+
##############################
- at HiMom:9:1:2:1158
+ at machine1:HiMom:abcdeACXX:9:1:2:1158 :Y:0:
NGGGTCCTTCATAGTTTTTTTCTACTTTCC
+
%0777646;099:::95;;;688::99###
- at HiMom:9:1:2:1238
+ at machine1:HiMom:abcdeACXX:9:1:2:1238 :N:0:
NTCCTTATATTCAATTATTAATATTTTTAC
+
##############################
- at HiMom:9:1:2:1275
+ at machine1:HiMom:abcdeACXX:9:1:2:1275 :Y:0:
NAGTGAAATAAGCCAGACACAGAAAGACAN
+
%/5204:99971773,44755-39717###
- at HiMom:9:1:2:1301
+ at machine1:HiMom:abcdeACXX:9:1:2:1301 :N:0:
NAGTAGACTGCATTAATTAATTGGAAGAGN
+
%0370)024263144:48;;##########
- at HiMom:9:1:2:1453
+ at machine1:HiMom:abcdeACXX:9:1:2:1453 :Y:0:
NATATCTTATTTTCTTTTCTTTCAGGCTCT
+
%.:7,,395255##################
- at HiMom:9:1:2:150
+ at machine1:HiMom:abcdeACXX:9:1:2:150 :N:0:
NAAGACTTGATTATATCCCTTGTATGANNN
+
##############################
- at HiMom:9:1:2:1592
+ at machine1:HiMom:abcdeACXX:9:1:2:1592 :Y:0:
NGAAAACTGGCACAAGACAAGGATGCCCTC
+
%,67786861,3466(8485868648583#
- at HiMom:9:1:2:1706
+ at machine1:HiMom:abcdeACXX:9:1:2:1706 :Y:0:
NGATATGTGGATACAGCTCACAAAGAGNNN
+
%,99:6/566999/7###############
- at HiMom:9:1:2:1722
+ at machine1:HiMom:abcdeACXX:9:1:2:1722 :N:0:
NAAAGAAAATTAAAGAAAAATATACACGTN
+
##############################
- at HiMom:9:1:2:1727
+ at machine1:HiMom:abcdeACXX:9:1:2:1727 :N:0:
NTATTGAAGGACTTTTGTATCCTCCTTATN
+
##############################
- at HiMom:9:1:2:1753
+ at machine1:HiMom:abcdeACXX:9:1:2:1753 :N:0:
NGTTCACACAAGGATAATATTTTTGATTAT
+
##############################
- at HiMom:9:1:2:1782
+ at machine1:HiMom:abcdeACXX:9:1:2:1782 :Y:0:
NACCAAGTGTTTGGAGTATGCTGCCTANNN
+
%0:::668885-5335/85###########
- at HiMom:9:1:2:1827
+ at machine1:HiMom:abcdeACXX:9:1:2:1827 :Y:0:
NAACCGAGGATGTACACTGTCCCTGTGAAA
+
##############################
- at HiMom:9:1:2:1932
+ at machine1:HiMom:abcdeACXX:9:1:2:1932 :Y:0:
NAGCGATCCTCCCGCCTCTGCCTCCCANNN
+
%,1545541455##################
- at HiMom:9:1:2:1946
+ at machine1:HiMom:abcdeACXX:9:1:2:1946 :N:0:
NATCTTCTGGAATTTCTAACAGCTTGGAAN
+
%0515.,.35<997################
- at HiMom:9:1:2:209
+ at machine1:HiMom:abcdeACXX:9:1:2:209 :N:0:
NGACTCAACTCCTGGGCTCCCTACGACCAT
+
##############################
- at HiMom:9:1:2:246
+ at machine1:HiMom:abcdeACXX:9:1:2:246 :N:0:
NGGAGGTTTCATTTAGCCGATATTGTGNNN
+
##############################
- at HiMom:9:1:2:25
+ at machine1:HiMom:abcdeACXX:9:1:2:25 :N:0:
NGCTTTGGCAAGACAAATCTCCCGTCTGGN
+
##############################
- at HiMom:9:1:2:307
+ at machine1:HiMom:abcdeACXX:9:1:2:307 :N:0:
NGGATGAACAGAAACTAAAATAACACANNN
+
##############################
- at HiMom:9:1:2:363
+ at machine1:HiMom:abcdeACXX:9:1:2:363 :N:0:
NATATTCTTTTTTTTTATTTATCAGATNNN
+
##############################
- at HiMom:9:1:2:449
+ at machine1:HiMom:abcdeACXX:9:1:2:449 :N:0:
NATTCTAATTCTAGGAAATTAACAATCNNN
+
%.9315<936970%0###############
- at HiMom:9:1:2:546
+ at machine1:HiMom:abcdeACXX:9:1:2:546 :N:0:
NGGTTGTGTCTCTCTCAGCCTTTGGGATCN
+
%,46888444685-35##############
- at HiMom:9:1:2:605
+ at machine1:HiMom:abcdeACXX:9:1:2:605 :Y:0:
NGCATTGAGCAGACGTGGCATCCAGATNNN
+
%)085222/55453################
- at HiMom:9:1:2:69
+ at machine1:HiMom:abcdeACXX:9:1:2:69 :N:0:
NTCAGTCTGCTGTTTTAAAAAAATACTGTG
+
##############################
- at HiMom:9:1:2:747
+ at machine1:HiMom:abcdeACXX:9:1:2:747 :N:0:
NAACAACAGCGGAAAATAATAAAAAAAAAN
+
##############################
- at HiMom:9:1:2:786
+ at machine1:HiMom:abcdeACXX:9:1:2:786 :Y:0:
NTAAACAATAATCTGATGATTTATAATCCN
+
%09<<<<;<;<8<9;<9<;<::<<::####
- at HiMom:9:1:2:858
+ at machine1:HiMom:abcdeACXX:9:1:2:858 :Y:0:
NAAACGTTGCTGATCTTCTGTTTTAAACTA
+
%/;7-222265366-6977035:::;626;
- at HiMom:9:1:2:943
+ at machine1:HiMom:abcdeACXX:9:1:2:943 :Y:0:
NAATACCAATAAACCTAGAATGTCTCATAC
+
%08<9646<6378744774:1005799<4#
- at HiMom:9:1:2:974
+ at machine1:HiMom:abcdeACXX:9:1:2:974 :Y:0:
NGATCAATGATCACATCTTTGGATATGTAT
+
%/9979<99:999::9;;:7511<<<77<<
- at HiMom:9:1:2:988
+ at machine1:HiMom:abcdeACXX:9:1:2:988 :Y:0:
NAAAGGAATGTTCAGCTCTGTGAGTTGAAC
+
%/92/04:2-2785-3875/404362-162
- at HiMom:9:1:3:1233
+ at machine1:HiMom:abcdeACXX:9:1:3:1233 :N:0:
NAACCAATTTCTTTACATACCAAATACGCC
+
##############################
- at HiMom:9:1:3:1294
+ at machine1:HiMom:abcdeACXX:9:1:3:1294 :N:0:
TGTAACTTTACTTTAGTTGCTTATTTGTAG
+
BA############################
- at HiMom:9:1:3:405
+ at machine1:HiMom:abcdeACXX:9:1:3:405 :N:0:
AAAAAACATAGAACGGGGTCAATATTTTAT
+
(?A>8(7B?<(:')?@)8(:(*:<8:0>'>
- at HiMom:9:1:3:579
+ at machine1:HiMom:abcdeACXX:9:1:3:579 :N:0:
NGAAAAATGACCACACTTGCCTCCTGAGAA
+
##############################
- at HiMom:9:1:3:673
+ at machine1:HiMom:abcdeACXX:9:1:3:673 :N:0:
TCCTCAAAAACAAGATAAAACGGTTGAAAT
+
>()>)''85BBC?#################
- at HiMom:9:1:3:890
+ at machine1:HiMom:abcdeACXX:9:1:3:890 :N:0:
TGCTTCTGTTTCCGTTAGCTAGATAAAGTT
+
##############################
- at HiMom:9:1:3:905
+ at machine1:HiMom:abcdeACXX:9:1:3:905 :N:0:
TGTTATGTTTAATTTTCTTTAGCACCCTTC
+
>7>?A:-<BA at 0>@:@8=A;5%7;9?=:9@
- at HiMom:9:1:3:918
+ at machine1:HiMom:abcdeACXX:9:1:3:918 :N:0:
TTTTCATTCCTAGTCATCCACCCCATCAGA
+
0()@A=:2>3:>(/((<22A>:0(20:@)@
- at HiMom:9:2:0:1073
+ at machine1:HiMom:abcdeACXX:9:2:0:1073 :N:0:
NNNNNANCACNNNCNNNCNCANNNCNNNNN
+
##############################
- at HiMom:9:2:0:1135
+ at machine1:HiMom:abcdeACXX:9:2:0:1135 :N:0:
NNNNNGNNGTNNNANNNTNTANNNGNNNNN
+
##############################
- at HiMom:9:2:0:1198
+ at machine1:HiMom:abcdeACXX:9:2:0:1198 :N:0:
NNNNNTNCTANNNTNNNCNCANNNANNNNN
+
##############################
- at HiMom:9:2:0:1278
+ at machine1:HiMom:abcdeACXX:9:2:0:1278 :N:0:
NNNNNNNNTANNNTNNNCNNANNNGNNNNN
+
##############################
- at HiMom:9:2:0:135
+ at machine1:HiMom:abcdeACXX:9:2:0:135 :N:0:
NNNNNNNNANNNNNNNNNNNGNNNNNNNNN
+
##############################
- at HiMom:9:2:0:1547
+ at machine1:HiMom:abcdeACXX:9:2:0:1547 :N:0:
NNNNNNNNCNNNNNNNNNNNGNNNANNNNN
+
##############################
- at HiMom:9:2:0:1598
+ at machine1:HiMom:abcdeACXX:9:2:0:1598 :N:0:
NNNNNNNNATNNNTNNNANNGNNNCNNNNN
+
##############################
- at HiMom:9:2:0:1620
+ at machine1:HiMom:abcdeACXX:9:2:0:1620 :N:0:
NNNNNNNNCANNNNNNNANNCNNNCNNNNN
+
##############################
- at HiMom:9:2:0:1668
+ at machine1:HiMom:abcdeACXX:9:2:0:1668 :N:0:
NNNNNANATANNNANNNGNTGNNNTNNNNN
+
##############################
- at HiMom:9:2:0:186
+ at machine1:HiMom:abcdeACXX:9:2:0:186 :N:0:
NNNNNNNNCCNNNANNNTNNTNNNTNNNNN
+
##############################
- at HiMom:9:2:0:205
+ at machine1:HiMom:abcdeACXX:9:2:0:205 :N:0:
NNNNNNNNANNNNNNNNTNNCNNNTNNNNN
+
##############################
- at HiMom:9:2:0:287
+ at machine1:HiMom:abcdeACXX:9:2:0:287 :N:0:
NNNNNNNNCCNNNCNNNTNNANNNANNNNN
+
##############################
- at HiMom:9:2:0:382
+ at machine1:HiMom:abcdeACXX:9:2:0:382 :N:0:
NNNNNNNNCANNNTNNNTNNANNNANNNNN
+
##############################
- at HiMom:9:2:0:441
+ at machine1:HiMom:abcdeACXX:9:2:0:441 :N:0:
NNNNNNNNTTNNNANNNANNTNNNTNNNNN
+
##############################
- at HiMom:9:2:0:50
+ at machine1:HiMom:abcdeACXX:9:2:0:50 :N:0:
NNNNNNNNTNNNNNNNNTNNGNNNGNNNNN
+
##############################
- at HiMom:9:2:0:501
+ at machine1:HiMom:abcdeACXX:9:2:0:501 :N:0:
NNNNNGNNAGNNNANNNCNCTNNNCNNNNN
+
##############################
- at HiMom:9:2:0:73
+ at machine1:HiMom:abcdeACXX:9:2:0:73 :N:0:
NNNNNANCATNNNGNNNANACNNNGNNNNN
+
##############################
- at HiMom:9:2:0:740
+ at machine1:HiMom:abcdeACXX:9:2:0:740 :N:0:
NNNNNNNNTTNNNANNNTNNANNNANNNNN
+
##############################
- at HiMom:9:2:0:766
+ at machine1:HiMom:abcdeACXX:9:2:0:766 :N:0:
NNNNNNNNTGNNNANNNANNTNNNTNNNNN
+
##############################
- at HiMom:9:2:0:87
+ at machine1:HiMom:abcdeACXX:9:2:0:87 :N:0:
NNNNNNNNGNNNNNNNNANNTNNNTNNNNN
+
##############################
- at HiMom:9:2:1:1004
+ at machine1:HiMom:abcdeACXX:9:2:1:1004 :N:0:
NATTTATCACTANANATCCGCAAACCCTCC
+
##############################
- at HiMom:9:2:1:1034
+ at machine1:HiMom:abcdeACXX:9:2:1:1034 :N:0:
NATCATTTTCATNCNTTTCACTGATACATT
+
%.737:887471%-%1:8555545;696::
- at HiMom:9:2:1:1159
+ at machine1:HiMom:abcdeACXX:9:2:1:1159 :N:0:
NNACTTNTAGNNNGNNNAAATNNCCNANNN
+
##############################
- at HiMom:9:2:1:1168
+ at machine1:HiMom:abcdeACXX:9:2:1:1168 :N:0:
NNTCTANCTTNNNTNNNATTGNNTTNTNNN
+
##############################
- at HiMom:9:2:1:1180
+ at machine1:HiMom:abcdeACXX:9:2:1:1180 :N:0:
NNATGGNCTTNNNCNNNAGAANNTCNANNN
+
##############################
- at HiMom:9:2:1:1214
+ at machine1:HiMom:abcdeACXX:9:2:1:1214 :N:0:
NAAAAAAAAAAANANTATAAGAAAGAATCA
+
%035:#########################
- at HiMom:9:2:1:1221
+ at machine1:HiMom:abcdeACXX:9:2:1:1221 :N:0:
NGGTCACACTCACATAGTGTTCAGAGCACT
+
##############################
- at HiMom:9:2:1:1306
+ at machine1:HiMom:abcdeACXX:9:2:1:1306 :N:0:
NNACATNAAANNNTNNNAACANNGTNANNN
+
##############################
- at HiMom:9:2:1:1351
+ at machine1:HiMom:abcdeACXX:9:2:1:1351 :N:0:
NNNNNCNATANNNTNNNANAANNNTNNNNN
+
##############################
- at HiMom:9:2:1:1424
+ at machine1:HiMom:abcdeACXX:9:2:1:1424 :N:0:
NNTCATNTAGNNNCNNNATGGNNGTNCNNN
+
##############################
- at HiMom:9:2:1:1452
+ at machine1:HiMom:abcdeACXX:9:2:1:1452 :N:0:
NGAAATTTGTAAAANCACCTGCAGAATACT
+
##############################
- at HiMom:9:2:1:1515
+ at machine1:HiMom:abcdeACXX:9:2:1:1515 :N:0:
NATTAAATATNANANNGTAATAATAATANN
+
%/9###########################
- at HiMom:9:2:1:1521
+ at machine1:HiMom:abcdeACXX:9:2:1:1521 :N:0:
NNACACNAAANNNGNNNATCTNNTTNCNNN
+
##############################
- at HiMom:9:2:1:1536
+ at machine1:HiMom:abcdeACXX:9:2:1:1536 :N:0:
NAGCAAAGACTTNGNACCAACCCAAATGTT
+
##############################
- at HiMom:9:2:1:1543
+ at machine1:HiMom:abcdeACXX:9:2:1:1543 :N:0:
NNTTGANATCNNNANNNAATANNTANCNNN
+
##############################
- at HiMom:9:2:1:1617
+ at machine1:HiMom:abcdeACXX:9:2:1:1617 :N:0:
NNCCATNATCNNNGNNNCCAGNNGTNTNNN
+
##############################
- at HiMom:9:2:1:1627
+ at machine1:HiMom:abcdeACXX:9:2:1:1627 :N:0:
NNTGGTNAGANNNCNNNAAAANNCANTNNN
+
##############################
- at HiMom:9:2:1:1646
+ at machine1:HiMom:abcdeACXX:9:2:1:1646 :N:0:
NTTAATTATANNNANNTAAACATTCTAANN
+
##############################
- at HiMom:9:2:1:1653
+ at machine1:HiMom:abcdeACXX:9:2:1:1653 :N:0:
NNAATTNAAANNNTNNNATCTNNAGNANNN
+
##############################
- at HiMom:9:2:1:1682
+ at machine1:HiMom:abcdeACXX:9:2:1:1682 :N:0:
NNTCTTNTTTNNNGNNNAAAANNAANTNNN
+
##############################
- at HiMom:9:2:1:170
+ at machine1:HiMom:abcdeACXX:9:2:1:170 :Y:0:
NAGAAGAAATGGGATCCTGCTGTGGCCAGT
+
%/888865284168866767663(6874/5
- at HiMom:9:2:1:1731
+ at machine1:HiMom:abcdeACXX:9:2:1:1731 :N:0:
NNTATANGAANNNTNNNTGCTNNAGNTNNN
+
##############################
- at HiMom:9:2:1:1755
+ at machine1:HiMom:abcdeACXX:9:2:1:1755 :N:0:
NNGTNANTCTNNNCNNNCNTGNNNGNANNN
+
##############################
- at HiMom:9:2:1:1812
+ at machine1:HiMom:abcdeACXX:9:2:1:1812 :N:0:
NNTTGCNCACNNNCNNNCCATNNAANGNNN
+
##############################
- at HiMom:9:2:1:1853
+ at machine1:HiMom:abcdeACXX:9:2:1:1853 :N:0:
NNATCTNTTCNNNANNNAGTGNNATNCNNN
+
##############################
- at HiMom:9:2:1:1919
+ at machine1:HiMom:abcdeACXX:9:2:1:1919 :N:0:
NNAATTNAAANNNANNNAGAANNAGNANNN
+
##############################
- at HiMom:9:2:1:1924
+ at machine1:HiMom:abcdeACXX:9:2:1:1924 :N:0:
NATATTCTGAAGNANNCCAATGAACCAAAN
+
%116<9579<7###################
- at HiMom:9:2:1:1933
+ at machine1:HiMom:abcdeACXX:9:2:1:1933 :N:0:
NAGGGTACATNTNCNNAATGTGCGGGTTNN
+
##############################
- at HiMom:9:2:1:1938
+ at machine1:HiMom:abcdeACXX:9:2:1:1938 :Y:0:
NAGTCCAGTGTCTCTGCTTCCGCAGGGACA
+
%/818865/058858644866457646668
- at HiMom:9:2:1:1950
+ at machine1:HiMom:abcdeACXX:9:2:1:1950 :N:0:
NNTTNANAAANNNCNNNTNCANNNTNCNNN
+
##############################
- at HiMom:9:2:1:1959
+ at machine1:HiMom:abcdeACXX:9:2:1:1959 :N:0:
NGACACATTCCTACNACAGAGAAAAATTTA
+
%*77;;<;<<:<;,%.::;:6:9::<4488
- at HiMom:9:2:1:1987
+ at machine1:HiMom:abcdeACXX:9:2:1:1987 :N:0:
NNATNGNACANNNCNNNTNGTNNNTNNNNN
+
##############################
- at HiMom:9:2:1:2006
+ at machine1:HiMom:abcdeACXX:9:2:1:2006 :N:0:
NNGTATNTGANNNGNNNCCTTNNAGNANNN
+
##############################
- at HiMom:9:2:1:211
+ at machine1:HiMom:abcdeACXX:9:2:1:211 :N:0:
NNCTGANACANNNGNNNTGCANNACNCNNN
+
##############################
- at HiMom:9:2:1:234
+ at machine1:HiMom:abcdeACXX:9:2:1:234 :N:0:
NAAGCCTGTGGGNANNCCCAGTGGGAGCGN
+
##############################
- at HiMom:9:2:1:242
+ at machine1:HiMom:abcdeACXX:9:2:1:242 :N:0:
NNGCTCNAGCNNNANNNATATNNTTNGNNN
+
##############################
- at HiMom:9:2:1:262
+ at machine1:HiMom:abcdeACXX:9:2:1:262 :N:0:
NNATTGNAATNNNCNNNTTCCNNATNTNNN
+
##############################
- at HiMom:9:2:1:298
+ at machine1:HiMom:abcdeACXX:9:2:1:298 :N:0:
NNTCAANTTGNNNTNNNCTGCNNTTNTNNN
+
##############################
- at HiMom:9:2:1:312
+ at machine1:HiMom:abcdeACXX:9:2:1:312 :N:0:
NNTTGCNAGANNNANNNAACTNNTGNANNN
+
##############################
- at HiMom:9:2:1:363
+ at machine1:HiMom:abcdeACXX:9:2:1:363 :Y:0:
NGAAAGGTTTTGCAGCATGTGCAAACTCAC
+
%-5565678:8177656503512/377856
- at HiMom:9:2:1:37
+ at machine1:HiMom:abcdeACXX:9:2:1:37 :N:0:
NTGTAAACGANNNCNNTTCCTGTTCAGCNN
+
##############################
- at HiMom:9:2:1:370
+ at machine1:HiMom:abcdeACXX:9:2:1:370 :N:0:
NNCTGGNAGCNNNTNNNCATANNAANCNNN
+
##############################
- at HiMom:9:2:1:377
+ at machine1:HiMom:abcdeACXX:9:2:1:377 :N:0:
NNAGAANGTGNNNTNNNAAATNNAANANNN
+
##############################
- at HiMom:9:2:1:414
+ at machine1:HiMom:abcdeACXX:9:2:1:414 :N:0:
NNTAGANAGCNNNANNNTCAGNNACNGNNN
+
##############################
- at HiMom:9:2:1:421
+ at machine1:HiMom:abcdeACXX:9:2:1:421 :N:0:
NNGTTANTTCNNNANNNCGTGNNATNCNNN
+
##############################
- at HiMom:9:2:1:428
+ at machine1:HiMom:abcdeACXX:9:2:1:428 :N:0:
NATGTGAATANTNANNTAGTTGGGATTCAN
+
##############################
- at HiMom:9:2:1:44
+ at machine1:HiMom:abcdeACXX:9:2:1:44 :N:0:
NACTACCTCANGNANNAAGCAGGTTCTAAN
+
##############################
- at HiMom:9:2:1:466
+ at machine1:HiMom:abcdeACXX:9:2:1:466 :N:0:
NACACTCACANCNANNTGTTTGGAATGANN
+
##############################
- at HiMom:9:2:1:555
+ at machine1:HiMom:abcdeACXX:9:2:1:555 :N:0:
NNCAATNTCTNNNGNNNTACANNCTNCNNN
+
##############################
- at HiMom:9:2:1:558
+ at machine1:HiMom:abcdeACXX:9:2:1:558 :N:0:
NAAAATATCANTNANNAATAAATAATCANN
+
##############################
- at HiMom:9:2:1:56
+ at machine1:HiMom:abcdeACXX:9:2:1:56 :N:0:
NNGCCANGGTNNNANNNTCACNNGGNCNNN
+
##############################
- at HiMom:9:2:1:569
+ at machine1:HiMom:abcdeACXX:9:2:1:569 :N:0:
NNAGGCNAGTNNNGNNNGTCCNNGTNANNN
+
##############################
- at HiMom:9:2:1:604
+ at machine1:HiMom:abcdeACXX:9:2:1:604 :N:0:
NATGATGAAACTCTNTCTCTACTAAAAATA
+
##############################
- at HiMom:9:2:1:628
+ at machine1:HiMom:abcdeACXX:9:2:1:628 :N:0:
NAGTATGCCCNCNCNNACCACTCCTATTNN
+
##############################
- at HiMom:9:2:1:64
+ at machine1:HiMom:abcdeACXX:9:2:1:64 :N:0:
NATTAATCTTNNNTNNGCACAATTCATTNN
+
##############################
- at HiMom:9:2:1:684
+ at machine1:HiMom:abcdeACXX:9:2:1:684 :N:0:
NAAAAATCAAATGANCATAATTTTATAAAA
+
##############################
- at HiMom:9:2:1:699
+ at machine1:HiMom:abcdeACXX:9:2:1:699 :N:0:
NNAATTNTTGNNNTNNNATTTNNGANTNNN
+
##############################
- at HiMom:9:2:1:714
+ at machine1:HiMom:abcdeACXX:9:2:1:714 :N:0:
NATTAACTTANANTNNACCACAACCTAANN
+
%.:###########################
- at HiMom:9:2:1:722
+ at machine1:HiMom:abcdeACXX:9:2:1:722 :N:0:
NNCCTCNCTGNNNCNNNCTGTNNTGNCNNN
+
##############################
- at HiMom:9:2:1:749
+ at machine1:HiMom:abcdeACXX:9:2:1:749 :N:0:
NNAGTGNTACNNNTNNNCTTGNNCTNTNNN
+
##############################
- at HiMom:9:2:1:760
+ at machine1:HiMom:abcdeACXX:9:2:1:760 :N:0:
NGTCTGTTTTATGTNAAATATTTTGTTTAA
+
##############################
- at HiMom:9:2:1:8
+ at machine1:HiMom:abcdeACXX:9:2:1:8 :N:0:
NNTGCGNTGGNNNCNNNAGGCNNTTNTNNN
+
##############################
- at HiMom:9:2:1:833
+ at machine1:HiMom:abcdeACXX:9:2:1:833 :N:0:
NNGAGCNCCTNNNANNNCTCCNNGANGNNN
+
##############################
- at HiMom:9:2:1:848
+ at machine1:HiMom:abcdeACXX:9:2:1:848 :N:0:
NNTACTNAGTNNNGNNNTGTTNNGCNTNNN
+
##############################
- at HiMom:9:2:1:893
+ at machine1:HiMom:abcdeACXX:9:2:1:893 :N:0:
NGAGACAGAGTCTCNCTCTGTTCCCTAGCC
+
##############################
- at HiMom:9:2:1:998
+ at machine1:HiMom:abcdeACXX:9:2:1:998 :N:0:
NNATGTNTGCNNNANNNTATANNGGNANNN
+
##############################
- at HiMom:9:2:2:0
+ at machine1:HiMom:abcdeACXX:9:2:2:0 :N:0:
NATTCCTTNANNNNNNNNNNNNNNNNNNNN
+
##############################
- at HiMom:9:2:2:131
+ at machine1:HiMom:abcdeACXX:9:2:2:131 :Y:0:
NATATATTGACAGCAGTCATGTTGTTGAAG
+
%0<<<:<959874492:96999969:7784
- at HiMom:9:2:2:1636
+ at machine1:HiMom:abcdeACXX:9:2:2:1636 :N:0:
NGTGTAAAAGTAGGGAAATACTATAGCAAG
+
##############################
- at HiMom:9:2:2:1974
+ at machine1:HiMom:abcdeACXX:9:2:2:1974 :N:0:
NACGCCAATACAAAAATGTTGAAGCTAGCT
+
##############################
- at HiMom:9:2:2:351
+ at machine1:HiMom:abcdeACXX:9:2:2:351 :N:0:
NGGGGTTGAGGTGTAAATAGAACATTTGTA
+
##############################
- at HiMom:9:2:2:646
+ at machine1:HiMom:abcdeACXX:9:2:2:646 :N:0:
NGAATCTAAGAAGACACAAAACTAAGGAAA
+
##############################
- at HiMom:9:2:2:828
+ at machine1:HiMom:abcdeACXX:9:2:2:828 :N:0:
NTCAAGTCAATTTGGGACTTGAAACAGCTC
+
##############################
- at HiMom:9:2:3:1529
+ at machine1:HiMom:abcdeACXX:9:2:3:1529 :N:0:
NTTATATGAATAGATAAATAAATAATCAAT
+
##############################
- at HiMom:9:2:3:179
+ at machine1:HiMom:abcdeACXX:9:2:3:179 :N:0:
CATTATTGTTAGACTGATTTTTTATAATCT
+
B@)104..*0-A(@@(<A9A<(+9)-=6(B
- at HiMom:9:2:3:198
+ at machine1:HiMom:abcdeACXX:9:2:3:198 :N:0:
TGTCATTTTCTTTGCCTTAATTGTTCTTCT
+
5 at CBB7-*<=####################
- at HiMom:9:2:3:2030
+ at machine1:HiMom:abcdeACXX:9:2:3:2030 :N:0:
CGAGATAATTTTTTAAAAAAAGTCCAAAAA
+
((@;()@==*7<(5A@<C>###########
- at HiMom:9:2:3:247
+ at machine1:HiMom:abcdeACXX:9:2:3:247 :N:0:
TGTACATGACCAGGTAATTTGGTTATGTGA
+
<@596353;)>@A7=:,A0'6>########
- at HiMom:9:2:3:4
+ at machine1:HiMom:abcdeACXX:9:2:3:4 :N:0:
AGAGGCAATAAGTTTTAANNNNNNNNNNNN
+
A>BA at 9BAB3AA##################
- at HiMom:9:2:3:862
+ at machine1:HiMom:abcdeACXX:9:2:3:862 :N:0:
NCTTTAAGAAATCATTCATTCTGCAAACAC
+
##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/NN.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/NN.barcode_1.fastq
index ab4d092..d03e8d4 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/NN.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/NN.barcode_1.fastq
@@ -1,892 +1,892 @@
- at HiMom:9:1:0:1038
+ at machine1:HiMom:abcdeACXX:9:1:0:1038 :N:0:
NNNNNGTN
+
########
- at HiMom:9:1:0:1093
+ at machine1:HiMom:abcdeACXX:9:1:0:1093 :N:0:
NNNNNTGN
+
########
- at HiMom:9:1:0:113
+ at machine1:HiMom:abcdeACXX:9:1:0:113 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:0:1193
+ at machine1:HiMom:abcdeACXX:9:1:0:1193 :N:0:
NNNNNGTN
+
########
- at HiMom:9:1:0:1291
+ at machine1:HiMom:abcdeACXX:9:1:0:1291 :N:0:
NNNNNGNN
+
########
- at HiMom:9:1:0:1307
+ at machine1:HiMom:abcdeACXX:9:1:0:1307 :N:0:
NNNNNTAN
+
########
- at HiMom:9:1:0:1434
+ at machine1:HiMom:abcdeACXX:9:1:0:1434 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:0:1475
+ at machine1:HiMom:abcdeACXX:9:1:0:1475 :N:0:
NNNNNCCN
+
########
- at HiMom:9:1:0:1690
+ at machine1:HiMom:abcdeACXX:9:1:0:1690 :N:0:
NNNNNANN
+
########
- at HiMom:9:1:0:1703
+ at machine1:HiMom:abcdeACXX:9:1:0:1703 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:0:1940
+ at machine1:HiMom:abcdeACXX:9:1:0:1940 :N:0:
NNNNNCNN
+
########
- at HiMom:9:1:0:2001
+ at machine1:HiMom:abcdeACXX:9:1:0:2001 :N:0:
NNNNNGAN
+
########
- at HiMom:9:1:0:205
+ at machine1:HiMom:abcdeACXX:9:1:0:205 :N:0:
NNNNNCGN
+
########
- at HiMom:9:1:0:275
+ at machine1:HiMom:abcdeACXX:9:1:0:275 :N:0:
NNNNNATN
+
########
- at HiMom:9:1:0:324
+ at machine1:HiMom:abcdeACXX:9:1:0:324 :N:0:
NNNNNGTN
+
########
- at HiMom:9:1:0:37
+ at machine1:HiMom:abcdeACXX:9:1:0:37 :N:0:
NNNNNGNN
+
########
- at HiMom:9:1:0:464
+ at machine1:HiMom:abcdeACXX:9:1:0:464 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:0:586
+ at machine1:HiMom:abcdeACXX:9:1:0:586 :N:0:
NNNNNCNN
+
########
- at HiMom:9:1:0:841
+ at machine1:HiMom:abcdeACXX:9:1:0:841 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:0:879
+ at machine1:HiMom:abcdeACXX:9:1:0:879 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:1013
+ at machine1:HiMom:abcdeACXX:9:1:1:1013 :N:0:
NNNNNGAN
+
########
- at HiMom:9:1:1:111
+ at machine1:HiMom:abcdeACXX:9:1:1:111 :N:0:
NNNNNCGN
+
########
- at HiMom:9:1:1:1153
+ at machine1:HiMom:abcdeACXX:9:1:1:1153 :N:0:
NNNNNCTN
+
########
- at HiMom:9:1:1:1184
+ at machine1:HiMom:abcdeACXX:9:1:1:1184 :N:0:
NNNNNAGN
+
########
- at HiMom:9:1:1:1241
+ at machine1:HiMom:abcdeACXX:9:1:1:1241 :N:0:
NNNNNCTN
+
########
- at HiMom:9:1:1:1243
+ at machine1:HiMom:abcdeACXX:9:1:1:1243 :N:0:
NNNNNTGN
+
########
- at HiMom:9:1:1:1247
+ at machine1:HiMom:abcdeACXX:9:1:1:1247 :N:0:
NNNNNACN
+
########
- at HiMom:9:1:1:1282
+ at machine1:HiMom:abcdeACXX:9:1:1:1282 :N:0:
NNNNNCCN
+
########
- at HiMom:9:1:1:132
+ at machine1:HiMom:abcdeACXX:9:1:1:132 :N:0:
NNNNNTGN
+
########
- at HiMom:9:1:1:1320
+ at machine1:HiMom:abcdeACXX:9:1:1:1320 :N:0:
NNNNNCGN
+
########
- at HiMom:9:1:1:1372
+ at machine1:HiMom:abcdeACXX:9:1:1:1372 :N:0:
NNNGNTTA
+
########
- at HiMom:9:1:1:1379
+ at machine1:HiMom:abcdeACXX:9:1:1:1379 :N:0:
NNNCNGAT
+
########
- at HiMom:9:1:1:1391
+ at machine1:HiMom:abcdeACXX:9:1:1:1391 :N:0:
NNNNNAGN
+
########
- at HiMom:9:1:1:140
+ at machine1:HiMom:abcdeACXX:9:1:1:140 :N:0:
NNNNNCAN
+
########
- at HiMom:9:1:1:1513
+ at machine1:HiMom:abcdeACXX:9:1:1:1513 :N:0:
NNNNNCTN
+
########
- at HiMom:9:1:1:1521
+ at machine1:HiMom:abcdeACXX:9:1:1:1521 :N:0:
NNNNNCCN
+
########
- at HiMom:9:1:1:155
+ at machine1:HiMom:abcdeACXX:9:1:1:155 :N:0:
NNNNNCAN
+
########
- at HiMom:9:1:1:1555
+ at machine1:HiMom:abcdeACXX:9:1:1:1555 :N:0:
NNNNNCAN
+
########
- at HiMom:9:1:1:164
+ at machine1:HiMom:abcdeACXX:9:1:1:164 :N:0:
NNNNNTTN
+
########
- at HiMom:9:1:1:1684
+ at machine1:HiMom:abcdeACXX:9:1:1:1684 :N:0:
NNNNNCGN
+
########
- at HiMom:9:1:1:1696
+ at machine1:HiMom:abcdeACXX:9:1:1:1696 :N:0:
NNNNNCTN
+
########
- at HiMom:9:1:1:170
+ at machine1:HiMom:abcdeACXX:9:1:1:170 :N:0:
NNNNNACN
+
########
- at HiMom:9:1:1:173
+ at machine1:HiMom:abcdeACXX:9:1:1:173 :N:0:
NNNNNCCN
+
########
- at HiMom:9:1:1:1733
+ at machine1:HiMom:abcdeACXX:9:1:1:1733 :N:0:
NNNNNGAN
+
########
- at HiMom:9:1:1:1770
+ at machine1:HiMom:abcdeACXX:9:1:1:1770 :N:0:
NNNNNTCN
+
########
- at HiMom:9:1:1:18
+ at machine1:HiMom:abcdeACXX:9:1:1:18 :N:0:
NNNNNCGN
+
########
- at HiMom:9:1:1:1815
+ at machine1:HiMom:abcdeACXX:9:1:1:1815 :N:0:
NNNTNGAC
+
########
- at HiMom:9:1:1:1836
+ at machine1:HiMom:abcdeACXX:9:1:1:1836 :N:0:
NNNNNGTN
+
########
- at HiMom:9:1:1:184
+ at machine1:HiMom:abcdeACXX:9:1:1:184 :N:0:
NNNNNGTN
+
########
- at HiMom:9:1:1:1886
+ at machine1:HiMom:abcdeACXX:9:1:1:1886 :Y:0:
NNNGNGCC
+
########
- at HiMom:9:1:1:1906
+ at machine1:HiMom:abcdeACXX:9:1:1:1906 :N:0:
NNNNNCGN
+
########
- at HiMom:9:1:1:1917
+ at machine1:HiMom:abcdeACXX:9:1:1:1917 :N:0:
NNNNNACN
+
########
- at HiMom:9:1:1:195
+ at machine1:HiMom:abcdeACXX:9:1:1:195 :N:0:
NNNNNCGN
+
########
- at HiMom:9:1:1:1954
+ at machine1:HiMom:abcdeACXX:9:1:1:1954 :N:0:
NNNNNCCN
+
########
- at HiMom:9:1:1:2
+ at machine1:HiMom:abcdeACXX:9:1:1:2 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:2011
+ at machine1:HiMom:abcdeACXX:9:1:1:2011 :N:0:
NNNGNTAG
+
########
- at HiMom:9:1:1:240
+ at machine1:HiMom:abcdeACXX:9:1:1:240 :N:0:
NNNNNGAN
+
########
- at HiMom:9:1:1:262
+ at machine1:HiMom:abcdeACXX:9:1:1:262 :N:0:
NNNNNCAN
+
########
- at HiMom:9:1:1:264
+ at machine1:HiMom:abcdeACXX:9:1:1:264 :N:0:
NNNNNCGA
+
########
- at HiMom:9:1:1:299
+ at machine1:HiMom:abcdeACXX:9:1:1:299 :N:0:
NNNNNCGN
+
########
- at HiMom:9:1:1:30
+ at machine1:HiMom:abcdeACXX:9:1:1:30 :N:0:
NNNNNACN
+
########
- at HiMom:9:1:1:353
+ at machine1:HiMom:abcdeACXX:9:1:1:353 :N:0:
NNNNNCGN
+
########
- at HiMom:9:1:1:367
+ at machine1:HiMom:abcdeACXX:9:1:1:367 :N:0:
NNNNNAGN
+
########
- at HiMom:9:1:1:41
+ at machine1:HiMom:abcdeACXX:9:1:1:41 :N:0:
NNNNNGAN
+
########
- at HiMom:9:1:1:416
+ at machine1:HiMom:abcdeACXX:9:1:1:416 :N:0:
NNNNNGAN
+
########
- at HiMom:9:1:1:483
+ at machine1:HiMom:abcdeACXX:9:1:1:483 :N:0:
NNNNNTAN
+
########
- at HiMom:9:1:1:486
+ at machine1:HiMom:abcdeACXX:9:1:1:486 :N:0:
NNNNNTGN
+
########
- at HiMom:9:1:1:495
+ at machine1:HiMom:abcdeACXX:9:1:1:495 :N:0:
NNNNNGAN
+
########
- at HiMom:9:1:1:508
+ at machine1:HiMom:abcdeACXX:9:1:1:508 :N:0:
NNNNNCTN
+
########
- at HiMom:9:1:1:517
+ at machine1:HiMom:abcdeACXX:9:1:1:517 :N:0:
NNNCNAGA
+
########
- at HiMom:9:1:1:535
+ at machine1:HiMom:abcdeACXX:9:1:1:535 :N:0:
NNNCNCGA
+
########
- at HiMom:9:1:1:55
+ at machine1:HiMom:abcdeACXX:9:1:1:55 :N:0:
NNNGNTTA
+
########
- at HiMom:9:1:1:554
+ at machine1:HiMom:abcdeACXX:9:1:1:554 :N:0:
NNNNNTAN
+
########
- at HiMom:9:1:1:567
+ at machine1:HiMom:abcdeACXX:9:1:1:567 :N:0:
NNNNNCCN
+
########
- at HiMom:9:1:1:59
+ at machine1:HiMom:abcdeACXX:9:1:1:59 :N:0:
NNNNNACN
+
########
- at HiMom:9:1:1:613
+ at machine1:HiMom:abcdeACXX:9:1:1:613 :N:0:
NNNNNAGN
+
########
- at HiMom:9:1:1:622
+ at machine1:HiMom:abcdeACXX:9:1:1:622 :N:0:
NNNNNAGN
+
########
- at HiMom:9:1:1:627
+ at machine1:HiMom:abcdeACXX:9:1:1:627 :N:0:
NNNNNGAN
+
########
- at HiMom:9:1:1:684
+ at machine1:HiMom:abcdeACXX:9:1:1:684 :N:0:
NNNNNGAN
+
########
- at HiMom:9:1:1:72
+ at machine1:HiMom:abcdeACXX:9:1:1:72 :N:0:
NNNTNGAC
+
########
- at HiMom:9:1:1:812
+ at machine1:HiMom:abcdeACXX:9:1:1:812 :N:0:
NNNNNGAN
+
########
- at HiMom:9:1:1:874
+ at machine1:HiMom:abcdeACXX:9:1:1:874 :N:0:
NNNNNGTN
+
########
- at HiMom:9:1:1:931
+ at machine1:HiMom:abcdeACXX:9:1:1:931 :N:0:
NNNNNCAN
+
########
- at HiMom:9:1:1:965
+ at machine1:HiMom:abcdeACXX:9:1:1:965 :N:0:
NNNTNTAA
+
########
- at HiMom:9:1:1:994
+ at machine1:HiMom:abcdeACXX:9:1:1:994 :N:0:
NNNNNCGN
+
########
- at HiMom:9:1:2:1158
+ at machine1:HiMom:abcdeACXX:9:1:2:1158 :Y:0:
NNCTTAGC
+
########
- at HiMom:9:1:2:1238
+ at machine1:HiMom:abcdeACXX:9:1:2:1238 :N:0:
NNCTAAGC
+
########
- at HiMom:9:1:2:1275
+ at machine1:HiMom:abcdeACXX:9:1:2:1275 :Y:0:
NNNANCTG
+
########
- at HiMom:9:1:2:1301
+ at machine1:HiMom:abcdeACXX:9:1:2:1301 :N:0:
NNNTAACA
+
########
- at HiMom:9:1:2:1453
+ at machine1:HiMom:abcdeACXX:9:1:2:1453 :Y:0:
NNACCAGG
+
########
- at HiMom:9:1:2:150
+ at machine1:HiMom:abcdeACXX:9:1:2:150 :N:0:
NNNANCCT
+
########
- at HiMom:9:1:2:1592
+ at machine1:HiMom:abcdeACXX:9:1:2:1592 :Y:0:
NNNGAGCC
+
########
- at HiMom:9:1:2:1706
+ at machine1:HiMom:abcdeACXX:9:1:2:1706 :Y:0:
NNNCNGAT
+
########
- at HiMom:9:1:2:1722
+ at machine1:HiMom:abcdeACXX:9:1:2:1722 :N:0:
NNNTCGAC
+
########
- at HiMom:9:1:2:1727
+ at machine1:HiMom:abcdeACXX:9:1:2:1727 :N:0:
NNNTNCTT
+
########
- at HiMom:9:1:2:1753
+ at machine1:HiMom:abcdeACXX:9:1:2:1753 :N:0:
NNTGCTTA
+
########
- at HiMom:9:1:2:1782
+ at machine1:HiMom:abcdeACXX:9:1:2:1782 :Y:0:
NNNTNAGC
+
########
- at HiMom:9:1:2:1827
+ at machine1:HiMom:abcdeACXX:9:1:2:1827 :Y:0:
NNCAACTG
+
########
- at HiMom:9:1:2:1932
+ at machine1:HiMom:abcdeACXX:9:1:2:1932 :Y:0:
NNNCNAGA
+
########
- at HiMom:9:1:2:1946
+ at machine1:HiMom:abcdeACXX:9:1:2:1946 :N:0:
NNNTNGAC
+
########
- at HiMom:9:1:2:209
+ at machine1:HiMom:abcdeACXX:9:1:2:209 :N:0:
NNCATTTC
+
########
- at HiMom:9:1:2:246
+ at machine1:HiMom:abcdeACXX:9:1:2:246 :N:0:
NNNANTTC
+
########
- at HiMom:9:1:2:25
+ at machine1:HiMom:abcdeACXX:9:1:2:25 :N:0:
NNNGATGA
+
########
- at HiMom:9:1:2:307
+ at machine1:HiMom:abcdeACXX:9:1:2:307 :N:0:
NNNTNGAC
+
########
- at HiMom:9:1:2:363
+ at machine1:HiMom:abcdeACXX:9:1:2:363 :N:0:
NNNTNCTT
+
########
- at HiMom:9:1:2:449
+ at machine1:HiMom:abcdeACXX:9:1:2:449 :N:0:
NNNGNTGT
+
########
- at HiMom:9:1:2:546
+ at machine1:HiMom:abcdeACXX:9:1:2:546 :N:0:
NNNANGTT
+
########
- at HiMom:9:1:2:605
+ at machine1:HiMom:abcdeACXX:9:1:2:605 :Y:0:
NNNTNGAC
+
########
- at HiMom:9:1:2:69
+ at machine1:HiMom:abcdeACXX:9:1:2:69 :N:0:
NNGGAGCC
+
########
- at HiMom:9:1:2:747
+ at machine1:HiMom:abcdeACXX:9:1:2:747 :N:0:
NNNCCAGG
+
########
- at HiMom:9:1:2:786
+ at machine1:HiMom:abcdeACXX:9:1:2:786 :Y:0:
NNNGATGT
+
########
- at HiMom:9:1:2:858
+ at machine1:HiMom:abcdeACXX:9:1:2:858 :Y:0:
NNACATCT
+
%%/57799
- at HiMom:9:1:2:943
+ at machine1:HiMom:abcdeACXX:9:1:2:943 :Y:0:
NNACCAGG
+
########
- at HiMom:9:1:2:974
+ at machine1:HiMom:abcdeACXX:9:1:2:974 :Y:0:
NNTATGTT
+
%%0::::<
- at HiMom:9:1:2:988
+ at machine1:HiMom:abcdeACXX:9:1:2:988 :Y:0:
NNTGGCGA
+
########
- at HiMom:9:1:3:1233
+ at machine1:HiMom:abcdeACXX:9:1:3:1233 :N:0:
CCAACAGG
+
########
- at HiMom:9:1:3:1294
+ at machine1:HiMom:abcdeACXX:9:1:3:1294 :N:0:
TCACAATG
+
*37<<@5<
- at HiMom:9:1:3:405
+ at machine1:HiMom:abcdeACXX:9:1:3:405 :N:0:
ACACAAGA
+
0(><=###
- at HiMom:9:1:3:579
+ at machine1:HiMom:abcdeACXX:9:1:3:579 :N:0:
AATCATGT
+
73######
- at HiMom:9:1:3:673
+ at machine1:HiMom:abcdeACXX:9:1:3:673 :N:0:
TGCCCAAA
+
(<######
- at HiMom:9:1:3:890
+ at machine1:HiMom:abcdeACXX:9:1:3:890 :N:0:
GTCACCAT
+
########
- at HiMom:9:1:3:905
+ at machine1:HiMom:abcdeACXX:9:1:3:905 :N:0:
ACATCCTA
+
AA78/<:#
- at HiMom:9:1:3:918
+ at machine1:HiMom:abcdeACXX:9:1:3:918 :N:0:
ACTACCTT
+
)?4B>###
- at HiMom:9:2:0:1073
+ at machine1:HiMom:abcdeACXX:9:2:0:1073 :N:0:
NNNNNCAN
+
########
- at HiMom:9:2:0:1135
+ at machine1:HiMom:abcdeACXX:9:2:0:1135 :N:0:
NNNNNAGN
+
########
- at HiMom:9:2:0:1198
+ at machine1:HiMom:abcdeACXX:9:2:0:1198 :N:0:
NNNNNCCN
+
########
- at HiMom:9:2:0:1278
+ at machine1:HiMom:abcdeACXX:9:2:0:1278 :N:0:
NNNNNTAN
+
########
- at HiMom:9:2:0:135
+ at machine1:HiMom:abcdeACXX:9:2:0:135 :N:0:
NNNNNCGN
+
########
- at HiMom:9:2:0:1547
+ at machine1:HiMom:abcdeACXX:9:2:0:1547 :N:0:
NNNNNCAN
+
########
- at HiMom:9:2:0:1598
+ at machine1:HiMom:abcdeACXX:9:2:0:1598 :N:0:
NNNNNAGN
+
########
- at HiMom:9:2:0:1620
+ at machine1:HiMom:abcdeACXX:9:2:0:1620 :N:0:
NNNNNTGN
+
########
- at HiMom:9:2:0:1668
+ at machine1:HiMom:abcdeACXX:9:2:0:1668 :N:0:
NNNNNCTN
+
########
- at HiMom:9:2:0:186
+ at machine1:HiMom:abcdeACXX:9:2:0:186 :N:0:
NNNNNCCN
+
########
- at HiMom:9:2:0:205
+ at machine1:HiMom:abcdeACXX:9:2:0:205 :N:0:
NNNNNAGN
+
########
- at HiMom:9:2:0:287
+ at machine1:HiMom:abcdeACXX:9:2:0:287 :N:0:
NNNNNGAN
+
########
- at HiMom:9:2:0:382
+ at machine1:HiMom:abcdeACXX:9:2:0:382 :N:0:
NNNNNTAN
+
########
- at HiMom:9:2:0:441
+ at machine1:HiMom:abcdeACXX:9:2:0:441 :N:0:
NNNNNAGN
+
########
- at HiMom:9:2:0:50
+ at machine1:HiMom:abcdeACXX:9:2:0:50 :N:0:
NNNNNGAN
+
########
- at HiMom:9:2:0:501
+ at machine1:HiMom:abcdeACXX:9:2:0:501 :N:0:
NNNNNTAN
+
########
- at HiMom:9:2:0:73
+ at machine1:HiMom:abcdeACXX:9:2:0:73 :N:0:
NNNNNCGN
+
########
- at HiMom:9:2:0:740
+ at machine1:HiMom:abcdeACXX:9:2:0:740 :N:0:
NNNNNGGN
+
########
- at HiMom:9:2:0:766
+ at machine1:HiMom:abcdeACXX:9:2:0:766 :N:0:
NNNNNCCN
+
########
- at HiMom:9:2:0:87
+ at machine1:HiMom:abcdeACXX:9:2:0:87 :N:0:
NNNNNCGN
+
########
- at HiMom:9:2:1:1004
+ at machine1:HiMom:abcdeACXX:9:2:1:1004 :N:0:
NNNGCCGA
+
########
- at HiMom:9:2:1:1034
+ at machine1:HiMom:abcdeACXX:9:2:1:1034 :N:0:
NNNAGCCT
+
########
- at HiMom:9:2:1:1159
+ at machine1:HiMom:abcdeACXX:9:2:1:1159 :N:0:
NNNTNGAC
+
########
- at HiMom:9:2:1:1168
+ at machine1:HiMom:abcdeACXX:9:2:1:1168 :N:0:
NNNGNTAG
+
########
- at HiMom:9:2:1:1180
+ at machine1:HiMom:abcdeACXX:9:2:1:1180 :N:0:
NNNTNAGC
+
########
- at HiMom:9:2:1:1214
+ at machine1:HiMom:abcdeACXX:9:2:1:1214 :N:0:
NNNCATGA
+
########
- at HiMom:9:2:1:1221
+ at machine1:HiMom:abcdeACXX:9:2:1:1221 :N:0:
NNGGATGT
+
########
- at HiMom:9:2:1:1306
+ at machine1:HiMom:abcdeACXX:9:2:1:1306 :N:0:
NNNANCTG
+
########
- at HiMom:9:2:1:1351
+ at machine1:HiMom:abcdeACXX:9:2:1:1351 :N:0:
NNNNNTTN
+
########
- at HiMom:9:2:1:1424
+ at machine1:HiMom:abcdeACXX:9:2:1:1424 :N:0:
NNNCNTCT
+
########
- at HiMom:9:2:1:1452
+ at machine1:HiMom:abcdeACXX:9:2:1:1452 :N:0:
NNAGATCC
+
########
- at HiMom:9:2:1:1515
+ at machine1:HiMom:abcdeACXX:9:2:1:1515 :N:0:
NNNGNATG
+
########
- at HiMom:9:2:1:1521
+ at machine1:HiMom:abcdeACXX:9:2:1:1521 :N:0:
NNNCNAGG
+
########
- at HiMom:9:2:1:1536
+ at machine1:HiMom:abcdeACXX:9:2:1:1536 :N:0:
NNACATCT
+
########
- at HiMom:9:2:1:1543
+ at machine1:HiMom:abcdeACXX:9:2:1:1543 :N:0:
NNNANTTC
+
########
- at HiMom:9:2:1:1617
+ at machine1:HiMom:abcdeACXX:9:2:1:1617 :N:0:
NNNCNAGG
+
########
- at HiMom:9:2:1:1627
+ at machine1:HiMom:abcdeACXX:9:2:1:1627 :N:0:
NNNANCTG
+
########
- at HiMom:9:2:1:1646
+ at machine1:HiMom:abcdeACXX:9:2:1:1646 :N:0:
NNNTNGAC
+
########
- at HiMom:9:2:1:1653
+ at machine1:HiMom:abcdeACXX:9:2:1:1653 :N:0:
NNNGNTGT
+
########
- at HiMom:9:2:1:1682
+ at machine1:HiMom:abcdeACXX:9:2:1:1682 :N:0:
NNNGNGCC
+
########
- at HiMom:9:2:1:170
+ at machine1:HiMom:abcdeACXX:9:2:1:170 :Y:0:
NNGAGCCT
+
########
- at HiMom:9:2:1:1731
+ at machine1:HiMom:abcdeACXX:9:2:1:1731 :N:0:
NNNTNAGC
+
########
- at HiMom:9:2:1:1755
+ at machine1:HiMom:abcdeACXX:9:2:1:1755 :N:0:
NNNNNCAN
+
########
- at HiMom:9:2:1:1812
+ at machine1:HiMom:abcdeACXX:9:2:1:1812 :N:0:
NNNCNTAT
+
########
- at HiMom:9:2:1:1853
+ at machine1:HiMom:abcdeACXX:9:2:1:1853 :N:0:
NNNCNCGA
+
########
- at HiMom:9:2:1:1919
+ at machine1:HiMom:abcdeACXX:9:2:1:1919 :N:0:
NNNANCTG
+
########
- at HiMom:9:2:1:1924
+ at machine1:HiMom:abcdeACXX:9:2:1:1924 :N:0:
NNNAACTG
+
########
- at HiMom:9:2:1:1933
+ at machine1:HiMom:abcdeACXX:9:2:1:1933 :N:0:
NNNTTAGC
+
########
- at HiMom:9:2:1:1938
+ at machine1:HiMom:abcdeACXX:9:2:1:1938 :Y:0:
NNCTCGAC
+
########
- at HiMom:9:2:1:1950
+ at machine1:HiMom:abcdeACXX:9:2:1:1950 :N:0:
NNNNNGTN
+
########
- at HiMom:9:2:1:1959
+ at machine1:HiMom:abcdeACXX:9:2:1:1959 :N:0:
NNTGCTTA
+
########
- at HiMom:9:2:1:1987
+ at machine1:HiMom:abcdeACXX:9:2:1:1987 :N:0:
NNNNNTAN
+
########
- at HiMom:9:2:1:2006
+ at machine1:HiMom:abcdeACXX:9:2:1:2006 :N:0:
NNNGNGCC
+
########
- at HiMom:9:2:1:211
+ at machine1:HiMom:abcdeACXX:9:2:1:211 :N:0:
NNNGNTGT
+
########
- at HiMom:9:2:1:234
+ at machine1:HiMom:abcdeACXX:9:2:1:234 :N:0:
NNNGCTTA
+
########
- at HiMom:9:2:1:242
+ at machine1:HiMom:abcdeACXX:9:2:1:242 :N:0:
NNNCNCGC
+
########
- at HiMom:9:2:1:262
+ at machine1:HiMom:abcdeACXX:9:2:1:262 :N:0:
NNNCNAGG
+
########
- at HiMom:9:2:1:298
+ at machine1:HiMom:abcdeACXX:9:2:1:298 :N:0:
NNNGNTAG
+
########
- at HiMom:9:2:1:312
+ at machine1:HiMom:abcdeACXX:9:2:1:312 :N:0:
NNNANGTT
+
########
- at HiMom:9:2:1:363
+ at machine1:HiMom:abcdeACXX:9:2:1:363 :Y:0:
NNTATGTT
+
%%.99999
- at HiMom:9:2:1:37
+ at machine1:HiMom:abcdeACXX:9:2:1:37 :N:0:
NNNGNCGA
+
########
- at HiMom:9:2:1:370
+ at machine1:HiMom:abcdeACXX:9:2:1:370 :N:0:
NNNANCAT
+
########
- at HiMom:9:2:1:377
+ at machine1:HiMom:abcdeACXX:9:2:1:377 :N:0:
NNNCNTCT
+
########
- at HiMom:9:2:1:414
+ at machine1:HiMom:abcdeACXX:9:2:1:414 :N:0:
NNNGNTTA
+
########
- at HiMom:9:2:1:421
+ at machine1:HiMom:abcdeACXX:9:2:1:421 :N:0:
NNNANCCT
+
########
- at HiMom:9:2:1:428
+ at machine1:HiMom:abcdeACXX:9:2:1:428 :N:0:
NNNATGTT
+
########
- at HiMom:9:2:1:44
+ at machine1:HiMom:abcdeACXX:9:2:1:44 :N:0:
NNNAGCGA
+
########
- at HiMom:9:2:1:466
+ at machine1:HiMom:abcdeACXX:9:2:1:466 :N:0:
NNNTNACA
+
########
- at HiMom:9:2:1:555
+ at machine1:HiMom:abcdeACXX:9:2:1:555 :N:0:
NNNCNGAT
+
########
- at HiMom:9:2:1:558
+ at machine1:HiMom:abcdeACXX:9:2:1:558 :N:0:
NNNANCGA
+
########
- at HiMom:9:2:1:56
+ at machine1:HiMom:abcdeACXX:9:2:1:56 :N:0:
NNNTNAGC
+
########
- at HiMom:9:2:1:569
+ at machine1:HiMom:abcdeACXX:9:2:1:569 :N:0:
NNNANCTG
+
########
- at HiMom:9:2:1:604
+ at machine1:HiMom:abcdeACXX:9:2:1:604 :N:0:
NNCAACTG
+
########
- at HiMom:9:2:1:628
+ at machine1:HiMom:abcdeACXX:9:2:1:628 :N:0:
NNNTAACA
+
########
- at HiMom:9:2:1:64
+ at machine1:HiMom:abcdeACXX:9:2:1:64 :N:0:
NNNANGTT
+
########
- at HiMom:9:2:1:684
+ at machine1:HiMom:abcdeACXX:9:2:1:684 :N:0:
NNAAACGA
+
########
- at HiMom:9:2:1:699
+ at machine1:HiMom:abcdeACXX:9:2:1:699 :N:0:
NNNCNCGA
+
########
- at HiMom:9:2:1:714
+ at machine1:HiMom:abcdeACXX:9:2:1:714 :N:0:
NNNAGCGA
+
########
- at HiMom:9:2:1:722
+ at machine1:HiMom:abcdeACXX:9:2:1:722 :N:0:
NNNCNAGG
+
########
- at HiMom:9:2:1:749
+ at machine1:HiMom:abcdeACXX:9:2:1:749 :N:0:
NNNTNGAC
+
########
- at HiMom:9:2:1:760
+ at machine1:HiMom:abcdeACXX:9:2:1:760 :N:0:
NNACAACA
+
########
- at HiMom:9:2:1:8
+ at machine1:HiMom:abcdeACXX:9:2:1:8 :N:0:
NNNANNNN
+
########
- at HiMom:9:2:1:833
+ at machine1:HiMom:abcdeACXX:9:2:1:833 :N:0:
NNNANCCT
+
########
- at HiMom:9:2:1:848
+ at machine1:HiMom:abcdeACXX:9:2:1:848 :N:0:
NNNANCGA
+
########
- at HiMom:9:2:1:893
+ at machine1:HiMom:abcdeACXX:9:2:1:893 :N:0:
NNCAATTC
+
########
- at HiMom:9:2:1:998
+ at machine1:HiMom:abcdeACXX:9:2:1:998 :N:0:
NNNANGTT
+
########
- at HiMom:9:2:2:0
+ at machine1:HiMom:abcdeACXX:9:2:2:0 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:2:131
+ at machine1:HiMom:abcdeACXX:9:2:2:131 :Y:0:
CACAATCC
+
AACCBCA@
- at HiMom:9:2:2:1636
+ at machine1:HiMom:abcdeACXX:9:2:2:1636 :N:0:
ATCAACCC
+
368?####
- at HiMom:9:2:2:1974
+ at machine1:HiMom:abcdeACXX:9:2:2:1974 :N:0:
AGCAATCT
+
>#######
- at HiMom:9:2:2:351
+ at machine1:HiMom:abcdeACXX:9:2:2:351 :N:0:
TGATAGAA
+
########
- at HiMom:9:2:2:646
+ at machine1:HiMom:abcdeACXX:9:2:2:646 :N:0:
ATCAATTA
+
((>4/406
- at HiMom:9:2:2:828
+ at machine1:HiMom:abcdeACXX:9:2:2:828 :N:0:
TATATCGA
+
########
- at HiMom:9:2:3:1529
+ at machine1:HiMom:abcdeACXX:9:2:3:1529 :N:0:
TAGAACCT
+
9)@73?B=
- at HiMom:9:2:3:179
+ at machine1:HiMom:abcdeACXX:9:2:3:179 :N:0:
GTTTATTA
+
########
- at HiMom:9:2:3:198
+ at machine1:HiMom:abcdeACXX:9:2:3:198 :N:0:
CAGGATCT
+
5)0*@782
- at HiMom:9:2:3:2030
+ at machine1:HiMom:abcdeACXX:9:2:3:2030 :N:0:
GATCAAGA
+
(((>(<@<
- at HiMom:9:2:3:247
+ at machine1:HiMom:abcdeACXX:9:2:3:247 :N:0:
CGGTAGCT
+
########
- at HiMom:9:2:3:4
+ at machine1:HiMom:abcdeACXX:9:2:3:4 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:3:862
+ at machine1:HiMom:abcdeACXX:9:2:3:862 :N:0:
TAACAAGA
+
4)=69)=@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/NN.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/NN.barcode_2.fastq
index 1929789..70b0ee2 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/NN.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/NN.barcode_2.fastq
@@ -1,892 +1,892 @@
- at HiMom:9:1:0:1038
+ at machine1:HiMom:abcdeACXX:9:1:0:1038 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:0:1093
+ at machine1:HiMom:abcdeACXX:9:1:0:1093 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:0:113
+ at machine1:HiMom:abcdeACXX:9:1:0:113 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:0:1193
+ at machine1:HiMom:abcdeACXX:9:1:0:1193 :N:0:
NNNNNGTN
+
########
- at HiMom:9:1:0:1291
+ at machine1:HiMom:abcdeACXX:9:1:0:1291 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:0:1307
+ at machine1:HiMom:abcdeACXX:9:1:0:1307 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:0:1434
+ at machine1:HiMom:abcdeACXX:9:1:0:1434 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:0:1475
+ at machine1:HiMom:abcdeACXX:9:1:0:1475 :N:0:
NNNNNCNN
+
########
- at HiMom:9:1:0:1690
+ at machine1:HiMom:abcdeACXX:9:1:0:1690 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:0:1703
+ at machine1:HiMom:abcdeACXX:9:1:0:1703 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:0:1940
+ at machine1:HiMom:abcdeACXX:9:1:0:1940 :N:0:
NNNNNCNN
+
########
- at HiMom:9:1:0:2001
+ at machine1:HiMom:abcdeACXX:9:1:0:2001 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:0:205
+ at machine1:HiMom:abcdeACXX:9:1:0:205 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:0:275
+ at machine1:HiMom:abcdeACXX:9:1:0:275 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:0:324
+ at machine1:HiMom:abcdeACXX:9:1:0:324 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:0:37
+ at machine1:HiMom:abcdeACXX:9:1:0:37 :N:0:
NNNNNGNN
+
########
- at HiMom:9:1:0:464
+ at machine1:HiMom:abcdeACXX:9:1:0:464 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:0:586
+ at machine1:HiMom:abcdeACXX:9:1:0:586 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:0:841
+ at machine1:HiMom:abcdeACXX:9:1:0:841 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:0:879
+ at machine1:HiMom:abcdeACXX:9:1:0:879 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:1013
+ at machine1:HiMom:abcdeACXX:9:1:1:1013 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:111
+ at machine1:HiMom:abcdeACXX:9:1:1:111 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:1153
+ at machine1:HiMom:abcdeACXX:9:1:1:1153 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:1184
+ at machine1:HiMom:abcdeACXX:9:1:1:1184 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:1241
+ at machine1:HiMom:abcdeACXX:9:1:1:1241 :N:0:
NNNNNCNN
+
########
- at HiMom:9:1:1:1243
+ at machine1:HiMom:abcdeACXX:9:1:1:1243 :N:0:
NNNNNTGN
+
########
- at HiMom:9:1:1:1247
+ at machine1:HiMom:abcdeACXX:9:1:1:1247 :N:0:
NNNNNANN
+
########
- at HiMom:9:1:1:1282
+ at machine1:HiMom:abcdeACXX:9:1:1:1282 :N:0:
NNNNNCNN
+
########
- at HiMom:9:1:1:132
+ at machine1:HiMom:abcdeACXX:9:1:1:132 :N:0:
NNNNNTNN
+
########
- at HiMom:9:1:1:1320
+ at machine1:HiMom:abcdeACXX:9:1:1:1320 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:1372
+ at machine1:HiMom:abcdeACXX:9:1:1:1372 :N:0:
NNNGNNNN
+
########
- at HiMom:9:1:1:1379
+ at machine1:HiMom:abcdeACXX:9:1:1:1379 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:1391
+ at machine1:HiMom:abcdeACXX:9:1:1:1391 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:140
+ at machine1:HiMom:abcdeACXX:9:1:1:140 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:1513
+ at machine1:HiMom:abcdeACXX:9:1:1:1513 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:1521
+ at machine1:HiMom:abcdeACXX:9:1:1:1521 :N:0:
NNNNNCCN
+
########
- at HiMom:9:1:1:155
+ at machine1:HiMom:abcdeACXX:9:1:1:155 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:1555
+ at machine1:HiMom:abcdeACXX:9:1:1:1555 :N:0:
NNNNNCNN
+
########
- at HiMom:9:1:1:164
+ at machine1:HiMom:abcdeACXX:9:1:1:164 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:1684
+ at machine1:HiMom:abcdeACXX:9:1:1:1684 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:1696
+ at machine1:HiMom:abcdeACXX:9:1:1:1696 :N:0:
NNNNNCTN
+
########
- at HiMom:9:1:1:170
+ at machine1:HiMom:abcdeACXX:9:1:1:170 :N:0:
NNNNNACN
+
########
- at HiMom:9:1:1:173
+ at machine1:HiMom:abcdeACXX:9:1:1:173 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:1733
+ at machine1:HiMom:abcdeACXX:9:1:1:1733 :N:0:
NNNNNGAN
+
########
- at HiMom:9:1:1:1770
+ at machine1:HiMom:abcdeACXX:9:1:1:1770 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:18
+ at machine1:HiMom:abcdeACXX:9:1:1:18 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:1815
+ at machine1:HiMom:abcdeACXX:9:1:1:1815 :N:0:
NNNTNNNN
+
########
- at HiMom:9:1:1:1836
+ at machine1:HiMom:abcdeACXX:9:1:1:1836 :N:0:
NNNNNGTN
+
########
- at HiMom:9:1:1:184
+ at machine1:HiMom:abcdeACXX:9:1:1:184 :N:0:
NNNNNGTN
+
########
- at HiMom:9:1:1:1886
+ at machine1:HiMom:abcdeACXX:9:1:1:1886 :Y:0:
NNNGNNNN
+
########
- at HiMom:9:1:1:1906
+ at machine1:HiMom:abcdeACXX:9:1:1:1906 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:1917
+ at machine1:HiMom:abcdeACXX:9:1:1:1917 :N:0:
NNNNNACN
+
########
- at HiMom:9:1:1:195
+ at machine1:HiMom:abcdeACXX:9:1:1:195 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:1954
+ at machine1:HiMom:abcdeACXX:9:1:1:1954 :N:0:
NNNNNCNN
+
########
- at HiMom:9:1:1:2
+ at machine1:HiMom:abcdeACXX:9:1:1:2 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:2011
+ at machine1:HiMom:abcdeACXX:9:1:1:2011 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:240
+ at machine1:HiMom:abcdeACXX:9:1:1:240 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:262
+ at machine1:HiMom:abcdeACXX:9:1:1:262 :N:0:
NNNNNCNN
+
########
- at HiMom:9:1:1:264
+ at machine1:HiMom:abcdeACXX:9:1:1:264 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:299
+ at machine1:HiMom:abcdeACXX:9:1:1:299 :N:0:
NNNNNCGN
+
########
- at HiMom:9:1:1:30
+ at machine1:HiMom:abcdeACXX:9:1:1:30 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:353
+ at machine1:HiMom:abcdeACXX:9:1:1:353 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:367
+ at machine1:HiMom:abcdeACXX:9:1:1:367 :N:0:
NNNNNANN
+
########
- at HiMom:9:1:1:41
+ at machine1:HiMom:abcdeACXX:9:1:1:41 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:416
+ at machine1:HiMom:abcdeACXX:9:1:1:416 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:483
+ at machine1:HiMom:abcdeACXX:9:1:1:483 :N:0:
NNNNNTAN
+
########
- at HiMom:9:1:1:486
+ at machine1:HiMom:abcdeACXX:9:1:1:486 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:495
+ at machine1:HiMom:abcdeACXX:9:1:1:495 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:508
+ at machine1:HiMom:abcdeACXX:9:1:1:508 :N:0:
NNNNNCNN
+
########
- at HiMom:9:1:1:517
+ at machine1:HiMom:abcdeACXX:9:1:1:517 :N:0:
NNNNNAGN
+
########
- at HiMom:9:1:1:535
+ at machine1:HiMom:abcdeACXX:9:1:1:535 :N:0:
NNNCNNNN
+
########
- at HiMom:9:1:1:55
+ at machine1:HiMom:abcdeACXX:9:1:1:55 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:554
+ at machine1:HiMom:abcdeACXX:9:1:1:554 :N:0:
NNNNNTAN
+
########
- at HiMom:9:1:1:567
+ at machine1:HiMom:abcdeACXX:9:1:1:567 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:59
+ at machine1:HiMom:abcdeACXX:9:1:1:59 :N:0:
NNNNNANN
+
########
- at HiMom:9:1:1:613
+ at machine1:HiMom:abcdeACXX:9:1:1:613 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:622
+ at machine1:HiMom:abcdeACXX:9:1:1:622 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:627
+ at machine1:HiMom:abcdeACXX:9:1:1:627 :N:0:
NNNNNGAN
+
########
- at HiMom:9:1:1:684
+ at machine1:HiMom:abcdeACXX:9:1:1:684 :N:0:
NNNNNGAN
+
########
- at HiMom:9:1:1:72
+ at machine1:HiMom:abcdeACXX:9:1:1:72 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:812
+ at machine1:HiMom:abcdeACXX:9:1:1:812 :N:0:
NNNNNGAN
+
########
- at HiMom:9:1:1:874
+ at machine1:HiMom:abcdeACXX:9:1:1:874 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:1:931
+ at machine1:HiMom:abcdeACXX:9:1:1:931 :N:0:
NNNNNCNN
+
########
- at HiMom:9:1:1:965
+ at machine1:HiMom:abcdeACXX:9:1:1:965 :N:0:
NNNTNNNN
+
########
- at HiMom:9:1:1:994
+ at machine1:HiMom:abcdeACXX:9:1:1:994 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:2:1158
+ at machine1:HiMom:abcdeACXX:9:1:2:1158 :Y:0:
NNNNTANN
+
########
- at HiMom:9:1:2:1238
+ at machine1:HiMom:abcdeACXX:9:1:2:1238 :N:0:
NNNNNAGN
+
########
- at HiMom:9:1:2:1275
+ at machine1:HiMom:abcdeACXX:9:1:2:1275 :Y:0:
NNNANNNN
+
########
- at HiMom:9:1:2:1301
+ at machine1:HiMom:abcdeACXX:9:1:2:1301 :N:0:
NNNTANNN
+
########
- at HiMom:9:1:2:1453
+ at machine1:HiMom:abcdeACXX:9:1:2:1453 :Y:0:
NNNNNNNN
+
########
- at HiMom:9:1:2:150
+ at machine1:HiMom:abcdeACXX:9:1:2:150 :N:0:
NNNANNNN
+
########
- at HiMom:9:1:2:1592
+ at machine1:HiMom:abcdeACXX:9:1:2:1592 :Y:0:
NNNGANNN
+
########
- at HiMom:9:1:2:1706
+ at machine1:HiMom:abcdeACXX:9:1:2:1706 :Y:0:
NNNCNNNN
+
########
- at HiMom:9:1:2:1722
+ at machine1:HiMom:abcdeACXX:9:1:2:1722 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:2:1727
+ at machine1:HiMom:abcdeACXX:9:1:2:1727 :N:0:
NNNTNNNN
+
########
- at HiMom:9:1:2:1753
+ at machine1:HiMom:abcdeACXX:9:1:2:1753 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:2:1782
+ at machine1:HiMom:abcdeACXX:9:1:2:1782 :Y:0:
NNNNNNNN
+
########
- at HiMom:9:1:2:1827
+ at machine1:HiMom:abcdeACXX:9:1:2:1827 :Y:0:
NNNNACNN
+
########
- at HiMom:9:1:2:1932
+ at machine1:HiMom:abcdeACXX:9:1:2:1932 :Y:0:
NNNCNNNN
+
########
- at HiMom:9:1:2:1946
+ at machine1:HiMom:abcdeACXX:9:1:2:1946 :N:0:
NNNNNGNN
+
########
- at HiMom:9:1:2:209
+ at machine1:HiMom:abcdeACXX:9:1:2:209 :N:0:
NNNATNNN
+
########
- at HiMom:9:1:2:246
+ at machine1:HiMom:abcdeACXX:9:1:2:246 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:2:25
+ at machine1:HiMom:abcdeACXX:9:1:2:25 :N:0:
NNNGNNNN
+
########
- at HiMom:9:1:2:307
+ at machine1:HiMom:abcdeACXX:9:1:2:307 :N:0:
NNNTNNNN
+
########
- at HiMom:9:1:2:363
+ at machine1:HiMom:abcdeACXX:9:1:2:363 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:2:449
+ at machine1:HiMom:abcdeACXX:9:1:2:449 :N:0:
NNNGNNNN
+
########
- at HiMom:9:1:2:546
+ at machine1:HiMom:abcdeACXX:9:1:2:546 :N:0:
NNNNNGNN
+
########
- at HiMom:9:1:2:605
+ at machine1:HiMom:abcdeACXX:9:1:2:605 :Y:0:
NNNTNNNN
+
########
- at HiMom:9:1:2:69
+ at machine1:HiMom:abcdeACXX:9:1:2:69 :N:0:
NNNNAGNN
+
########
- at HiMom:9:1:2:747
+ at machine1:HiMom:abcdeACXX:9:1:2:747 :N:0:
NNNNNNNN
+
########
- at HiMom:9:1:2:786
+ at machine1:HiMom:abcdeACXX:9:1:2:786 :Y:0:
NNNGNNNN
+
########
- at HiMom:9:1:2:858
+ at machine1:HiMom:abcdeACXX:9:1:2:858 :Y:0:
NNNNATNN
+
%%/57799
- at HiMom:9:1:2:943
+ at machine1:HiMom:abcdeACXX:9:1:2:943 :Y:0:
NNNCCNNN
+
########
- at HiMom:9:1:2:974
+ at machine1:HiMom:abcdeACXX:9:1:2:974 :Y:0:
NNNATNNN
+
%%0::::<
- at HiMom:9:1:2:988
+ at machine1:HiMom:abcdeACXX:9:1:2:988 :Y:0:
NNNGGNNN
+
########
- at HiMom:9:1:3:1233
+ at machine1:HiMom:abcdeACXX:9:1:3:1233 :N:0:
NNNACNNN
+
########
- at HiMom:9:1:3:1294
+ at machine1:HiMom:abcdeACXX:9:1:3:1294 :N:0:
TCNNNNNN
+
*37<<@5<
- at HiMom:9:1:3:405
+ at machine1:HiMom:abcdeACXX:9:1:3:405 :N:0:
NNNNNAGN
+
0(><=###
- at HiMom:9:1:3:579
+ at machine1:HiMom:abcdeACXX:9:1:3:579 :N:0:
NNNNATNN
+
73######
- at HiMom:9:1:3:673
+ at machine1:HiMom:abcdeACXX:9:1:3:673 :N:0:
NNNCCNNN
+
(<######
- at HiMom:9:1:3:890
+ at machine1:HiMom:abcdeACXX:9:1:3:890 :N:0:
NNCANNNN
+
########
- at HiMom:9:1:3:905
+ at machine1:HiMom:abcdeACXX:9:1:3:905 :N:0:
ACNNNNNN
+
AA78/<:#
- at HiMom:9:1:3:918
+ at machine1:HiMom:abcdeACXX:9:1:3:918 :N:0:
NNNNNCTN
+
)?4B>###
- at HiMom:9:2:0:1073
+ at machine1:HiMom:abcdeACXX:9:2:0:1073 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:0:1135
+ at machine1:HiMom:abcdeACXX:9:2:0:1135 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:0:1198
+ at machine1:HiMom:abcdeACXX:9:2:0:1198 :N:0:
NNNNNCCN
+
########
- at HiMom:9:2:0:1278
+ at machine1:HiMom:abcdeACXX:9:2:0:1278 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:0:135
+ at machine1:HiMom:abcdeACXX:9:2:0:135 :N:0:
NNNNNCNN
+
########
- at HiMom:9:2:0:1547
+ at machine1:HiMom:abcdeACXX:9:2:0:1547 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:0:1598
+ at machine1:HiMom:abcdeACXX:9:2:0:1598 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:0:1620
+ at machine1:HiMom:abcdeACXX:9:2:0:1620 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:0:1668
+ at machine1:HiMom:abcdeACXX:9:2:0:1668 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:0:186
+ at machine1:HiMom:abcdeACXX:9:2:0:186 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:0:205
+ at machine1:HiMom:abcdeACXX:9:2:0:205 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:0:287
+ at machine1:HiMom:abcdeACXX:9:2:0:287 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:0:382
+ at machine1:HiMom:abcdeACXX:9:2:0:382 :N:0:
NNNNNTNN
+
########
- at HiMom:9:2:0:441
+ at machine1:HiMom:abcdeACXX:9:2:0:441 :N:0:
NNNNNAGN
+
########
- at HiMom:9:2:0:50
+ at machine1:HiMom:abcdeACXX:9:2:0:50 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:0:501
+ at machine1:HiMom:abcdeACXX:9:2:0:501 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:0:73
+ at machine1:HiMom:abcdeACXX:9:2:0:73 :N:0:
NNNNNCNN
+
########
- at HiMom:9:2:0:740
+ at machine1:HiMom:abcdeACXX:9:2:0:740 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:0:766
+ at machine1:HiMom:abcdeACXX:9:2:0:766 :N:0:
NNNNNCCN
+
########
- at HiMom:9:2:0:87
+ at machine1:HiMom:abcdeACXX:9:2:0:87 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:1:1004
+ at machine1:HiMom:abcdeACXX:9:2:1:1004 :N:0:
NNNNNCGN
+
########
- at HiMom:9:2:1:1034
+ at machine1:HiMom:abcdeACXX:9:2:1:1034 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:1:1159
+ at machine1:HiMom:abcdeACXX:9:2:1:1159 :N:0:
NNNTNNNN
+
########
- at HiMom:9:2:1:1168
+ at machine1:HiMom:abcdeACXX:9:2:1:1168 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:1:1180
+ at machine1:HiMom:abcdeACXX:9:2:1:1180 :N:0:
NNNNNAGN
+
########
- at HiMom:9:2:1:1214
+ at machine1:HiMom:abcdeACXX:9:2:1:1214 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:1:1221
+ at machine1:HiMom:abcdeACXX:9:2:1:1221 :N:0:
NNNNNTGN
+
########
- at HiMom:9:2:1:1306
+ at machine1:HiMom:abcdeACXX:9:2:1:1306 :N:0:
NNNNNCNN
+
########
- at HiMom:9:2:1:1351
+ at machine1:HiMom:abcdeACXX:9:2:1:1351 :N:0:
NNNNNTNN
+
########
- at HiMom:9:2:1:1424
+ at machine1:HiMom:abcdeACXX:9:2:1:1424 :N:0:
NNNCNNNN
+
########
- at HiMom:9:2:1:1452
+ at machine1:HiMom:abcdeACXX:9:2:1:1452 :N:0:
NNNNATNN
+
########
- at HiMom:9:2:1:1515
+ at machine1:HiMom:abcdeACXX:9:2:1:1515 :N:0:
NNNNNANN
+
########
- at HiMom:9:2:1:1521
+ at machine1:HiMom:abcdeACXX:9:2:1:1521 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:1:1536
+ at machine1:HiMom:abcdeACXX:9:2:1:1536 :N:0:
NNANNNNN
+
########
- at HiMom:9:2:1:1543
+ at machine1:HiMom:abcdeACXX:9:2:1:1543 :N:0:
NNNANNNN
+
########
- at HiMom:9:2:1:1617
+ at machine1:HiMom:abcdeACXX:9:2:1:1617 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:1:1627
+ at machine1:HiMom:abcdeACXX:9:2:1:1627 :N:0:
NNNANNNN
+
########
- at HiMom:9:2:1:1646
+ at machine1:HiMom:abcdeACXX:9:2:1:1646 :N:0:
NNNTNNNN
+
########
- at HiMom:9:2:1:1653
+ at machine1:HiMom:abcdeACXX:9:2:1:1653 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:1:1682
+ at machine1:HiMom:abcdeACXX:9:2:1:1682 :N:0:
NNNNNGNN
+
########
- at HiMom:9:2:1:170
+ at machine1:HiMom:abcdeACXX:9:2:1:170 :Y:0:
NNNAGNNN
+
########
- at HiMom:9:2:1:1731
+ at machine1:HiMom:abcdeACXX:9:2:1:1731 :N:0:
NNNNNAGN
+
########
- at HiMom:9:2:1:1755
+ at machine1:HiMom:abcdeACXX:9:2:1:1755 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:1:1812
+ at machine1:HiMom:abcdeACXX:9:2:1:1812 :N:0:
NNNCNNNN
+
########
- at HiMom:9:2:1:1853
+ at machine1:HiMom:abcdeACXX:9:2:1:1853 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:1:1919
+ at machine1:HiMom:abcdeACXX:9:2:1:1919 :N:0:
NNNANNNN
+
########
- at HiMom:9:2:1:1924
+ at machine1:HiMom:abcdeACXX:9:2:1:1924 :N:0:
NNNAANNN
+
########
- at HiMom:9:2:1:1933
+ at machine1:HiMom:abcdeACXX:9:2:1:1933 :N:0:
NNNTNNNN
+
########
- at HiMom:9:2:1:1938
+ at machine1:HiMom:abcdeACXX:9:2:1:1938 :Y:0:
NNCTNNNN
+
########
- at HiMom:9:2:1:1950
+ at machine1:HiMom:abcdeACXX:9:2:1:1950 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:1:1959
+ at machine1:HiMom:abcdeACXX:9:2:1:1959 :N:0:
NNNNCTNN
+
########
- at HiMom:9:2:1:1987
+ at machine1:HiMom:abcdeACXX:9:2:1:1987 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:1:2006
+ at machine1:HiMom:abcdeACXX:9:2:1:2006 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:1:211
+ at machine1:HiMom:abcdeACXX:9:2:1:211 :N:0:
NNNNNTGN
+
########
- at HiMom:9:2:1:234
+ at machine1:HiMom:abcdeACXX:9:2:1:234 :N:0:
NNNNCTNN
+
########
- at HiMom:9:2:1:242
+ at machine1:HiMom:abcdeACXX:9:2:1:242 :N:0:
NNNCNNNN
+
########
- at HiMom:9:2:1:262
+ at machine1:HiMom:abcdeACXX:9:2:1:262 :N:0:
NNNCNNNN
+
########
- at HiMom:9:2:1:298
+ at machine1:HiMom:abcdeACXX:9:2:1:298 :N:0:
NNNGNNNN
+
########
- at HiMom:9:2:1:312
+ at machine1:HiMom:abcdeACXX:9:2:1:312 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:1:363
+ at machine1:HiMom:abcdeACXX:9:2:1:363 :Y:0:
NNTNNNNN
+
%%.99999
- at HiMom:9:2:1:37
+ at machine1:HiMom:abcdeACXX:9:2:1:37 :N:0:
NNNGNNNN
+
########
- at HiMom:9:2:1:370
+ at machine1:HiMom:abcdeACXX:9:2:1:370 :N:0:
NNNANNNN
+
########
- at HiMom:9:2:1:377
+ at machine1:HiMom:abcdeACXX:9:2:1:377 :N:0:
NNNNNTNN
+
########
- at HiMom:9:2:1:414
+ at machine1:HiMom:abcdeACXX:9:2:1:414 :N:0:
NNNGNNNN
+
########
- at HiMom:9:2:1:421
+ at machine1:HiMom:abcdeACXX:9:2:1:421 :N:0:
NNNANNNN
+
########
- at HiMom:9:2:1:428
+ at machine1:HiMom:abcdeACXX:9:2:1:428 :N:0:
NNNANNNN
+
########
- at HiMom:9:2:1:44
+ at machine1:HiMom:abcdeACXX:9:2:1:44 :N:0:
NNNAGNNN
+
########
- at HiMom:9:2:1:466
+ at machine1:HiMom:abcdeACXX:9:2:1:466 :N:0:
NNNTNNNN
+
########
- at HiMom:9:2:1:555
+ at machine1:HiMom:abcdeACXX:9:2:1:555 :N:0:
NNNCNNNN
+
########
- at HiMom:9:2:1:558
+ at machine1:HiMom:abcdeACXX:9:2:1:558 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:1:56
+ at machine1:HiMom:abcdeACXX:9:2:1:56 :N:0:
NNNNNANN
+
########
- at HiMom:9:2:1:569
+ at machine1:HiMom:abcdeACXX:9:2:1:569 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:1:604
+ at machine1:HiMom:abcdeACXX:9:2:1:604 :N:0:
NNCNNNNN
+
########
- at HiMom:9:2:1:628
+ at machine1:HiMom:abcdeACXX:9:2:1:628 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:1:64
+ at machine1:HiMom:abcdeACXX:9:2:1:64 :N:0:
NNNNNGTN
+
########
- at HiMom:9:2:1:684
+ at machine1:HiMom:abcdeACXX:9:2:1:684 :N:0:
NNAANNNN
+
########
- at HiMom:9:2:1:699
+ at machine1:HiMom:abcdeACXX:9:2:1:699 :N:0:
NNNCNNNN
+
########
- at HiMom:9:2:1:714
+ at machine1:HiMom:abcdeACXX:9:2:1:714 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:1:722
+ at machine1:HiMom:abcdeACXX:9:2:1:722 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:1:749
+ at machine1:HiMom:abcdeACXX:9:2:1:749 :N:0:
NNNNNGNN
+
########
- at HiMom:9:2:1:760
+ at machine1:HiMom:abcdeACXX:9:2:1:760 :N:0:
NNNNAANN
+
########
- at HiMom:9:2:1:8
+ at machine1:HiMom:abcdeACXX:9:2:1:8 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:1:833
+ at machine1:HiMom:abcdeACXX:9:2:1:833 :N:0:
NNNNNCCN
+
########
- at HiMom:9:2:1:848
+ at machine1:HiMom:abcdeACXX:9:2:1:848 :N:0:
NNNANNNN
+
########
- at HiMom:9:2:1:893
+ at machine1:HiMom:abcdeACXX:9:2:1:893 :N:0:
NNNAANNN
+
########
- at HiMom:9:2:1:998
+ at machine1:HiMom:abcdeACXX:9:2:1:998 :N:0:
NNNNNGNN
+
########
- at HiMom:9:2:2:0
+ at machine1:HiMom:abcdeACXX:9:2:2:0 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:2:131
+ at machine1:HiMom:abcdeACXX:9:2:2:131 :Y:0:
NNNAANNN
+
AACCBCA@
- at HiMom:9:2:2:1636
+ at machine1:HiMom:abcdeACXX:9:2:2:1636 :N:0:
NNNAANNN
+
368?####
- at HiMom:9:2:2:1974
+ at machine1:HiMom:abcdeACXX:9:2:2:1974 :N:0:
NGCNNNNN
+
>#######
- at HiMom:9:2:2:351
+ at machine1:HiMom:abcdeACXX:9:2:2:351 :N:0:
NNNNNGAN
+
########
- at HiMom:9:2:2:646
+ at machine1:HiMom:abcdeACXX:9:2:2:646 :N:0:
NTCNNNNN
+
((>4/406
- at HiMom:9:2:2:828
+ at machine1:HiMom:abcdeACXX:9:2:2:828 :N:0:
NNNNNCGN
+
########
- at HiMom:9:2:3:1529
+ at machine1:HiMom:abcdeACXX:9:2:3:1529 :N:0:
NAGNNNNN
+
9)@73?B=
- at HiMom:9:2:3:179
+ at machine1:HiMom:abcdeACXX:9:2:3:179 :N:0:
NNNTANNN
+
########
- at HiMom:9:2:3:198
+ at machine1:HiMom:abcdeACXX:9:2:3:198 :N:0:
NNNNNTCN
+
5)0*@782
- at HiMom:9:2:3:2030
+ at machine1:HiMom:abcdeACXX:9:2:3:2030 :N:0:
NNNCANNN
+
(((>(<@<
- at HiMom:9:2:3:247
+ at machine1:HiMom:abcdeACXX:9:2:3:247 :N:0:
CGNNNNNN
+
########
- at HiMom:9:2:3:4
+ at machine1:HiMom:abcdeACXX:9:2:3:4 :N:0:
NNNNNNNN
+
########
- at HiMom:9:2:3:862
+ at machine1:HiMom:abcdeACXX:9:2:3:862 :N:0:
TANNNNNN
+
4)=69)=@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGC.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGC.1.fastq
index 5e65408..e93c230 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGC.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGC.1.fastq
@@ -1,32 +1,32 @@
- at HiMom:7:1:2:737
+ at machine1:HiMom:abcdeACXX:7:1:2:737 :N:0:TACTTAGC
NAAAACAATTAAAATAAATGCTTAAAATCA
+
##############################
- at HiMom:7:1:2:85
+ at machine1:HiMom:abcdeACXX:7:1:2:85 :N:0:TACTTAGC
NGATAAAGTACAATGCTAATCACTTAAGAT
+
%.52353046874+'01999975;:9255;
- at HiMom:7:1:3:1574
+ at machine1:HiMom:abcdeACXX:7:1:3:1574 :Y:0:TACTTAGC
NTTATTCCTTAGGAAATTTTAAATTCTGTA
+
%0955357999999:99::99102::9:3:
- at HiMom:7:2:2:101
+ at machine1:HiMom:abcdeACXX:7:2:2:101 :Y:0:TACTTAGC
NGTTAATTTAGGGAAATTTGTTTGTATTTT
+
%,3:969;<52718;<<<768;::9;999;
- at HiMom:7:2:2:12
+ at machine1:HiMom:abcdeACXX:7:2:2:12 :N:0:TACTTAGC
NATGCATTGTAATTTAATAGAGTGAAATGG
+
##############################
- at HiMom:7:2:3:1844
+ at machine1:HiMom:abcdeACXX:7:2:3:1844 :N:0:TACTTAGC
NGGACTACAAGCGCACGCCACATGCTCAGC
+
##############################
- at HiMom:7:2:3:728
+ at machine1:HiMom:abcdeACXX:7:2:3:728 :N:0:TACTTAGC
TGCCTCCTTGGAGAGGGCCGCAAAGCCAGG
+
=>=7?A?7'50>/996:;<+>AA at 7+8B67
- at HiMom:7:2:3:80
+ at machine1:HiMom:abcdeACXX:7:2:3:80 :Y:0:TACTTAGC
AGGCAGGATGAAATTTTGTCTATTTATTCA
+
@9:B at B@?B at ABABBBB??7AABBBBBB?A
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGC.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGC.barcode_1.fastq
index 4bc5a8b..6fd2760 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGC.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGC.barcode_1.fastq
@@ -1,32 +1,32 @@
- at HiMom:7:1:2:737
+ at machine1:HiMom:abcdeACXX:7:1:2:737 :N:0:TACTTAGC
TACTTAGC
+
BCCCBCBB
- at HiMom:7:1:2:85
+ at machine1:HiMom:abcdeACXX:7:1:2:85 :N:0:TACTTAGC
TACTTAGC
+
B>(>B=B2
- at HiMom:7:1:3:1574
+ at machine1:HiMom:abcdeACXX:7:1:3:1574 :Y:0:TACTTAGC
TACTTAGC
+
@ACBBC at A
- at HiMom:7:2:2:101
+ at machine1:HiMom:abcdeACXX:7:2:2:101 :Y:0:TACTTAGC
TACTTAGC
+
BB=CCCC?
- at HiMom:7:2:2:12
+ at machine1:HiMom:abcdeACXX:7:2:2:12 :N:0:TACTTAGC
TACTTAGC
+
A8%9<=##
- at HiMom:7:2:3:1844
+ at machine1:HiMom:abcdeACXX:7:2:3:1844 :N:0:TACTTAGC
TACTTAGC
+
B?BC>:@@
- at HiMom:7:2:3:728
+ at machine1:HiMom:abcdeACXX:7:2:3:728 :N:0:TACTTAGC
TACTTAGC
+
BBCA>B7#
- at HiMom:7:2:3:80
+ at machine1:HiMom:abcdeACXX:7:2:3:80 :Y:0:TACTTAGC
TACTTAGC
+
B at 9ABA@8
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGCCACATCCT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGCCACATCCT.1.fastq
index 7461810..9536869 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGCCACATCCT.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGCCACATCCT.1.fastq
@@ -1,32 +1,32 @@
- at HiMom:9:1:2:737
+ at machine1:HiMom:abcdeACXX:9:1:2:737 :N:0:TACTTAGCCACATCCT
NAAAACAATTAAAATAAATGCTTAAAATCA
+
##############################
- at HiMom:9:1:2:85
+ at machine1:HiMom:abcdeACXX:9:1:2:85 :N:0:TACTTAGCCACATCCT
NGATAAAGTACAATGCTAATCACTTAAGAT
+
%.52353046874+'01999975;:9255;
- at HiMom:9:1:3:1574
+ at machine1:HiMom:abcdeACXX:9:1:3:1574 :Y:0:TACTTAGCCACATCCT
NTTATTCCTTAGGAAATTTTAAATTCTGTA
+
%0955357999999:99::99102::9:3:
- at HiMom:9:2:2:101
+ at machine1:HiMom:abcdeACXX:9:2:2:101 :Y:0:TACTTAGCCACATCCT
NGTTAATTTAGGGAAATTTGTTTGTATTTT
+
%,3:969;<52718;<<<768;::9;999;
- at HiMom:9:2:2:12
+ at machine1:HiMom:abcdeACXX:9:2:2:12 :N:0:TACTTAGCCACATCCT
NATGCATTGTAATTTAATAGAGTGAAATGG
+
##############################
- at HiMom:9:2:3:1844
+ at machine1:HiMom:abcdeACXX:9:2:3:1844 :N:0:TACTTAGCCACATCCT
NGGACTACAAGCGCACGCCACATGCTCAGC
+
##############################
- at HiMom:9:2:3:728
+ at machine1:HiMom:abcdeACXX:9:2:3:728 :N:0:TACTTAGCCACATCCT
TGCCTCCTTGGAGAGGGCCGCAAAGCCAGG
+
=>=7?A?7'50>/996:;<+>AA at 7+8B67
- at HiMom:9:2:3:80
+ at machine1:HiMom:abcdeACXX:9:2:3:80 :Y:0:TACTTAGCCACATCCT
AGGCAGGATGAAATTTTGTCTATTTATTCA
+
@9:B at B@?B at ABABBBB??7AABBBBBB?A
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGCCACATCCT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGCCACATCCT.barcode_1.fastq
index 96d4dbe..431c08a 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGCCACATCCT.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGCCACATCCT.barcode_1.fastq
@@ -1,32 +1,32 @@
- at HiMom:9:1:2:737
+ at machine1:HiMom:abcdeACXX:9:1:2:737 :N:0:TACTTAGCCACATCCT
TACTTAGC
+
BCCCBCBB
- at HiMom:9:1:2:85
+ at machine1:HiMom:abcdeACXX:9:1:2:85 :N:0:TACTTAGCCACATCCT
TACTTAGC
+
B>(>B=B2
- at HiMom:9:1:3:1574
+ at machine1:HiMom:abcdeACXX:9:1:3:1574 :Y:0:TACTTAGCCACATCCT
TACTTAGC
+
@ACBBC at A
- at HiMom:9:2:2:101
+ at machine1:HiMom:abcdeACXX:9:2:2:101 :Y:0:TACTTAGCCACATCCT
TACTTAGC
+
BB=CCCC?
- at HiMom:9:2:2:12
+ at machine1:HiMom:abcdeACXX:9:2:2:12 :N:0:TACTTAGCCACATCCT
TACTTAGC
+
A8%9<=##
- at HiMom:9:2:3:1844
+ at machine1:HiMom:abcdeACXX:9:2:3:1844 :N:0:TACTTAGCCACATCCT
TACTTAGC
+
B?BC>:@@
- at HiMom:9:2:3:728
+ at machine1:HiMom:abcdeACXX:9:2:3:728 :N:0:TACTTAGCCACATCCT
TACTTAGC
+
BBCA>B7#
- at HiMom:9:2:3:80
+ at machine1:HiMom:abcdeACXX:9:2:3:80 :Y:0:TACTTAGCCACATCCT
TACTTAGC
+
B at 9ABA@8
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGCCACATCCT.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGCCACATCCT.barcode_2.fastq
index cb349a6..35c71fa 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGCCACATCCT.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGCCACATCCT.barcode_2.fastq
@@ -1,32 +1,32 @@
- at HiMom:9:1:2:737
+ at machine1:HiMom:abcdeACXX:9:1:2:737 :N:0:TACTTAGCCACATCCT
CACATCCT
+
BCCCBCBB
- at HiMom:9:1:2:85
+ at machine1:HiMom:abcdeACXX:9:1:2:85 :N:0:TACTTAGCCACATCCT
CACATCCT
+
B>(>B=B2
- at HiMom:9:1:3:1574
+ at machine1:HiMom:abcdeACXX:9:1:3:1574 :Y:0:TACTTAGCCACATCCT
CACATCCT
+
@ACBBC at A
- at HiMom:9:2:2:101
+ at machine1:HiMom:abcdeACXX:9:2:2:101 :Y:0:TACTTAGCCACATCCT
CACATCCT
+
BB=CCCC?
- at HiMom:9:2:2:12
+ at machine1:HiMom:abcdeACXX:9:2:2:12 :N:0:TACTTAGCCACATCCT
CACATCCT
+
A8%9<=##
- at HiMom:9:2:3:1844
+ at machine1:HiMom:abcdeACXX:9:2:3:1844 :N:0:TACTTAGCCACATCCT
CACATCCT
+
B?BC>:@@
- at HiMom:9:2:3:728
+ at machine1:HiMom:abcdeACXX:9:2:3:728 :N:0:TACTTAGCCACATCCT
CACATCCT
+
BBCA>B7#
- at HiMom:9:2:3:80
+ at machine1:HiMom:abcdeACXX:9:2:3:80 :Y:0:TACTTAGCCACATCCT
CACATCCT
+
B at 9ABA@8
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATG.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATG.1.fastq
index 4ce046c..a6de675 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATG.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATG.1.fastq
@@ -1,28 +1,28 @@
- at HiMom:7:1:3:1328
+ at machine1:HiMom:abcdeACXX:7:1:3:1328 :N:0:TCGGAATG
GCTACCAACCCCACTCCTAGATGAAAGACC
+
068,=@)=AA82 at C@8;;@3;8/<<#####
- at HiMom:7:1:3:2037
+ at machine1:HiMom:abcdeACXX:7:1:3:2037 :N:0:TCGGAATG
CATCCTGTAACAAAGTGTTTATAGTTTTCA
+
:@9 at B6<?A>(>AB@<*)=<CBA:>51:7A
- at HiMom:7:1:3:695
+ at machine1:HiMom:abcdeACXX:7:1:3:695 :Y:0:TCGGAATG
TGATACTGCCTTTGCAAAAATTATAACAGT
+
;>ABBCC<?ACCBBBCCCCBBACBAABB<A
- at HiMom:7:2:2:220
+ at machine1:HiMom:abcdeACXX:7:2:2:220 :Y:0:TCGGAATG
NAATAAACCTCTTTCTTTGATAAATTACCC
+
%.5:78335567:525<736:9868;8###
- at HiMom:7:2:3:567
+ at machine1:HiMom:abcdeACXX:7:2:3:567 :Y:0:TCGGAATG
TATCTTCACATAAAAACTACACAAAGCATT
+
BCB<ACBB at BCCBBCB<BB<@;?BB>=BBB
- at HiMom:7:2:3:663
+ at machine1:HiMom:abcdeACXX:7:2:3:663 :N:0:TCGGAATG
AAAAGCATGTTGCTCAGTAAAAGCAAATAG
+
##############################
- at HiMom:7:2:3:922
+ at machine1:HiMom:abcdeACXX:7:2:3:922 :Y:0:TCGGAATG
ATTTCTGTCTGACTTTTCCAAATGTGCTAT
+
AABB@>>>@>9@>AAAA>;@BB@@53;BBB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATG.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATG.barcode_1.fastq
index 5641882..a0c3335 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATG.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATG.barcode_1.fastq
@@ -1,28 +1,28 @@
- at HiMom:7:1:3:1328
+ at machine1:HiMom:abcdeACXX:7:1:3:1328 :N:0:TCGGAATG
TCGGAATG
+
A@@2=?83
- at HiMom:7:1:3:2037
+ at machine1:HiMom:abcdeACXX:7:1:3:2037 :N:0:TCGGAATG
TCGGAATG
+
?<):=@=@
- at HiMom:7:1:3:695
+ at machine1:HiMom:abcdeACXX:7:1:3:695 :Y:0:TCGGAATG
TCGGAATG
+
B?;BBB=?
- at HiMom:7:2:2:220
+ at machine1:HiMom:abcdeACXX:7:2:2:220 :Y:0:TCGGAATG
TCGGAATG
+
BA==@@?;
- at HiMom:7:2:3:567
+ at machine1:HiMom:abcdeACXX:7:2:3:567 :Y:0:TCGGAATG
TCGGAATG
+
@?@?AB@<
- at HiMom:7:2:3:663
+ at machine1:HiMom:abcdeACXX:7:2:3:663 :N:0:TCGGAATG
TCGGAATG
+
=<23<C=8
- at HiMom:7:2:3:922
+ at machine1:HiMom:abcdeACXX:7:2:3:922 :Y:0:TCGGAATG
TCGGAATG
+
BA<ABC?;
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATGATTATGTT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATGATTATGTT.1.fastq
index f8fb381..89321f1 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATGATTATGTT.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATGATTATGTT.1.fastq
@@ -1,28 +1,28 @@
- at HiMom:9:1:3:1328
+ at machine1:HiMom:abcdeACXX:9:1:3:1328 :N:0:TCGGAATGATTATGTT
GCTACCAACCCCACTCCTAGATGAAAGACC
+
068,=@)=AA82 at C@8;;@3;8/<<#####
- at HiMom:9:1:3:2037
+ at machine1:HiMom:abcdeACXX:9:1:3:2037 :N:0:TCGGAATGATTATGTT
CATCCTGTAACAAAGTGTTTATAGTTTTCA
+
:@9 at B6<?A>(>AB@<*)=<CBA:>51:7A
- at HiMom:9:1:3:695
+ at machine1:HiMom:abcdeACXX:9:1:3:695 :Y:0:TCGGAATGATTATGTT
TGATACTGCCTTTGCAAAAATTATAACAGT
+
;>ABBCC<?ACCBBBCCCCBBACBAABB<A
- at HiMom:9:2:2:220
+ at machine1:HiMom:abcdeACXX:9:2:2:220 :Y:0:TCGGAATGATTATGTT
NAATAAACCTCTTTCTTTGATAAATTACCC
+
%.5:78335567:525<736:9868;8###
- at HiMom:9:2:3:567
+ at machine1:HiMom:abcdeACXX:9:2:3:567 :Y:0:TCGGAATGATTATGTT
TATCTTCACATAAAAACTACACAAAGCATT
+
BCB<ACBB at BCCBBCB<BB<@;?BB>=BBB
- at HiMom:9:2:3:663
+ at machine1:HiMom:abcdeACXX:9:2:3:663 :N:0:TCGGAATGATTATGTT
AAAAGCATGTTGCTCAGTAAAAGCAAATAG
+
##############################
- at HiMom:9:2:3:922
+ at machine1:HiMom:abcdeACXX:9:2:3:922 :Y:0:TCGGAATGATTATGTT
ATTTCTGTCTGACTTTTCCAAATGTGCTAT
+
AABB@>>>@>9@>AAAA>;@BB@@53;BBB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATGATTATGTT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATGATTATGTT.barcode_1.fastq
index 31d5dca..90a3a06 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATGATTATGTT.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATGATTATGTT.barcode_1.fastq
@@ -1,28 +1,28 @@
- at HiMom:9:1:3:1328
+ at machine1:HiMom:abcdeACXX:9:1:3:1328 :N:0:TCGGAATGATTATGTT
TCGGAATG
+
A@@2=?83
- at HiMom:9:1:3:2037
+ at machine1:HiMom:abcdeACXX:9:1:3:2037 :N:0:TCGGAATGATTATGTT
TCGGAATG
+
?<):=@=@
- at HiMom:9:1:3:695
+ at machine1:HiMom:abcdeACXX:9:1:3:695 :Y:0:TCGGAATGATTATGTT
TCGGAATG
+
B?;BBB=?
- at HiMom:9:2:2:220
+ at machine1:HiMom:abcdeACXX:9:2:2:220 :Y:0:TCGGAATGATTATGTT
TCGGAATG
+
BA==@@?;
- at HiMom:9:2:3:567
+ at machine1:HiMom:abcdeACXX:9:2:3:567 :Y:0:TCGGAATGATTATGTT
TCGGAATG
+
@?@?AB@<
- at HiMom:9:2:3:663
+ at machine1:HiMom:abcdeACXX:9:2:3:663 :N:0:TCGGAATGATTATGTT
TCGGAATG
+
=<23<C=8
- at HiMom:9:2:3:922
+ at machine1:HiMom:abcdeACXX:9:2:3:922 :Y:0:TCGGAATGATTATGTT
TCGGAATG
+
BA<ABC?;
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATGATTATGTT.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATGATTATGTT.barcode_2.fastq
index bc60db3..08a7f9f 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATGATTATGTT.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATGATTATGTT.barcode_2.fastq
@@ -1,28 +1,28 @@
- at HiMom:9:1:3:1328
+ at machine1:HiMom:abcdeACXX:9:1:3:1328 :N:0:TCGGAATGATTATGTT
ATTATGTT
+
A@@2=?83
- at HiMom:9:1:3:2037
+ at machine1:HiMom:abcdeACXX:9:1:3:2037 :N:0:TCGGAATGATTATGTT
ATTATGTT
+
?<):=@=@
- at HiMom:9:1:3:695
+ at machine1:HiMom:abcdeACXX:9:1:3:695 :Y:0:TCGGAATGATTATGTT
ATTATGTT
+
B?;BBB=?
- at HiMom:9:2:2:220
+ at machine1:HiMom:abcdeACXX:9:2:2:220 :Y:0:TCGGAATGATTATGTT
ATTATGTT
+
BA==@@?;
- at HiMom:9:2:3:567
+ at machine1:HiMom:abcdeACXX:9:2:3:567 :Y:0:TCGGAATGATTATGTT
ATTATGTT
+
@?@?AB@<
- at HiMom:9:2:3:663
+ at machine1:HiMom:abcdeACXX:9:2:3:663 :N:0:TCGGAATGATTATGTT
ATTATGTT
+
=<23<C=8
- at HiMom:9:2:3:922
+ at machine1:HiMom:abcdeACXX:9:2:3:922 :Y:0:TCGGAATGATTATGTT
ATTATGTT
+
BA<ABC?;
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGA.1.fastq
index 41eb3d7..9af8df3 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGA.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGA.1.fastq
@@ -1,20 +1,20 @@
- at HiMom:7:1:3:1406
+ at machine1:HiMom:abcdeACXX:7:1:3:1406 :N:0:TCTGGCGA
NAAAATGCCAGATAAATTTTATGTAAAACC
+
%1<<97227467::77(7;;;503<9:972
- at HiMom:7:1:3:1717
+ at machine1:HiMom:abcdeACXX:7:1:3:1717 :Y:0:TCTGGCGA
NAAACAGACTTGTTTCTTGTAATAATTATG
+
%/;;89689:999<76:8399:9:::::##
- at HiMom:7:2:3:2004
+ at machine1:HiMom:abcdeACXX:7:2:3:2004 :N:0:TCTGGCGA
NAAGACTACCTTGCTGAAATAGGGCATTTA
+
%.:875459;4-743(29;;5139266###
- at HiMom:7:2:3:695
+ at machine1:HiMom:abcdeACXX:7:2:3:695 :Y:0:TCTGGCGA
NCAACTCCAAGACACATAATTGTCAGATTC
+
%/:::95578589969:::;6559748;82
- at HiMom:7:2:3:987
+ at machine1:HiMom:abcdeACXX:7:2:3:987 :N:0:TCTGGCGA
AAGAGCAATATTTTCTTTCACTATATTATT
+
*@<@@?A at 0)7448)?C@)@4)9:@#####
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGA.barcode_1.fastq
index ec30d59..f2ad3a3 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGA.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGA.barcode_1.fastq
@@ -1,20 +1,20 @@
- at HiMom:7:1:3:1406
+ at machine1:HiMom:abcdeACXX:7:1:3:1406 :N:0:TCTGGCGA
TCTGGCGA
+
AA=;5@=@
- at HiMom:7:1:3:1717
+ at machine1:HiMom:abcdeACXX:7:1:3:1717 :Y:0:TCTGGCGA
TCTGGCGA
+
AB=11;A@
- at HiMom:7:2:3:2004
+ at machine1:HiMom:abcdeACXX:7:2:3:2004 :N:0:TCTGGCGA
TCTGGCGA
+
@?>/>BBB
- at HiMom:7:2:3:695
+ at machine1:HiMom:abcdeACXX:7:2:3:695 :Y:0:TCTGGCGA
TCTGGCGA
+
AA?>9=@A
- at HiMom:7:2:3:987
+ at machine1:HiMom:abcdeACXX:7:2:3:987 :N:0:TCTGGCGA
TCTCGCGA
+
0<(.(;1@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGAAGTTGCTT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGAAGTTGCTT.1.fastq
index 4dc8df5..83ca136 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGAAGTTGCTT.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGAAGTTGCTT.1.fastq
@@ -1,20 +1,20 @@
- at HiMom:9:1:3:1406
+ at machine1:HiMom:abcdeACXX:9:1:3:1406 :N:0:TCTGGCGAAGTTGCTT
NAAAATGCCAGATAAATTTTATGTAAAACC
+
%1<<97227467::77(7;;;503<9:972
- at HiMom:9:1:3:1717
+ at machine1:HiMom:abcdeACXX:9:1:3:1717 :Y:0:TCTGGCGAAGTTGCTT
NAAACAGACTTGTTTCTTGTAATAATTATG
+
%/;;89689:999<76:8399:9:::::##
- at HiMom:9:2:3:2004
+ at machine1:HiMom:abcdeACXX:9:2:3:2004 :N:0:TCTGGCGAAGTTGCTT
NAAGACTACCTTGCTGAAATAGGGCATTTA
+
%.:875459;4-743(29;;5139266###
- at HiMom:9:2:3:695
+ at machine1:HiMom:abcdeACXX:9:2:3:695 :Y:0:TCTGGCGAAGTTGCTT
NCAACTCCAAGACACATAATTGTCAGATTC
+
%/:::95578589969:::;6559748;82
- at HiMom:9:2:3:987
+ at machine1:HiMom:abcdeACXX:9:2:3:987 :N:0:TCTGGCGAAGTTGCTT
AAGAGCAATATTTTCTTTCACTATATTATT
+
*@<@@?A at 0)7448)?C@)@4)9:@#####
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGAAGTTGCTT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGAAGTTGCTT.barcode_1.fastq
index d61d604..80e639a 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGAAGTTGCTT.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGAAGTTGCTT.barcode_1.fastq
@@ -1,20 +1,20 @@
- at HiMom:9:1:3:1406
+ at machine1:HiMom:abcdeACXX:9:1:3:1406 :N:0:TCTGGCGAAGTTGCTT
TCTGGCGA
+
AA=;5@=@
- at HiMom:9:1:3:1717
+ at machine1:HiMom:abcdeACXX:9:1:3:1717 :Y:0:TCTGGCGAAGTTGCTT
TCTGGCGA
+
AB=11;A@
- at HiMom:9:2:3:2004
+ at machine1:HiMom:abcdeACXX:9:2:3:2004 :N:0:TCTGGCGAAGTTGCTT
TCTGGCGA
+
@?>/>BBB
- at HiMom:9:2:3:695
+ at machine1:HiMom:abcdeACXX:9:2:3:695 :Y:0:TCTGGCGAAGTTGCTT
TCTGGCGA
+
AA?>9=@A
- at HiMom:9:2:3:987
+ at machine1:HiMom:abcdeACXX:9:2:3:987 :N:0:TCTGGCGAAGTTGCTT
TCTCGCGA
+
0<(.(;1@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGAAGTTGCTT.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGAAGTTGCTT.barcode_2.fastq
index 6feb177..deecd6b 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGAAGTTGCTT.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGAAGTTGCTT.barcode_2.fastq
@@ -1,20 +1,20 @@
- at HiMom:9:1:3:1406
+ at machine1:HiMom:abcdeACXX:9:1:3:1406 :N:0:TCTGGCGAAGTTGCTT
AGTTGCTT
+
AA=;5@=@
- at HiMom:9:1:3:1717
+ at machine1:HiMom:abcdeACXX:9:1:3:1717 :Y:0:TCTGGCGAAGTTGCTT
AGTTGCTT
+
AB=11;A@
- at HiMom:9:2:3:2004
+ at machine1:HiMom:abcdeACXX:9:2:3:2004 :N:0:TCTGGCGAAGTTGCTT
AGTTGCTT
+
@?>/>BBB
- at HiMom:9:2:3:695
+ at machine1:HiMom:abcdeACXX:9:2:3:695 :Y:0:TCTGGCGAAGTTGCTT
AGTTGCTT
+
AA?>9=@A
- at HiMom:9:2:3:987
+ at machine1:HiMom:abcdeACXX:9:2:3:987 :N:0:TCTGGCGAAGTTGCTT
AGTTGCTT
+
0<(.(;1@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGAC.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGAC.1.fastq
index e9f86b6..9037a85 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGAC.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGAC.1.fastq
@@ -1,20 +1,20 @@
- at HiMom:7:1:2:52
+ at machine1:HiMom:abcdeACXX:7:1:2:52 :N:0:TGCTCGAC
NAAGTATAATGTAGAGACGCTTGTATTGTC
+
##############################
- at HiMom:7:1:3:1348
+ at machine1:HiMom:abcdeACXX:7:1:3:1348 :Y:0:TGCTCGAC
NATATTGATTCTTCCTACCCATGAGTATGG
+
%1;;78.+389999888;;89118;7;8##
- at HiMom:7:1:3:1981
+ at machine1:HiMom:abcdeACXX:7:1:3:1981 :Y:0:TGCTCGAC
AGCCTGTCTGTAGAAAAAATACAAAAATTA
+
@3;=;8/@=:8B8=BBBBB:B?BBABB?:B
- at HiMom:7:2:2:115
+ at machine1:HiMom:abcdeACXX:7:2:2:115 :N:0:TGCTCGAC
NGATGTGCTACACACTTTCAAACAAACAGA
+
%0:500&/99;69727::995313374484
- at HiMom:7:2:3:317
+ at machine1:HiMom:abcdeACXX:7:2:3:317 :Y:0:TGCTCGAC
AGAGAGAAATGTGGCATATGAGTATCACCT
+
@4>BBB?ABCAB@>>ACBB?B<AABBCBBB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGAC.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGAC.barcode_1.fastq
index 6b9259f..70798ff 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGAC.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGAC.barcode_1.fastq
@@ -1,20 +1,20 @@
- at HiMom:7:1:2:52
+ at machine1:HiMom:abcdeACXX:7:1:2:52 :N:0:TGCTCGAC
TGCTCGAC
+
:;;;:;=;
- at HiMom:7:1:3:1348
+ at machine1:HiMom:abcdeACXX:7:1:3:1348 :Y:0:TGCTCGAC
TGCTCGAC
+
B9??@7 at 5
- at HiMom:7:1:3:1981
+ at machine1:HiMom:abcdeACXX:7:1:3:1981 :Y:0:TGCTCGAC
TGCTCGAC
+
=*@1;@BB
- at HiMom:7:2:2:115
+ at machine1:HiMom:abcdeACXX:7:2:2:115 :N:0:TGCTCGAC
TGCTCGAC
+
BA=>=@@=
- at HiMom:7:2:3:317
+ at machine1:HiMom:abcdeACXX:7:2:3:317 :Y:0:TGCTCGAC
TGCTCGAC
+
BAABBA<=
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGACAGCAATTC.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGACAGCAATTC.1.fastq
index b832e3d..2710293 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGACAGCAATTC.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGACAGCAATTC.1.fastq
@@ -1,20 +1,20 @@
- at HiMom:9:1:2:52
+ at machine1:HiMom:abcdeACXX:9:1:2:52 :N:0:TGCTCGACAGCAATTC
NAAGTATAATGTAGAGACGCTTGTATTGTC
+
##############################
- at HiMom:9:1:3:1348
+ at machine1:HiMom:abcdeACXX:9:1:3:1348 :Y:0:TGCTCGACAGCAATTC
NATATTGATTCTTCCTACCCATGAGTATGG
+
%1;;78.+389999888;;89118;7;8##
- at HiMom:9:1:3:1981
+ at machine1:HiMom:abcdeACXX:9:1:3:1981 :Y:0:TGCTCGACAGCAATTC
AGCCTGTCTGTAGAAAAAATACAAAAATTA
+
@3;=;8/@=:8B8=BBBBB:B?BBABB?:B
- at HiMom:9:2:2:115
+ at machine1:HiMom:abcdeACXX:9:2:2:115 :N:0:TGCTCGACAGCAATTC
NGATGTGCTACACACTTTCAAACAAACAGA
+
%0:500&/99;69727::995313374484
- at HiMom:9:2:3:317
+ at machine1:HiMom:abcdeACXX:9:2:3:317 :Y:0:TGCTCGACAGCAATTC
AGAGAGAAATGTGGCATATGAGTATCACCT
+
@4>BBB?ABCAB@>>ACBB?B<AABBCBBB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGACAGCAATTC.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGACAGCAATTC.barcode_1.fastq
index 44c1b02..62cf80e 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGACAGCAATTC.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGACAGCAATTC.barcode_1.fastq
@@ -1,20 +1,20 @@
- at HiMom:9:1:2:52
+ at machine1:HiMom:abcdeACXX:9:1:2:52 :N:0:TGCTCGACAGCAATTC
TGCTCGAC
+
:;;;:;=;
- at HiMom:9:1:3:1348
+ at machine1:HiMom:abcdeACXX:9:1:3:1348 :Y:0:TGCTCGACAGCAATTC
TGCTCGAC
+
B9??@7 at 5
- at HiMom:9:1:3:1981
+ at machine1:HiMom:abcdeACXX:9:1:3:1981 :Y:0:TGCTCGACAGCAATTC
TGCTCGAC
+
=*@1;@BB
- at HiMom:9:2:2:115
+ at machine1:HiMom:abcdeACXX:9:2:2:115 :N:0:TGCTCGACAGCAATTC
TGCTCGAC
+
BA=>=@@=
- at HiMom:9:2:3:317
+ at machine1:HiMom:abcdeACXX:9:2:3:317 :Y:0:TGCTCGACAGCAATTC
TGCTCGAC
+
BAABBA<=
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGACAGCAATTC.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGACAGCAATTC.barcode_2.fastq
index efe4857..bf38ef7 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGACAGCAATTC.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGACAGCAATTC.barcode_2.fastq
@@ -1,20 +1,20 @@
- at HiMom:9:1:2:52
+ at machine1:HiMom:abcdeACXX:9:1:2:52 :N:0:TGCTCGACAGCAATTC
AGCAATTC
+
:;;;:;=;
- at HiMom:9:1:3:1348
+ at machine1:HiMom:abcdeACXX:9:1:3:1348 :Y:0:TGCTCGACAGCAATTC
AGCAATTC
+
B9??@7 at 5
- at HiMom:9:1:3:1981
+ at machine1:HiMom:abcdeACXX:9:1:3:1981 :Y:0:TGCTCGACAGCAATTC
AGCAATTC
+
=*@1;@BB
- at HiMom:9:2:2:115
+ at machine1:HiMom:abcdeACXX:9:2:2:115 :N:0:TGCTCGACAGCAATTC
AGCAATTC
+
BA=>=@@=
- at HiMom:9:2:3:317
+ at machine1:HiMom:abcdeACXX:9:2:3:317 :Y:0:TGCTCGACAGCAATTC
AGCAATTC
+
BAABBA<=
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGAT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGAT.1.fastq
index 297c7d0..610e71c 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGAT.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGAT.1.fastq
@@ -1,16 +1,16 @@
- at HiMom:7:1:2:950
+ at machine1:HiMom:abcdeACXX:7:1:2:950 :Y:0:TGTCGGAT
NGTGTGTGTTTTTAGAGATGCCTTTTAGAA
+
%-7463817999<999998876999;6579
- at HiMom:7:2:3:1389
+ at machine1:HiMom:abcdeACXX:7:2:3:1389 :Y:0:TGTCGGAT
TATCGATCTCCTGACCTCGTGATCCACCCA
+
ACBCBCB?CBB at 6ABCB@)B>CBBCC at 4;5
- at HiMom:7:2:3:143
+ at machine1:HiMom:abcdeACXX:7:2:3:143 :Y:0:TGTCGGAT
AAAATCAATTCTGAAATGATTACATATTTT
+
BBBACBBACB=B?BBBBCBBCBBBBBBCBB
- at HiMom:7:2:3:898
+ at machine1:HiMom:abcdeACXX:7:2:3:898 :Y:0:TGTCGGAT
TAACATTCCCACAGTGCTTGCCACAGAGCC
+
ACCCCCC at C@@B@);>;BBCC=@BC?B@;>
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGAT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGAT.barcode_1.fastq
index 506485e..8c96032 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGAT.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGAT.barcode_1.fastq
@@ -1,16 +1,16 @@
- at HiMom:7:1:2:950
+ at machine1:HiMom:abcdeACXX:7:1:2:950 :Y:0:TGTCGGAT
TGTCGGAT
+
@@=A:AAA
- at HiMom:7:2:3:1389
+ at machine1:HiMom:abcdeACXX:7:2:3:1389 :Y:0:TGTCGGAT
TGTCGGAT
+
?2ACA at B<
- at HiMom:7:2:3:143
+ at machine1:HiMom:abcdeACXX:7:2:3:143 :Y:0:TGTCGGAT
TGTCGGAT
+
A>AB??=B
- at HiMom:7:2:3:898
+ at machine1:HiMom:abcdeACXX:7:2:3:898 :Y:0:TGTCGGAT
TGTCGGAT
+
>8>A@=<@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGATACCAACTG.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGATACCAACTG.1.fastq
index c23aaab..97566b5 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGATACCAACTG.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGATACCAACTG.1.fastq
@@ -1,16 +1,16 @@
- at HiMom:9:1:2:950
+ at machine1:HiMom:abcdeACXX:9:1:2:950 :Y:0:TGTCGGATACCAACTG
NGTGTGTGTTTTTAGAGATGCCTTTTAGAA
+
%-7463817999<999998876999;6579
- at HiMom:9:2:3:1389
+ at machine1:HiMom:abcdeACXX:9:2:3:1389 :Y:0:TGTCGGATACCAACTG
TATCGATCTCCTGACCTCGTGATCCACCCA
+
ACBCBCB?CBB at 6ABCB@)B>CBBCC at 4;5
- at HiMom:9:2:3:143
+ at machine1:HiMom:abcdeACXX:9:2:3:143 :Y:0:TGTCGGATACCAACTG
AAAATCAATTCTGAAATGATTACATATTTT
+
BBBACBBACB=B?BBBBCBBCBBBBBBCBB
- at HiMom:9:2:3:898
+ at machine1:HiMom:abcdeACXX:9:2:3:898 :Y:0:TGTCGGATACCAACTG
TAACATTCCCACAGTGCTTGCCACAGAGCC
+
ACCCCCC at C@@B@);>;BBCC=@BC?B@;>
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGATACCAACTG.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGATACCAACTG.barcode_1.fastq
index 7815673..780d300 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGATACCAACTG.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGATACCAACTG.barcode_1.fastq
@@ -1,16 +1,16 @@
- at HiMom:9:1:2:950
+ at machine1:HiMom:abcdeACXX:9:1:2:950 :Y:0:TGTCGGATACCAACTG
TGTCGGAT
+
@@=A:AAA
- at HiMom:9:2:3:1389
+ at machine1:HiMom:abcdeACXX:9:2:3:1389 :Y:0:TGTCGGATACCAACTG
TGTCGGAT
+
?2ACA at B<
- at HiMom:9:2:3:143
+ at machine1:HiMom:abcdeACXX:9:2:3:143 :Y:0:TGTCGGATACCAACTG
TGTCGGAT
+
A>AB??=B
- at HiMom:9:2:3:898
+ at machine1:HiMom:abcdeACXX:9:2:3:898 :Y:0:TGTCGGATACCAACTG
TGTCGGAT
+
>8>A@=<@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGATACCAACTG.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGATACCAACTG.barcode_2.fastq
index d120dc2..1a9029a 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGATACCAACTG.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGATACCAACTG.barcode_2.fastq
@@ -1,16 +1,16 @@
- at HiMom:9:1:2:950
+ at machine1:HiMom:abcdeACXX:9:1:2:950 :Y:0:TGTCGGATACCAACTG
ACCAACTG
+
@@=A:AAA
- at HiMom:9:2:3:1389
+ at machine1:HiMom:abcdeACXX:9:2:3:1389 :Y:0:TGTCGGATACCAACTG
ACCAACTG
+
?2ACA at B<
- at HiMom:9:2:3:143
+ at machine1:HiMom:abcdeACXX:9:2:3:143 :Y:0:TGTCGGATACCAACTG
ACCAACTG
+
A>AB??=B
- at HiMom:9:2:3:898
+ at machine1:HiMom:abcdeACXX:9:2:3:898 :Y:0:TGTCGGATACCAACTG
ACCAACTG
+
>8>A@=<@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGA.1.fastq
index 1dcdad0..d696f12 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGA.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGA.1.fastq
@@ -1,20 +1,20 @@
- at HiMom:7:1:2:309
+ at machine1:HiMom:abcdeACXX:7:1:2:309 :Y:0:TTCGCTGA
NAATGGCCATGCTGCCCAAAGTATTTTATA
+
%.705699:5-227759996717:::9:9:
- at HiMom:7:1:2:63
+ at machine1:HiMom:abcdeACXX:7:1:2:63 :Y:0:TTCGCTGA
NGAGTGGAATGGAATGGAGTGGAATGGCTT
+
%,/66818682811553536525875686#
- at HiMom:7:1:3:880
+ at machine1:HiMom:abcdeACXX:7:1:3:880 :N:0:TTCGCTGA
ATGAGTGAGAAATAGAAGTCCTAAGTAGAT
+
B@=;/75>)>?B@=3>@=<.2=B at 2@>49B
- at HiMom:7:2:2:669
+ at machine1:HiMom:abcdeACXX:7:2:2:669 :N:0:TTCGCTGA
NGGCTGAAGCAGGAGGGTCACTTGAGCCAA
+
##############################
- at HiMom:7:2:2:775
+ at machine1:HiMom:abcdeACXX:7:2:2:775 :Y:0:TTCGCTGA
NGTTTATAATTGTGAGTTAAAAATCTAAAA
+
%,-78:8:968:45524<<636;<:<<<<<
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGA.barcode_1.fastq
index dd6c8f1..6a7b76c 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGA.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGA.barcode_1.fastq
@@ -1,20 +1,20 @@
- at HiMom:7:1:2:309
+ at machine1:HiMom:abcdeACXX:7:1:2:309 :Y:0:TTCGCTGA
NTCGCTGA
+
########
- at HiMom:7:1:2:63
+ at machine1:HiMom:abcdeACXX:7:1:2:63 :Y:0:TTCGCTGA
TTCGCTGA
+
7@=B<C@#
- at HiMom:7:1:3:880
+ at machine1:HiMom:abcdeACXX:7:1:3:880 :N:0:TTCGCTGA
TTCGCTGA
+
>@62;A==
- at HiMom:7:2:2:669
+ at machine1:HiMom:abcdeACXX:7:2:2:669 :N:0:TTCGCTGA
TTCGCTGA
+
B>BB at BB9
- at HiMom:7:2:2:775
+ at machine1:HiMom:abcdeACXX:7:2:2:775 :Y:0:TTCGCTGA
TTCGCTGA
+
BCC6ABBC
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGAAAGGATGT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGAAAGGATGT.1.fastq
index 479d31e..68353f1 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGAAAGGATGT.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGAAAGGATGT.1.fastq
@@ -1,20 +1,20 @@
- at HiMom:9:1:2:309
+ at machine1:HiMom:abcdeACXX:9:1:2:309 :Y:0:TTCGCTGAAAGGATGT
NAATGGCCATGCTGCCCAAAGTATTTTATA
+
%.705699:5-227759996717:::9:9:
- at HiMom:9:1:2:63
+ at machine1:HiMom:abcdeACXX:9:1:2:63 :Y:0:TTCGCTGAAAGGATGT
NGAGTGGAATGGAATGGAGTGGAATGGCTT
+
%,/66818682811553536525875686#
- at HiMom:9:1:3:880
+ at machine1:HiMom:abcdeACXX:9:1:3:880 :N:0:TTCGCTGAAAGGATGT
ATGAGTGAGAAATAGAAGTCCTAAGTAGAT
+
B@=;/75>)>?B@=3>@=<.2=B at 2@>49B
- at HiMom:9:2:2:669
+ at machine1:HiMom:abcdeACXX:9:2:2:669 :N:0:TTCGCTGAAAGGATGT
NGGCTGAAGCAGGAGGGTCACTTGAGCCAA
+
##############################
- at HiMom:9:2:2:775
+ at machine1:HiMom:abcdeACXX:9:2:2:775 :Y:0:TTCGCTGAAAGGATGT
NGTTTATAATTGTGAGTTAAAAATCTAAAA
+
%,-78:8:968:45524<<636;<:<<<<<
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGAAAGGATGT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGAAAGGATGT.barcode_1.fastq
index 93688bf..233f520 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGAAAGGATGT.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGAAAGGATGT.barcode_1.fastq
@@ -1,20 +1,20 @@
- at HiMom:9:1:2:309
+ at machine1:HiMom:abcdeACXX:9:1:2:309 :Y:0:TTCGCTGAAAGGATGT
NTCGCTGA
+
########
- at HiMom:9:1:2:63
+ at machine1:HiMom:abcdeACXX:9:1:2:63 :Y:0:TTCGCTGAAAGGATGT
TTCGCTGA
+
7@=B<C@#
- at HiMom:9:1:3:880
+ at machine1:HiMom:abcdeACXX:9:1:3:880 :N:0:TTCGCTGAAAGGATGT
TTCGCTGA
+
>@62;A==
- at HiMom:9:2:2:669
+ at machine1:HiMom:abcdeACXX:9:2:2:669 :N:0:TTCGCTGAAAGGATGT
TTCGCTGA
+
B>BB at BB9
- at HiMom:9:2:2:775
+ at machine1:HiMom:abcdeACXX:9:2:2:775 :Y:0:TTCGCTGAAAGGATGT
TTCGCTGA
+
BCC6ABBC
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGAAAGGATGT.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGAAAGGATGT.barcode_2.fastq
index cf196c5..491006d 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGAAAGGATGT.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGAAAGGATGT.barcode_2.fastq
@@ -1,20 +1,20 @@
- at HiMom:9:1:2:309
+ at machine1:HiMom:abcdeACXX:9:1:2:309 :Y:0:TTCGCTGAAAGGATGT
AAGGATGT
+
########
- at HiMom:9:1:2:63
+ at machine1:HiMom:abcdeACXX:9:1:2:63 :Y:0:TTCGCTGAAAGGATGT
AAGGATGT
+
7@=B<C@#
- at HiMom:9:1:3:880
+ at machine1:HiMom:abcdeACXX:9:1:3:880 :N:0:TTCGCTGAAAGGATGT
AAGGATGT
+
>@62;A==
- at HiMom:9:2:2:669
+ at machine1:HiMom:abcdeACXX:9:2:2:669 :N:0:TTCGCTGAAAGGATGT
AAGGATGT
+
B>BB at BB9
- at HiMom:9:2:2:775
+ at machine1:HiMom:abcdeACXX:9:2:2:775 :Y:0:TTCGCTGAAAGGATGT
AAGGATGT
+
BCC6ABBC
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCT.1.fastq
index 999312d..644b059 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCT.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCT.1.fastq
@@ -1,24 +1,24 @@
- at HiMom:7:1:3:1155
+ at machine1:HiMom:abcdeACXX:7:1:3:1155 :N:0:TTGAGCCT
NCAGCGAAAGAAGTACCAGGGTATGGGAAG
+
##############################
- at HiMom:7:2:2:1559
+ at machine1:HiMom:abcdeACXX:7:2:2:1559 :Y:0:TTGAGCCT
NACAGAAGGGAAAAGGTCACAGACTAAAGA
+
%//6;;;8849;:91,35::757:4:;:9:
- at HiMom:7:2:2:488
+ at machine1:HiMom:abcdeACXX:7:2:2:488 :Y:0:TTGAGCCT
NTGGGAAACTAAACCCCATGAGGGCAGAGC
+
%/2/156666785445255551/12545/4
- at HiMom:7:2:3:1101
+ at machine1:HiMom:abcdeACXX:7:2:3:1101 :Y:0:TTGAGCCT
AAGATTATATGAGTATAATGGAGCTATTTG
+
B<38>B=>>B==30ABBA886;?;AAA@@>
- at HiMom:7:2:3:1123
+ at machine1:HiMom:abcdeACXX:7:2:3:1123 :N:0:TTGAGCCT
NCCTCTTCCACAACTTCCTTCTTCTCCTTT
+
%.23)7475776876486:;67348867:8
- at HiMom:7:2:3:782
+ at machine1:HiMom:abcdeACXX:7:2:3:782 :Y:0:TTGAGCCT
AGCCATGGGCATATAGAATCACTGTAAACA
+
B at BBBB>7;BCBCBB at BBB?BB>:=BAB at B
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCT.barcode_1.fastq
index 895c3e6..33c23ba 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCT.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCT.barcode_1.fastq
@@ -1,24 +1,24 @@
- at HiMom:7:1:3:1155
+ at machine1:HiMom:abcdeACXX:7:1:3:1155 :N:0:TTGAGCCT
TTGAGCCT
+
########
- at HiMom:7:2:2:1559
+ at machine1:HiMom:abcdeACXX:7:2:2:1559 :Y:0:TTGAGCCT
TTGAGCCT
+
A at 5@@4BC
- at HiMom:7:2:2:488
+ at machine1:HiMom:abcdeACXX:7:2:2:488 :Y:0:TTGAGCCT
TTGAGCCT
+
@>=@@;@A
- at HiMom:7:2:3:1101
+ at machine1:HiMom:abcdeACXX:7:2:3:1101 :Y:0:TTGAGCCT
TTGAGCCT
+
7 at 57<*5=
- at HiMom:7:2:3:1123
+ at machine1:HiMom:abcdeACXX:7:2:3:1123 :N:0:TTGAGCCT
TTGAGCCT
+
B at 67(.AA
- at HiMom:7:2:3:782
+ at machine1:HiMom:abcdeACXX:7:2:3:782 :Y:0:TTGAGCCT
TTGAGCCT
+
BAAA<;B?
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCTAACTTGAC.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCTAACTTGAC.1.fastq
index b160fac..0377752 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCTAACTTGAC.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCTAACTTGAC.1.fastq
@@ -1,24 +1,24 @@
- at HiMom:9:1:3:1155
+ at machine1:HiMom:abcdeACXX:9:1:3:1155 :N:0:TTGAGCCTAACTTGAC
NCAGCGAAAGAAGTACCAGGGTATGGGAAG
+
##############################
- at HiMom:9:2:2:1559
+ at machine1:HiMom:abcdeACXX:9:2:2:1559 :Y:0:TTGAGCCTAACTTGAC
NACAGAAGGGAAAAGGTCACAGACTAAAGA
+
%//6;;;8849;:91,35::757:4:;:9:
- at HiMom:9:2:2:488
+ at machine1:HiMom:abcdeACXX:9:2:2:488 :Y:0:TTGAGCCTAACTTGAC
NTGGGAAACTAAACCCCATGAGGGCAGAGC
+
%/2/156666785445255551/12545/4
- at HiMom:9:2:3:1101
+ at machine1:HiMom:abcdeACXX:9:2:3:1101 :Y:0:TTGAGCCTAACTTGAC
AAGATTATATGAGTATAATGGAGCTATTTG
+
B<38>B=>>B==30ABBA886;?;AAA@@>
- at HiMom:9:2:3:1123
+ at machine1:HiMom:abcdeACXX:9:2:3:1123 :N:0:TTGAGCCTAACTTGAC
NCCTCTTCCACAACTTCCTTCTTCTCCTTT
+
%.23)7475776876486:;67348867:8
- at HiMom:9:2:3:782
+ at machine1:HiMom:abcdeACXX:9:2:3:782 :Y:0:TTGAGCCTAACTTGAC
AGCCATGGGCATATAGAATCACTGTAAACA
+
B at BBBB>7;BCBCBB at BBB?BB>:=BAB at B
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCTAACTTGAC.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCTAACTTGAC.barcode_1.fastq
index e2d9850..2f53965 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCTAACTTGAC.barcode_1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCTAACTTGAC.barcode_1.fastq
@@ -1,24 +1,24 @@
- at HiMom:9:1:3:1155
+ at machine1:HiMom:abcdeACXX:9:1:3:1155 :N:0:TTGAGCCTAACTTGAC
TTGAGCCT
+
########
- at HiMom:9:2:2:1559
+ at machine1:HiMom:abcdeACXX:9:2:2:1559 :Y:0:TTGAGCCTAACTTGAC
TTGAGCCT
+
A at 5@@4BC
- at HiMom:9:2:2:488
+ at machine1:HiMom:abcdeACXX:9:2:2:488 :Y:0:TTGAGCCTAACTTGAC
TTGAGCCT
+
@>=@@;@A
- at HiMom:9:2:3:1101
+ at machine1:HiMom:abcdeACXX:9:2:3:1101 :Y:0:TTGAGCCTAACTTGAC
TTGAGCCT
+
7 at 57<*5=
- at HiMom:9:2:3:1123
+ at machine1:HiMom:abcdeACXX:9:2:3:1123 :N:0:TTGAGCCTAACTTGAC
TTGAGCCT
+
B at 67(.AA
- at HiMom:9:2:3:782
+ at machine1:HiMom:abcdeACXX:9:2:3:782 :Y:0:TTGAGCCTAACTTGAC
TTGAGCCT
+
BAAA<;B?
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCTAACTTGAC.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCTAACTTGAC.barcode_2.fastq
index 4e52ec9..e424db6 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCTAACTTGAC.barcode_2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCTAACTTGAC.barcode_2.fastq
@@ -1,24 +1,24 @@
- at HiMom:9:1:3:1155
+ at machine1:HiMom:abcdeACXX:9:1:3:1155 :N:0:TTGAGCCTAACTTGAC
AACTTGAC
+
########
- at HiMom:9:2:2:1559
+ at machine1:HiMom:abcdeACXX:9:2:2:1559 :Y:0:TTGAGCCTAACTTGAC
AACTTGAC
+
A at 5@@4BC
- at HiMom:9:2:2:488
+ at machine1:HiMom:abcdeACXX:9:2:2:488 :Y:0:TTGAGCCTAACTTGAC
AACTTGAC
+
@>=@@;@A
- at HiMom:9:2:3:1101
+ at machine1:HiMom:abcdeACXX:9:2:3:1101 :Y:0:TTGAGCCTAACTTGAC
AACTTGAC
+
7 at 57<*5=
- at HiMom:9:2:3:1123
+ at machine1:HiMom:abcdeACXX:9:2:3:1123 :N:0:TTGAGCCTAACTTGAC
AACTTGAC
+
B at 67(.AA
- at HiMom:9:2:3:782
+ at machine1:HiMom:abcdeACXX:9:2:3:782 :Y:0:TTGAGCCTAACTTGAC
AACTTGAC
+
BAAA<;B?
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/nonBarcoded.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/nonBarcoded.1.fastq
index 758b666..4d09170 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/nonBarcoded.1.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/nonBarcoded.1.fastq
@@ -1,240 +1,240 @@
- at HiMom:1:1:1793:1011/1
+ at machine1:HiMom:abcdeACXX:1:1:1793:1011 1:N:0:
ANNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNN
+
(%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%%%%%%%%%%%%1%%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%
- at HiMom:1:1:1793:1420/1
+ at machine1:HiMom:abcdeACXX:1:1:1793:1420 1:N:0:
GNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNN
+
=%%%%%%%%%%%%%%%%%%%%=%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%
- at HiMom:1:1:1793:1441/1
+ at machine1:HiMom:abcdeACXX:1:1:1793:1441 1:N:0:
CNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNN
+
(%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%%%%%%%%%%%%+%%%%%%%%%%%%%%%%%%%%%5%%%%%%%%%%
- at HiMom:1:1:1793:1483/1
+ at machine1:HiMom:abcdeACXX:1:1:1793:1483 1:N:0:
GNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNANNNNNNNNNN
+
:%%%%%%%%%%%%%%%%%%%%=%%%%%%%%%%%%%%%%%%%%%/%%%%%%%%%%%%%%%%%%%%%8%%%%%%%%%%
- at HiMom:1:1:1793:1495/1
+ at machine1:HiMom:abcdeACXX:1:1:1793:1495 1:N:0:
GNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
+
7%%%%%%%%%%%%%%%%%%%%.%%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%
- at HiMom:1:1:1793:1527/1
+ at machine1:HiMom:abcdeACXX:1:1:1793:1527 1:N:0:
GNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNN
+
.%%%%%%%%%%%%%%%%%%%%(%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%%
- at HiMom:1:1:1793:1545/1
+ at machine1:HiMom:abcdeACXX:1:1:1793:1545 1:N:0:
CNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
+
)%%%%%%%%%%%%%%%%%%%%)%%%%%%%%%%%%%%%%%%%%%)%%%%%%%%%%%%%%%%%%%%%1%%%%%%%%%%
- at HiMom:1:1:1793:1583/1
+ at machine1:HiMom:abcdeACXX:1:1:1793:1583 1:N:0:
GNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNN
+
:%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%%
- at HiMom:1:1:1793:1596/1
+ at machine1:HiMom:abcdeACXX:1:1:1793:1596 1:N:0:
GNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNN
+
5%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%5%%%%%%%%%%
- at HiMom:1:1:1793:1602/1
+ at machine1:HiMom:abcdeACXX:1:1:1793:1602 1:N:0:
CNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNN
+
<%%%%%%%%%%%%%%%%%%%%(%%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%%%%%%%%%%%%(%%%%%%%%%%
- at HiMom:1:1:1793:1658/1
+ at machine1:HiMom:abcdeACXX:1:1:1793:1658 1:N:0:
CNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNN
+
(%%%%%%%%%%%%%%%%%%%%=%%%%%%%%%%%%%%%%%%%%%=%%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%%
- at HiMom:1:1:1793:1681/1
+ at machine1:HiMom:abcdeACXX:1:1:1793:1681 1:N:0:
CNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNANNNNNNNNNN
+
?%%%%%%%%%%%%%%%%%%%%)%%%%%%%%%%%%%%%%%%%%%&%%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%%
- at HiMom:1:1:1793:1718/1
+ at machine1:HiMom:abcdeACXX:1:1:1793:1718 1:N:0:
GNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
+
:%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%)%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%
- at HiMom:1:1:1793:1745/1
+ at machine1:HiMom:abcdeACXX:1:1:1793:1745 1:N:0:
CNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNN
+
1%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%%%%%%%%%%%%7%%%%%%%%%%%%%%%%%%%%%1%%%%%%%%%%
- at HiMom:1:1:1793:1777/1
+ at machine1:HiMom:abcdeACXX:1:1:1793:1777 1:N:0:
GNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
+
:%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%:%%%%%%%%%%%%%%%%%%%%%1%%%%%%%%%%
- at HiMom:1:1:1793:1813/1
+ at machine1:HiMom:abcdeACXX:1:1:1793:1813 1:N:0:
GNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
+
7%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%1%%%%%%%%%%%%%%%%%%%%%.%%%%%%%%%%
- at HiMom:1:1:1793:1916/1
+ at machine1:HiMom:abcdeACXX:1:1:1793:1916 1:N:0:
GNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
+
<%%%%%%%%%%%%%%%%%%%%6%%%%%%%%%%%%%%%%%%%%%=%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%
- at HiMom:1:1:1793:1959/1
+ at machine1:HiMom:abcdeACXX:1:1:1793:1959 1:N:0:
GNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
+
<%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%%%%%%%%%%%%.%%%%%%%%%%
- at HiMom:1:1:1793:602/1
+ at machine1:HiMom:abcdeACXX:1:1:1793:602 1:N:0:
TNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNANNNNNNNNNN
+
<%%%%%%%%%%%%%%%%%%%%>%%%%%%%%%%%%%%%%%%%%%7%%%%%%%%%%%%%%%%%%%%%2%%%%%%%%%%
- at HiMom:1:1:1793:808/1
+ at machine1:HiMom:abcdeACXX:1:1:1793:808 1:N:0:
TNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNN
+
:%%%%%%%%%%%%%%%%%%%%?%%%%%%%%%%%%%%%%%%%%%?%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%
- at HiMom:1:2:1793:1117/1
+ at machine1:HiMom:abcdeACXX:1:2:1793:1117 1:N:0:
GNGGGNNNNNNNCNGGTCGTTAGCAAGTGATGGCTGTGTTCTGTATCTTTATTGTGGCGACACTTACATGACTGGA
+
3%;B7%%%%%%%=%9C*'5@?BCB><.9>?@BA)>>(B<3@)@4?B<8)5>67<6A5+5-0.(84-8637,7/7%)
- at HiMom:1:2:1793:1329/1
+ at machine1:HiMom:abcdeACXX:1:2:1793:1329 1:N:0:
CNTCTNNNNNNNTNGATGCAGTAACTGGAAATATAGAAGATGCTGTGACTCCATTTGAATCTATAAAAAGCGTTGT
+
8%805%%%%%%%3%9?*7?(1(90'80;4(:??<<+9:5+/=A85,/=?3)=')6-+*,5=/902-2-0+5-%,-0
- at HiMom:1:2:1793:1354/1
+ at machine1:HiMom:abcdeACXX:1:2:1793:1354 1:N:0:
TNGCTNNNNNNNGNGGCGCCGCGAAGCGCACGGCGCCGACGCAGGGGGAAGGCGGGACATACACGACCCGCGAGCG
+
1%;A;%%%%%%%8%(5;@B7;(;*8;(8@;@<9/81((77*<(8 at -3<'(5=;(7((<')'<.0(/*(7/.2(9>1
- at HiMom:1:2:1793:1455/1
+ at machine1:HiMom:abcdeACXX:1:2:1793:1455 1:N:0:
CNTTCNNNNNNNGNGACTGCAGTTGCTGTTGCCCATTAAGACCTTGAGAAAAGGCTTGCCTGCCCTTCGTCTGACT
+
?%8=?%%%%%%%:%9'=?@C*@2'=B<;/(;=%?,89'80(=B9=>7145.-(7B-)38/5)'=%5-=:/57)%6%
- at HiMom:1:2:1793:1478/1
+ at machine1:HiMom:abcdeACXX:1:2:1793:1478 1:N:0:
TNTTTNNNNNNNCNAATTTTACCTCATAAAATTTTTTGAGGTTTGATGTATGTCTCTGTCTTATCAATAATGAGGC
+
=%?C?%%%%%%%*%+, at CCB>BCBBA@=778BCBCBCB?BC?BCA4AC@;@C at CBCBBACA:)=B>';64=>6=AC
- at HiMom:1:2:1793:1793/1
+ at machine1:HiMom:abcdeACXX:1:2:1793:1793 1:N:0:
CNCCANNNNNNNCNGGGCCCTTTGTCTAAAGTCTGAATCAGCATTTGGATTTAGCCCTAATAGAGCCTGTTCATCC
+
=%?%)%%%%%%%=%68>BBB9?>@:B:)2(7:A84'67>5;>/67889'385,9@?=-+(327+3@>8777</15@
- at HiMom:1:2:1793:1812/1
+ at machine1:HiMom:abcdeACXX:1:2:1793:1812 1:N:0:
CNCTCNNNNNNNCNGCATACTTAACAAGTCTGATCTTGCTTATAGAAATTGGATCTTACTACTTCATTCTCAGAAT
+
(%?B>%%%%%%%?%>B7=- at BB;=@07B at CBB5?CBBBCB?+>:B944?BB at 1@CBB9/=7B at AB=@@BB@(>(8<
- at HiMom:1:2:1793:1893/1
+ at machine1:HiMom:abcdeACXX:1:2:1793:1893 1:N:0:
GNTCCNNNNNNNANTCCCCGTGGATGAAAATGCTGTACATGTTCTTGTTGATAACAATGGGCAAGGTCTAGGACAG
+
0%;C<%%%%%%%)%9CC@(>?C at 1=A7(00=BCAB96A><A?@CAAB at AA5>7AB1'6>7>B9.9B7B5)7;5B<>
- at HiMom:1:2:1793:1909/1
+ at machine1:HiMom:abcdeACXX:1:2:1793:1909 1:N:0:
GNCCTNNNNNNNCNCTCACACCGCCCCCCTTCTCACCTGCCCTGCGTAACCTGTACTGACTGCCCACTCCTCACCC
+
(%<@8%%%%%%%*%;(8@;*>7;*.(<B>5(.5@/*>93;(2@=-:'5>)0=+1;'5:';/(;1@*>,(;';((:)
- at HiMom:1:2:1793:1931/1
+ at machine1:HiMom:abcdeACXX:1:2:1793:1931 1:N:0:
GNCTANNNNNNNTNCACTGTCGACACCGCACACGGGGCATACCCACATCAAAGCAGTCCCCCAAGTCCCTGCGCAG
+
<%8.'%%%%%%%&%.(<B**(>3*775(*(;'.6''+;'&1(9.).*(7;5/'2(64A70>0.,23@)0%'5=<*'
- at HiMom:1:2:1793:1969/1
+ at machine1:HiMom:abcdeACXX:1:2:1793:1969 1:N:0:
TNCGCNNNNNNNANCCCTGACTGGCAAGGCGGTGGCGGCTCCAGTGAAGGCTCCCCGTGTTCTTAAAGACTAGCGC
+
5%8((%%%%%%%1%;BBB>+)7BBB?-?10 at B7BBB9A@@A379'?*39BA4@>);'5:'BBAA;>2>A6+9+@*<
- at HiMom:1:2:1793:2004/1
+ at machine1:HiMom:abcdeACXX:1:2:1793:2004 1:N:0:
GNGTTNNNNNNNCNTACTGGCATTTACTGTTTAACATCACACACCAAGCCAGGTTATTTCACACTCCTGCTACTGG
+
8%13<%%%%%%%:%?CCBBB?(>CCCCCBA@*9+ at +@C at +*1?;8 at +3*@*8C4 at 4>C>7 at 8115?),CC<7@?:A
- at HiMom:1:2:1793:2031/1
+ at machine1:HiMom:abcdeACXX:1:2:1793:2031 1:N:0:
CNCCGNNNNNNNGNGGTGCATGGGCTCCAACGTGGTGTCCTGTGGAGCTGTTGGGCCTGGGCAGGCGGCACAGATC
+
:%'*:%%%%%%%:%:B;B@(<BBAB9BA3AAB9A@,B1(==A6 at A/??;=5=?A3%273<4A,;7;:=;+&&/,/3
- at HiMom:1:2:1793:2038/1
+ at machine1:HiMom:abcdeACXX:1:2:1793:2038 1:N:0:
GNGCGNNNNNNNGNCACCTTGGTACTGGGTGATGGGGAGGCACTGAATGGGCTTCAAGTCCTCAAACGCCTGATCT
+
?%:-;%%%%%%%.%=)@CCACB=8ABCB?7@&>B?AC=?CB9C4AAA>>6==>>;%5>3%:/:%,3.;@0,9*-1;
- at HiMom:1:2:1793:310/1
+ at machine1:HiMom:abcdeACXX:1:2:1793:310 1:N:0:
CNGGANNNNNNNTNGAACCTTTGGCAAGGCTGCTCTTACGAGTCCTCTCGCCCTGTTCCACCTATCCCCATAGCTA
+
(%5;'%%%%%%%(%.*0 at 99@AB>CA5):=:A1;A<3':-''.'3';('5>BC at B=A(A<>511(6B?,''(<&-*
- at HiMom:1:2:1793:404/1
+ at machine1:HiMom:abcdeACXX:1:2:1793:404 1:N:0:
CNCCCNNNNNNNTNCAATGCTATGCAGTATGTCTTCTTATCTCTGTCTTCAAGAGCATCCTCTGTCAGTCCTACAT
+
:%)?0%%%%%%%9%*/0%,8.-->>>>9@?=975(=4/%0?74'/''39%-?8828,4412=0168;2+9A:74'5
- at HiMom:1:2:1793:475/1
+ at machine1:HiMom:abcdeACXX:1:2:1793:475 1:N:0:
CNGGGNNNNNNNCNCCCCCCTAGGCAATATGCTACTGCATATATATTTGGTCTAGATATATAACAAGTTACTACTG
+
?%9?3%%%%%%%0%<<%5;(2*7<@?(1')6>7?,7=7@*)6)35'7:7)%%,'3(.(+2++482.:))-%0-''2
- at HiMom:1:2:1793:666/1
+ at machine1:HiMom:abcdeACXX:1:2:1793:666 1:N:0:
CNGAGNNNNNNNTNGGGTAGGAAACACAGCCTTGCTCCACAGCGCACTGTCAGCAAGACGCTCCTTTCTTCGGAGA
+
?%9(9%%%%%%%%%7)9..<::>3>1;77<B05??)B>0=12(2A6=4:4956?/%5-%-;1;6542;/-&(26,(
- at HiMom:1:2:1793:829/1
+ at machine1:HiMom:abcdeACXX:1:2:1793:829 1:N:0:
TNGGCNNNNNNNCNTGGGCAAGCACCTGACCAGCAACAGCCCCCGCCTGGTGCAGCACTGCCTGTGGACCCTGCGC
+
;%;>*%%%%%%%<%:BAB at 0;BBBBBB@;@B at A@;*@*>BBBBBABBA?@3@@;<(5 at AAB@:>.=;,<BB;<BAB
- at HiMom:1:2:1794:490/1
+ at machine1:HiMom:abcdeACXX:1:2:1794:490 1:N:0:
CNTCCNNNNNNNTNTATTTACTATTTTCTGATTTTTAAAATGACAGTGGCAATTACCATTTATACTGTGTTATTTG
+
?%8C?%%%%%%%9%6(=?:(=@BAA@@B at A<<<<=@=;5?@9+?A@:?9 at 5&1=>A?+:6668=A9?7?9?=<9=6
- at HiMom:1:3:1793:1031/1
+ at machine1:HiMom:abcdeACXX:1:3:1793:1031 1:N:0:
CNACTNNNNNNNGNNGCATTGGAGAAGAACCAAGCTGGCTCTCTAAGGAAGTGCACACGAGTTGGAACACATATTC
+
?%<?(%%%%%%%:%%=B47?B=6?=2?/00 at 8), at BB=3,>).'50;:72))1)5=:)<19%)+(%5?:=;7.)1'
- at HiMom:1:3:1793:1143/1
+ at machine1:HiMom:abcdeACXX:1:3:1793:1143 1:N:0:
TNGGGNNNNNNNTNCATGGTGAGGAAGAGTCGGAAGCAGGCATGCGGCTGCAGGGAATGCAACTTCTTCTCCATCG
+
:%(B3%%%%%%%:%=BCCC<CBBB<CCB3*@?BBBAA*=B at 9@?B?8<3;>3;A;+2:9<43:<;?9>A:8<+%<%
- at HiMom:1:3:1793:1282/1
+ at machine1:HiMom:abcdeACXX:1:3:1793:1282 1:N:0:
GNTAGNNNNNNNCNGGACTCTGGCGTCACCTTTGGCGCTGAGCGCCCCAGGCCCGCCAGCCCGCCCGCCCACTGCC
+
<%;(.%%%%%%%(%.6.(;B at 55+9>*8@(>*@;(.;@75'5';;@;;*4<5<2*@;/><@5>5(16;1;7)',..
- at HiMom:1:3:1793:1301/1
+ at machine1:HiMom:abcdeACXX:1:3:1793:1301 1:N:0:
GNAGGNNNNNNNTNCAGGGTTGAGGTATTCTTAGGTTAGCCGAGCTCTTTCCTCCTTTCCCCCCCCCTCTCCCCCA
+
?%*:3%%%%%%%(%;*9)>3+-*-@=)3?CCBAA;)A8 at 2*25;A7,52=B;(=)47)=BC;+:C@)2 at 0=BA9(9
- at HiMom:1:3:1793:1311/1
+ at machine1:HiMom:abcdeACXX:1:3:1793:1311 1:N:0:
GNTATNNNNNNNTNTTCCTTCAGTCTGCACAAAGATTAAGGTAATTTACAGTCAATCTGTGAATGAATGTTGAGAC
+
<%()<%%%%%%%7%<<BCBCCCABCCCC at CBB?BCCCCCBC>AACC?*@.BAB8*@CCCBC@:@?7?ABAA??B8B
- at HiMom:1:3:1793:1326/1
+ at machine1:HiMom:abcdeACXX:1:3:1793:1326 1:N:0:
GNCCANNNNNNNCNTCTTGGGCTCCACACCATTACCAGCATCAGAGGCAGGGGAACACAATCTGCTGCCTTATAAG
+
?%?@7%%%%%%%?%3C=+;.<@+@@8A?AC@@ABBB at BCB?+?;?-5- at BA92-7B<?-2/,*@A2?BB;A5?1'4
- at HiMom:1:3:1793:1389/1
+ at machine1:HiMom:abcdeACXX:1:3:1793:1389 1:N:0:
GNGGGNNNNNNNGNCGCAGGTGGGGATGGGCACCCTCACAGCTTCCCTGGACCTTAGTTTTGTTGGGGTTCAGTCC
+
:%<B;%%%%%%%7%;A at 1@>.>BB@:;ABAABBBBB<+<7?@8 at BBBBA72@>2<(>5+=7906A<;5*3<2 at -(4
- at HiMom:1:3:1793:1405/1
+ at machine1:HiMom:abcdeACXX:1:3:1793:1405 1:N:0:
GNTGGNNNNNNNTNGCTGAGATGCTCTTTAACCAAAGGAGGAAAGAGAGGAGACCAAGGGCCAGCTGGTTGGTTGT
+
7%1C=%%%%%%%8%8CA=2@?ABB6BABBABBC;:>BB>B at 9(;A=@?B>3?)@A?=5(7?@1>B=A;(=@@,1=3
- at HiMom:1:3:1793:141/1
+ at machine1:HiMom:abcdeACXX:1:3:1793:141 1:N:0:
TNCTCNNNNNNNCNCTTAGCAGTGCGCCCCCCGAGCGCGGCACAGGGGCCAGGGAGACAGAGGACACCGGGATCTC
+
;%;9,%%%%%%%,%52(((3.8(+/*/B at 1<1((=.&4+9+/(::11+(&7600+.+A4'*%%%-%:/,%%,'9'B
- at HiMom:1:3:1793:1507/1
+ at machine1:HiMom:abcdeACXX:1:3:1793:1507 1:N:0:
GNGTGNNNNNNNTNGTTGCCAGCCTGCTGCCCGCCATCCTGGTCTTCATTCTCATCTTCATGGAGACACAGATCAC
+
=%==8%%%%%%%?%5ABABBABCCBBCBBCCCBC at 09ACB==;CBB at 0;>ABBBACA>?'9A==>)@)?9;63?5@
- at HiMom:1:3:1793:1557/1
+ at machine1:HiMom:abcdeACXX:1:3:1793:1557 1:N:0:
GNGGANNNNNNNCNTCGAGCCATTCCACTCCCGCCCGGGCACCAACAGCCAAACGCACGCTCATCAAAAAGGCCGA
+
(%;*(%%%%%%%;%5>/(4?A;=6(><1*@1*-@@>/*0 at 9)9?>2.=8'<,8<,1((%:1<?+(.08'+55B?:%
- at HiMom:1:3:1793:1570/1
+ at machine1:HiMom:abcdeACXX:1:3:1793:1570 1:N:0:
GNTCTNNNNNNNTNTCTCCACTCTGCTGCCCTACCTCTCGGAGTCTTCTACCGCGTCTAACTAGTCATATTTACAA
+
6%3B6%%%%%%%,%'C@@BC>1?B at CC?C at CAB@B@?6&BACA4,?*<B@>1'13,<B;)@BB3'?%)+:A@;CB@
- at HiMom:1:3:1793:1617/1
+ at machine1:HiMom:abcdeACXX:1:3:1793:1617 1:N:0:
CNGAANNNNNNNTNCGCCTTCTTCTTCAACTCGGAGCTGCTGAGCGCTGTGCGCTTCGCCCTGGGCAAGGGCCGCG
+
:%75'%%%%%%%3%;;BA><A;=B;7 at 84>'9>:90<,7<,61132%*8//3471'349+6,36+:&+462+.&.%
- at HiMom:1:3:1793:1709/1
+ at machine1:HiMom:abcdeACXX:1:3:1793:1709 1:N:0:
GNGGGNNNNNNNTNCCATTGGTTTCTGAAAGTATTCACATCATTTGGGATACCAGATAGCTCAATACTCTCTGAGT
+
8%>B<%%%%%%%:%?B8BBBB?BBCAC?@6 at 1;AB@*@<>B9>?@@B?9<4BB8 at 82)<C at CA:?8B at C@C@?/='
- at HiMom:1:3:1793:1738/1
+ at machine1:HiMom:abcdeACXX:1:3:1793:1738 1:N:0:
GNGCCNNNNNNNGNCTCTTGGGGAATATCTGAGGCTCTGTGGTCACCCACAGACCCGTTACTCCTTTAGGTGTCTG
+
?%:C?%%%%%%%8%=BCABBBBC?BBCBCBBBBBC at C?A1AB.?3?A2)@880@@)0%96?9 at B;><+=>5 at 0>=@
- at HiMom:1:3:1793:1779/1
+ at machine1:HiMom:abcdeACXX:1:3:1793:1779 1:N:0:
GNGCANNNNNNNCNTGCGTATATTTACAGATATATATACAGAATTGTTTGCTCTGAGCCATTTATAAGCACTTACT
+
=%5A0%%%%%%%?%)9*>'=@::>BBB:B@;7AAA at 7@=3/.*:?@8;,<*;B4=ABBC?).=4>(;BA=CA:-?;
- at HiMom:1:3:1793:1793/1
+ at machine1:HiMom:abcdeACXX:1:3:1793:1793 1:N:0:
CNTCTNNNNNNNANNATGGGCTTTCTACAGCCTGCTTACCACTAACAGTAAGGAATCTTTCATAAACACACCTCAG
+
:%1 at 6%%%%%%%&%%'-;:)62(9=)=>3)0A9>@501??:=5:583466.451,9 at 952<,94.2;88+2=8;3,
- at HiMom:1:3:1793:1859/1
+ at machine1:HiMom:abcdeACXX:1:3:1793:1859 1:N:0:
GNGAGNNNNNNNANCCAAGCATCTATCCCAGTGTGGGGGCTGAGGCTGCGAGAGGAAAGCGGGGACGGAAGACGGG
+
<%((;%%%%%%%<%(;=<B96<@B3?BBB=B11(A;BB/(0=-:?9)@-=,12<=2>>:@8@':%8<=.52(82(+
- at HiMom:1:3:1793:1898/1
+ at machine1:HiMom:abcdeACXX:1:3:1793:1898 1:N:0:
GNACANNNNNNNGNAATATGGGCTTATCCAACCCAACCAAGATGGAGAGTGAGGGGGTTGTCCCTGGGCCCAAGGC
+
:%/=(%%%%%%%:%*/<1=5;BBBAAACCA8ABCAACB;)@?BBB+B6?4B:A7;??16@=BA?9509B?@-+844
- at HiMom:1:3:1793:456/1
+ at machine1:HiMom:abcdeACXX:1:3:1793:456 1:N:0:
CNTATNNNNNNNCNNCGGGTACCACAGTTGAGGACTGACATTCTGAACCCTGATGTTTCTAAAGAAACGACAGTAT
+
?%6 at 8%%%%%%%?%%?@?@6AAA??6<>>@6/7?A??6><<8=@252;>@84<9>58@?7.-6;78;<4'9-<:68
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/nonBarcoded.2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/nonBarcoded.2.fastq
index b5499f1..8e9b24a 100644
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/nonBarcoded.2.fastq
+++ b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/nonBarcoded.2.fastq
@@ -1,240 +1,240 @@
- at HiMom:1:1:1793:1011/2
+ at machine1:HiMom:abcdeACXX:1:1:1793:1011 2:N:0:
ANNNTNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
+
3%%%%%%%%%%%%%%%%%%%%(%%%%%%%%%%%%%%%%%%%%%?%%%%%%%%%%%%%%%%%%%%%*%%%%%%%%%%
- at HiMom:1:1:1793:1420/2
+ at machine1:HiMom:abcdeACXX:1:1:1793:1420 2:N:0:
CNNNANNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNN
+
?%%%*%%%%%%%%%%%%%%%%,%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%.%%%%%%%%%%
- at HiMom:1:1:1793:1441/2
+ at machine1:HiMom:abcdeACXX:1:1:1793:1441 2:N:0:
CNNNANNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNN
+
<%%%(%%%%%%%%%%%%%%%%'%%%%%%%%%%%%%%%%%%%%%:%%%%%%%%%%%%%%%%%%%%%&%%%%%%%%%%
- at HiMom:1:1:1793:1483/2
+ at machine1:HiMom:abcdeACXX:1:1:1793:1483 2:N:0:
GNNNANNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
+
<%%%%%%%%%%%%%%%%%%%%0%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%>%%%%%%%%%%
- at HiMom:1:1:1793:1495/2
+ at machine1:HiMom:abcdeACXX:1:1:1793:1495 2:N:0:
ANNNTNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
+
)%%%*%%%%%%%%%%%%%%%%(%%%%%%%%%%%%%%%%%%%%%:%%%%%%%%%%%%%%%%%%%%%4%%%%%%%%%%
- at HiMom:1:1:1793:1527/2
+ at machine1:HiMom:abcdeACXX:1:1:1793:1527 2:N:0:
CNNNCNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNN
+
:%%%*%%%%%%%%%%%%%%%%7%%%%%%%%%%%%%%%%%%%%%5%%%%%%%%%%%%%%%%%%%%%*%%%%%%%%%%
- at HiMom:1:1:1793:1545/2
+ at machine1:HiMom:abcdeACXX:1:1:1793:1545 2:N:0:
CNNNTNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNN
+
5%%%*%%%%%%%%%%%%%%%%2%%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%
- at HiMom:1:1:1793:1583/2
+ at machine1:HiMom:abcdeACXX:1:1:1793:1583 2:N:0:
CNNNTNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNN
+
<%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%%%%%%%%%%%%&%%%%%%%%%%
- at HiMom:1:1:1793:1596/2
+ at machine1:HiMom:abcdeACXX:1:1:1793:1596 2:N:0:
CNNNCNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
+
<%%%+%%%%%%%%%%%%%%%%5%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%+%%%%%%%%%%
- at HiMom:1:1:1793:1602/2
+ at machine1:HiMom:abcdeACXX:1:1:1793:1602 2:N:0:
CNNNGNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
+
;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%8%%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%
- at HiMom:1:1:1793:1658/2
+ at machine1:HiMom:abcdeACXX:1:1:1793:1658 2:N:0:
TNNNCNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
+
:%%%+%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%
- at HiMom:1:1:1793:1681/2
+ at machine1:HiMom:abcdeACXX:1:1:1793:1681 2:N:0:
ANNNANNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNN
+
)%%%(%%%%%%%%%%%%%%%%7%%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%%%%%%%%%%%%%4%%%%%%%%%%
- at HiMom:1:1:1793:1718/2
+ at machine1:HiMom:abcdeACXX:1:1:1793:1718 2:N:0:
ANNNANNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNN
+
(%%%%%%%%%%%%%%%%%%%%/%%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%%%%%%%%%%%%%(%%%%%%%%%%
- at HiMom:1:1:1793:1745/2
+ at machine1:HiMom:abcdeACXX:1:1:1793:1745 2:N:0:
ANNNTNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNN
+
(%%%%%%%%%%%%%%%%%%%%(%%%%%%%%%%%%%%%%%%%%%4%%%%%%%%%%%%%%%%%%%%%0%%%%%%%%%%
- at HiMom:1:1:1793:1777/2
+ at machine1:HiMom:abcdeACXX:1:1:1793:1777 2:N:0:
ANNNANNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
+
)%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%%%%%%%%%%%%(%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%
- at HiMom:1:1:1793:1813/2
+ at machine1:HiMom:abcdeACXX:1:1:1793:1813 2:N:0:
CNNNCNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
+
<%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%*%%%%%%%%%%%%%%%%%%%%%:%%%%%%%%%%
- at HiMom:1:1:1793:1916/2
+ at machine1:HiMom:abcdeACXX:1:1:1793:1916 2:N:0:
CNNNANNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
+
(%%%(%%%%%%%%%%%%%%%%0%%%%%%%%%%%%%%%%%%%%%5%%%%%%%%%%%%%%%%%%%%%4%%%%%%%%%%
- at HiMom:1:1:1793:1959/2
+ at machine1:HiMom:abcdeACXX:1:1:1793:1959 2:N:0:
ANNNCNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
+
1%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%
- at HiMom:1:1:1793:602/2
+ at machine1:HiMom:abcdeACXX:1:1:1793:602 2:N:0:
CNNNANNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNN
+
?%%%&%%%%%%%%%%%%%%%%;%%%%%%%%%%%%%%%%%%%%%:%%%%%%%%%%%%%%%%%%%%%6%%%%%%%%%%
- at HiMom:1:1:1793:808/2
+ at machine1:HiMom:abcdeACXX:1:1:1793:808 2:N:0:
CNNNANNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNN
+
<%%%%%%%%%%%%%%%%%%%%.%%%%%%%%%%%%%%%%%%%%%.%%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%
- at HiMom:1:2:1793:1117/2
+ at machine1:HiMom:abcdeACXX:1:2:1793:1117 2:N:0:
TTCTTCAGCTGTATTGAAGTATAATTTACAATACAGTACAATTCATATATTTTAATTGTATAATTTAATGACTTTG
+
+4 at .:B=?<'<?@2+=38A4+;>.3:9A>(7??A09(0>((0=A::;,;+/(:+*769)..'09>.%+2-4>-'(7
- at HiMom:1:2:1793:1329/2
+ at machine1:HiMom:abcdeACXX:1:2:1793:1329 2:N:0:
GAGCCCCGCGTCTGTCTCAGAGAACTTTTGCATTCTTCTTGTTCTCCAGGAGAAACGGCATCATCTTCCATGTCTT
+
A@=*BC at -+:6B8'6 at BC@C>,;2)5BBBBB>;BCBBC at 6@@BAACCB>B;8)07*<@=':C><<9A@(68@=B59
- at HiMom:1:2:1793:1354/2
+ at machine1:HiMom:abcdeACXX:1:2:1793:1354 2:N:0:
CTGAACCTCAAGTCTCCACCAATCAGAATCTGGGGGAGGGCGCGCGTGCAGGGAGCCGCCTGCTCTCCACCTTCGC
+
A24(06/+.2(21?49?:-+(5&8&5**4?1'13..0'.'%,,98&%(60&.++1(&+A,,0..8.18(.0&+,,/
- at HiMom:1:2:1793:1455/2
+ at machine1:HiMom:abcdeACXX:1:2:1793:1455 2:N:0:
GGAAACCAACCCCTCACATGGTAACCCGCTCCAACCCGCACGCCCTGTTCGGCCCCTGACCCGGCCCCCCGGCGCA
+
>/,+'<:''',5'3(59'+.705,/8 at 94(,+'5@;'%7%%;3>86.*%04&'%17(&.5%%+%,>0624*%,*:%
- at HiMom:1:2:1793:1478/2
+ at machine1:HiMom:abcdeACXX:1:2:1793:1478 2:N:0:
CAGCCATTCAAATCCAGTATTTTTTAAGCCTCATTATTGATAAGACAGAGACATACATCACACCTCAACACCTTTT
+
A:;C?'7<>(0*8B?*:4-4;A><8+-9BB>?/;;7:<702'+:(?/9(92<+12<,5;&'.>@<?*&%*&%3865
- at HiMom:1:2:1793:1793/2
+ at machine1:HiMom:abcdeACXX:1:2:1793:1793 2:N:0:
GTTTATAACTTCTTCTGTGGGATCAGCGGGCACGCCTCTTCCCACCAGCACACTACACGTCTACCAGCGCGGATGG
+
B?A>.90)(<@CB?C at B8BA>?=?*<&:@?=%;ABB:&85&=+>A=%7&+'. at 3&9&,=2&810626B7'<5%->:
- at HiMom:1:2:1793:1812/2
+ at machine1:HiMom:abcdeACXX:1:2:1793:1812 2:N:0:
TCCAGCATGAAGATAATGGCTAATACCAAAGCAGCCTTTTTGCTGTGGTAGGAAGATAATGGCTAATAAAAATGAG
+
BCCCCB9A at ++@4?7+?CBCA@)=)''/2)8@)=?(;??AA=&=B at BB02<9.)3).%0-2<5&/+*1%(:'*,%9
- at HiMom:1:2:1793:1893/2
+ at machine1:HiMom:abcdeACXX:1:2:1793:1893 2:N:0:
GGGCAGGGGGCTTTTTCTCACTCTCTCTCATATCTTCTAGGGTAACTACATGAACACACGCTTCTCTCCCCTTCCG
+
ABBB4=BBB:)=B<AAC?C>)?C at C?CBB3;)<C at BC9(>?A3 at -@=)@6@=4'?4(425C9=B<C at CB@(07((:
- at HiMom:1:2:1793:1909/2
+ at machine1:HiMom:abcdeACXX:1:2:1793:1909 2:N:0:
CTCACACCCACACCCCCCCCAATCCCACCCCCGGACACCACACCCCTCCAACTTCCCCCCCCGAGCGCAGCCGGGG
+
B16+:&3:(%+'4+&6;/2(%,/29.'5,,--,('&.''%%,&.1+%*:%%1%%%%,((%'&(%(247-*%+11&%
- at HiMom:1:2:1793:1931/2
+ at machine1:HiMom:abcdeACXX:1:2:1793:1931 2:N:0:
CTGAAGCGCCACCGCCGCGGCGTGGCGGGCCCCGCGCACCACCTCTTCCCGTCCTCTACCGGCCCTGGCCACGCCC
+
9+&'411'41,0'1/.%'%&9(0,%,'--%%-'%%.''.,((.+,(%-3+++,/(*+&'3,+*-%%**.&%,0'*(
- at HiMom:1:2:1793:1969/2
+ at machine1:HiMom:abcdeACXX:1:2:1793:1969 2:N:0:
GAGAACTCTCTGTGTAGTTGTGACTTCCATCCTTCCGCAACAGTAGTAAGGACCGCGACTTCTGACCACATTGACC
+
:%===(,=B>=:-;7<B/?@8@=:8==>'.,=86 at B@A,,+07-(9'35>?58//?;-'+.8(50'619('''+/9
- at HiMom:1:2:1793:2004/2
+ at machine1:HiMom:abcdeACXX:1:2:1793:2004 2:N:0:
GAACTTGACTATCTCTTCTAATTTTATTGTTTATTTTGTGTTTACTGCCCAGCTACTTCCCACCTTCCACTTGCTT
+
B?4 at C@<+>=57'3B>=)?4>BBA?+=@B@>7-;@@@A=B::7?4<>?*?<8B83A?=>(>;BB1A.%-@@:8 at 5=
- at HiMom:1:2:1793:2031/2
+ at machine1:HiMom:abcdeACXX:1:2:1793:2031 2:N:0:
TGCCAGTAGTTTTGGGTCAAGCCCTCACCTGATTCCACGCTTCATAGCTTCAGCCGTTCCCATCATACTACTAGCT
+
BBBC=>==B=@@@@BB5@)-=CBA9'/B@=>16 at BB)(8'4=A54-=B:8@(;?(9'0?A7'1A.96>3/'4235-
- at HiMom:1:2:1793:2038/2
+ at machine1:HiMom:abcdeACXX:1:2:1793:2038 2:N:0:
CCTGTGTCTCAGTGAGCCTTCAGTGCAACATACGGGTAAGAGCAGCCTTCTCTTCACTGAGATGAGACCCCCCCAC
+
B>626.288?89.5'5??60,477.3'%%)+112.21.&21330/75*)55(5+./,2*%-,/1)162/2'55662
- at HiMom:1:2:1793:310/2
+ at machine1:HiMom:abcdeACXX:1:2:1793:310 2:N:0:
CGAAACTTGGGTCAGTAAACTGGTGAAGCTGACCTATTTGGCAAGCAGCATGATTCGGAAGCGCGGCAGGCAGAGT
+
?(5 at BB*>57 at 6B@*34)?=6B@()'18%'?=@A*:@?4 at +(4>A;8<'/@=366A@;/7@(-'()7(1(8(2'''
- at HiMom:1:2:1793:404/2
+ at machine1:HiMom:abcdeACXX:1:2:1793:404 2:N:0:
ACATGAATCCTCTCCCACAGGAATTATTCAGCTTACCGCGAGTACGCTTCCGTGTTGGAAAGATTCAACTCACCCC
+
;'7B62:2(=/8<>A at 9A=88>6<==:4?%5A8=;>@*73,.%6?<'%%5;+)%%-2'1)&%5(-937&0)%%0=B
- at HiMom:1:2:1793:475/2
+ at machine1:HiMom:abcdeACXX:1:2:1793:475 2:N:0:
AACTTTTTTACGCAATGTTAATATTCAACTCTTCCTTCCAATAGAAATTTTCTGCTGCTTTTCTTGCTCGTGCTAG
+
BCB77433)@1)@*:>A9+>401>@?:*@6=(6C8*/2@<(2A8%)6?;97 at 9+9;<'3/4)-15:34+)'8'2--
- at HiMom:1:2:1793:666/2
+ at machine1:HiMom:abcdeACXX:1:2:1793:666 2:N:0:
ATTTTTGCTTTCCTTGGCCCCCACCAATTTATACATCTCCATTTTCCGACCTCTGGACTAACTGCTTGCTCAGCAC
+
6;BAC?AB@@>@8;@>@BBBBA:@B8=?;1>6 at AA<B4AB:94<;=,0'<@<A87)7B=73@;3)'/69(<,67'%
- at HiMom:1:2:1793:829/2
+ at machine1:HiMom:abcdeACXX:1:2:1793:829 2:N:0:
TCGCTGTTGTTGCATGTCAGGTTGGAGAGTGTGCCCGTGGCCCCGGTGCGGCCGGTGGCCGCCCCCCCCCCCCGCC
+
AB at BBA=AB?AA@)8@=@)>=>=A>3=0>4A3ABB at 6+<><(<'88*8%:8%:4%52(8%(55%4>2<7;*;2%7%
- at HiMom:1:2:1794:490/2
+ at machine1:HiMom:abcdeACXX:1:2:1794:490 2:N:0:
ATAAACTTGAAAATAATTTTCTATGATACAGCTTTCAGGTAGAAAAATGAATTTTCGTCGTGTTTAACAATGTTGT
+
ABBCBCAAC@;5@@77BBB?CCBBB?@BCBBCAB@@3<A6>>)99?0<B at 6?>@@BB6A9>B5A<@6<%+>@<<:0
- at HiMom:1:3:1793:1031/2
+ at machine1:HiMom:abcdeACXX:1:3:1793:1031 2:N:0:
CCCATACCAGCACAGAGCATACAGAAACACAGAAAAAATATTCCCAGTAAAACATGTGCAACTGTCCAGGCAGTCG
+
+5AA at 92+>4AABBA6@;'(-;<=22)B8@@@7>A@<583498 at 62-45:-8>8;:0081*956-;7.)*%.4))0
- at HiMom:1:3:1793:1143/2
+ at machine1:HiMom:abcdeACXX:1:3:1793:1143 2:N:0:
CTGCAGAGCAGTTGTGGCACTGGGCTTTGGCCACTCAAACTCAGGCTGGTCCGGAACCTCCCCCACCCCGCCCCAC
+
A==B59>>A at 8/7=,19:+:'344A..366?A9=4>168?1:113;42,%7:3-&177&59=;8&,=2%(8+7%%2
- at HiMom:1:3:1793:1282/2
+ at machine1:HiMom:abcdeACXX:1:3:1793:1282 2:N:0:
AAGCACACCAAGCTTCCCGCAGCTGCGGCGCCCCCGCTCCAAGGCCAGCAGCTGCCCCCTCTGCCCCCACCCCCTC
+
(*579.1(.//>B at -17+=../@9=*=(.(.;<.1'>;<:'''7=;'.':==:551938*7.7;:%7:'';@;609
- at HiMom:1:3:1793:1301/2
+ at machine1:HiMom:abcdeACXX:1:3:1793:1301 2:N:0:
GCATTGCGTCCATCTCTTTACAGAAGAACTCAGCCCACACCCTAGAATGTACACCTTTGGAAAAAGGAGAAGTGCT
+
=(6;9*AA;*BCBCCCABB at CB@)??@>@BBBCCCA6 at 8?CC>9@>=?@-2)9AB;6>>;5334=3=7+6-14?=-
- at HiMom:1:3:1793:1311/2
+ at machine1:HiMom:abcdeACXX:1:3:1793:1311 2:N:0:
CAGCAAAAGTGCCGGCTAGTCCGGTTTGTTGAAAATACAGTAGAAAAGCTGATTCTGGTTATCTCTCTCAGGACAA
+
B<ABBA4=A1?CCBB*B9?:>'>@)?A@<AA74;A@?B=>)'6'61<58(:/75A?7(0===@=@4*7%355/>40
- at HiMom:1:3:1793:1326/2
+ at machine1:HiMom:abcdeACXX:1:3:1793:1326 2:N:0:
CAAGATCATACTAACACACTCCAGCCTGGGCAACAGAGTGGGACTCTGTATCCAAAAAAAATTCTCTACCAACTAC
+
BABB==BA?@CB??BBCCCCBB- at AC0B<,CCCCA at 4<@A;;AC+CBCA,BCA1=A:=9<=A,C?+<?B?3<B,?C
- at HiMom:1:3:1793:1389/2
+ at machine1:HiMom:abcdeACXX:1:3:1793:1389 2:N:0:
ACCACAGGCACCACCAGCCACGGACCCACGCCTGCCACTCCCCACCCCCCCCCCCCCAGCCACGCCACCGTCCCAC
+
7@>*@0:3 at 2@@7BB=ABB3B=5%;B>(>0%:;<A=0@=8';&(:?A>2>7%<;%:A;3@>+.*%%.+<0/:)>-)
- at HiMom:1:3:1793:1405/2
+ at machine1:HiMom:abcdeACXX:1:3:1793:1405 2:N:0:
GCCTTGTTTGGCCCTGATCTCTGACTTCTAGAGCCCCAGCTGCTGGCGGCTGCTGGGATATCCTCCCCGCTCGGGT
+
@BBBBBA@@9BBBBA11=BBBBBABBBBB9=9BBBBB9ABABB@*=B@@719.2=33%822@>'':A5%1+%77%(
- at HiMom:1:3:1793:141/2
+ at machine1:HiMom:abcdeACXX:1:3:1793:141 2:N:0:
CTCTCCCGCGCCTGCTACGGAGCCCGCTCGGGGGGGCCACGCCGCTCCCGAGGACGTAGCACCTCCTCCACTCACG
+
4:-*695*:&7(.333?9*'(@(6.((%%,;62+*..(./0(>3/&%14(,1((0-6&15%%.6>(&'%+20&+3(
- at HiMom:1:3:1793:1507/2
+ at machine1:HiMom:abcdeACXX:1:3:1793:1507 2:N:0:
CAGAGCGCGTTGGCGTGAGTGACAGAGCGGCCAGTGGCCGCCGCCCACCCGCCCACGCCCCCGAGGGCCCCCCTGC
+
@11+1?4>44344=533,252.;11,->4.&7.**,-5++.,(.7*&,1*%%%.*(%...,*%*+,%%+1(&+%,.
- at HiMom:1:3:1793:1557/2
+ at machine1:HiMom:abcdeACXX:1:3:1793:1557 2:N:0:
CGGCTTTTTTTTTATTGAGACCAGCTCCTGCCCTACCCCCGCGGCTGCGGAGCAAGGTCCCCTTCATGCGCCCCCC
+
5&0/(7*3>96=9)<*+%'+5,/%'&7%7+675%'%%+09*(*'2(5%%,&(.&,%%(,6%(&'7&+&,&-,+554
- at HiMom:1:3:1793:1570/2
+ at machine1:HiMom:abcdeACXX:1:3:1793:1570 2:N:0:
CAGACACCTTTCATATCTTTATGGCAACTTAATTTTTGGCCTTTTATCACTCTGTCATACCAGCATTCTGCCGTCA
+
A@>;B at CB549'34=9B;?>/A@?8@@;=<(9/5++<74B;B<%..;C-(.8?@(>'9@>><6>(4;<%*.(.*=:
- at HiMom:1:3:1793:1617/2
+ at machine1:HiMom:abcdeACXX:1:3:1793:1617 2:N:0:
GTGGTCATAACTGTTTCTGGACCCATTTGAACTTCATCTGAATATAGAAATCTCAGCAGCGCCCGGACGGCTGCGG
+
A<CBAB4>=, at BB@BAC at B=*A@*+>ABB94BB at B;>B?;>@@5A;B=046C@@(6A9;A2A<'90'(:-?%3:/:
- at HiMom:1:3:1793:1709/2
+ at machine1:HiMom:abcdeACXX:1:3:1793:1709 2:N:0:
AGCCACTGTCCCGTGTATAACTTGGCATTAGAGCACCAGGTCTGTTGGATGGTGGTGGCAGGCCCAATTAATTTTT
+
,?@)7 at B@6BCCC;C?@A;+ at A;BBB=;BA at 6@B6B@(>B8CAA6<B?69B?(B=-:@>-7 at 85:%.))3&73-%)
- at HiMom:1:3:1793:1738/2
+ at machine1:HiMom:abcdeACXX:1:3:1793:1738 2:N:0:
TCCCTGACTGGATACAGGCAGCTGACCCCTTCTCCCGACACCTCAAGGAGTAACTGGGCTGTTGGTGACCCCCGAC
+
ABBBBA at BBBA<B7B at ABBAB;(:';BBA=A at 0@@*90@)@B<(>)>>(>(+;@9@:%;*<(54 at +.%3@(>5(%'
- at HiMom:1:3:1793:1779/2
+ at machine1:HiMom:abcdeACXX:1:3:1793:1779 2:N:0:
CACTGAAATGTTTAGGACCATATTATAAGTAAGTACTTATCAATGTACTTTAGGACCATATTATAAGTAAGTGCTT
+
=:AB>(>64A=;27A@=B@)=64@@:5)@9<)=:BBB@:='?'9B*BC>)67B at AC@;=9>)0@*8?:40:<BC=<
- at HiMom:1:3:1793:1793/2
+ at machine1:HiMom:abcdeACXX:1:3:1793:1793 2:N:0:
GCTCAAATTTGTGCTACCAATGATATCGAGTTTATAGCAAATTTTCTACGGGAAGTCTATGCGGCAATTTTCTCAT
+
BCA=8+3?C=A-8A@:ACB?,@;8;@+@*@;C3,8)8C?+9=;2*=+='2A?898*+0%())18)42:?A7B>?':
- at HiMom:1:3:1793:1859/2
+ at machine1:HiMom:abcdeACXX:1:3:1793:1859 2:N:0:
CGATTTTTAAGGACCCCGTGCCTCTGGGGGCCGATGAACTCCACGATGGGACGCACCTGGAGCTCTACCATCAATA
+
BB55A9?@>.(7AAAB?3,A>A=A>A6@?>29(434(.'0B?2:?266<2/,91:B9.1)06451//&&78A10,2
- at HiMom:1:3:1793:1898/2
+ at machine1:HiMom:abcdeACXX:1:3:1793:1898 2:N:0:
CCGGCCAAGCAGGCATGTGTGAATGAACGTGGCCGCTGACTCAGAACAGAGGACATCCCAGGGCCGCAAGCGCGGA
+
BB>ABB3=;>&5(1%2=4=552-',37A=,41>1(1',+.37'1,&9/331(/9/'6.+''0,(%,2&(.1,//.(
- at HiMom:1:3:1793:456/2
+ at machine1:HiMom:abcdeACXX:1:3:1793:456 2:N:0:
TCCATCCACTTCCCTGAGCCTCAGAAAAGGGCAAGGCATGGCTCACATACTCTCAGCCACGGCCTGGCCTGCTGCC
+
BBB<ABB at BBBBBB=@@ABB?B5 at 777=;;ABA9A;B?=><BB at 6@AA?B>B9>*>AA9A53?>(%89(.9>;<:(
diff --git a/testdata/net/sf/picard/io/5newline5.txt b/testdata/net/sf/picard/io/5newline5.txt
new file mode 100644
index 0000000..53ff652
--- /dev/null
+++ b/testdata/net/sf/picard/io/5newline5.txt
@@ -0,0 +1,2 @@
+
+
\ No newline at end of file
diff --git a/testdata/net/sf/picard/io/empty.txt b/testdata/net/sf/picard/io/empty.txt
new file mode 100644
index 0000000..e69de29
diff --git a/testdata/net/sf/picard/sam/fastq2bam/ok-paired/illumina-sanger_full_range_as_sanger-62.fastq b/testdata/net/sf/picard/sam/fastq2bam/ok-paired/illumina-sanger_full_range_as_sanger-62.fastq
new file mode 100644
index 0000000..21e8837
--- /dev/null
+++ b/testdata/net/sf/picard/sam/fastq2bam/ok-paired/illumina-sanger_full_range_as_sanger-62.fastq
@@ -0,0 +1,4 @@
+ at FAKE0001 Original version has PHRED scores from 93 to 0 inclusive (in that order)
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG
++
+ at ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
\ No newline at end of file
diff --git a/testdata/net/sf/picard/sam/fastq2bam/ok-paired/pair1.txt b/testdata/net/sf/picard/sam/fastq2bam/ok-paired/pair1.txt
index 2842b77..3313312 100644
--- a/testdata/net/sf/picard/sam/fastq2bam/ok-paired/pair1.txt
+++ b/testdata/net/sf/picard/sam/fastq2bam/ok-paired/pair1.txt
@@ -17,4 +17,4 @@ AAAAAAAAAAAAA
@record:5/1
AAAAAAAAAAAAA
+
-1111111111111
+1111111111111
\ No newline at end of file
diff --git a/testdata/net/sf/picard/sam/fastq2bam/ok-paired/s_1_1_sequence.txt b/testdata/net/sf/picard/sam/fastq2bam/ok-paired/s_1_1_sequence.txt
new file mode 100644
index 0000000..08bdd49
--- /dev/null
+++ b/testdata/net/sf/picard/sam/fastq2bam/ok-paired/s_1_1_sequence.txt
@@ -0,0 +1,40 @@
+ at SL-XBG:1:1:4:1663#0/1
+TGGTCTTTCTGATCACAAGAANTATGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:1663#0/1
+abbaabbbbbbaaaabb\BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:661#0/1
+TAAAGAAACAATTGAGAAGTGNGATANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:661#0/1
+Z[^b````aaabbaU^VBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:33#0/1
+GTGGGCAGTCCGTAGATGTGGNGGGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:33#0/1
+`_aaaaaa_a`aaa`\`aBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:548#0/1
+ATAGAGAGGTAGAGTTTTTTTNGTGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:548#0/1
+`bbbbbabb_bbbb_bab`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:1390#0/1
+CATGTCTGCCTCTTCTGCCAGNGGTCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:1390#0/1
+aa_`^`babaaaa^baabBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:1529#0/1
+CAGTTCAGGGCCAGGCACTCCNGGCCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:1529#0/1
+``a^`a_^TS]aaaaaaaaBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:1223#0/1
+CCTGGTGTTTGCCATTCTCTCNCCTGCNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:1223#0/1
+abbaa^b`babaaaba_bbaBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:972#0/1
+TGGAACCACTGAATGGAGTCGNTCTCANGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:972#0/1
+Tbbabbbbbbbabab_[V_bBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:1877#0/1
+GCACCTGTAATCCCAGCTACTNTGGAGNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:1877#0/1
+abbbababaabaaa^aabaaBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:2003#0/1
+GGCAGATGGACAACGCCTAATNATCACNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:2003#0/1
+aaa_abbb_Za^abbbba[`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
\ No newline at end of file
diff --git a/testdata/net/sf/picard/sam/fastq2bam/ok-paired/s_1_2_sequence.txt b/testdata/net/sf/picard/sam/fastq2bam/ok-paired/s_1_2_sequence.txt
new file mode 100644
index 0000000..1179d65
--- /dev/null
+++ b/testdata/net/sf/picard/sam/fastq2bam/ok-paired/s_1_2_sequence.txt
@@ -0,0 +1,41 @@
+
+ at SL-XBG:1:1:4:1663#0/2
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:1663#0/2
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:661#0/2
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:661#0/2
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:33#0/2
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:33#0/2
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:548#0/2
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:548#0/2
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:1390#0/2
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:1390#0/2
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:1529#0/2
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:1529#0/2
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:1223#0/2
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:1223#0/2
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:972#0/2
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:972#0/2
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:1877#0/2
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:1877#0/2
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:2003#0/2
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:2003#0/2
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
\ No newline at end of file
diff --git a/testdata/net/sf/picard/sam/fastq2bam/ok-paired/s_1_sequence.txt b/testdata/net/sf/picard/sam/fastq2bam/ok-paired/s_1_sequence.txt
new file mode 100644
index 0000000..a29f542
--- /dev/null
+++ b/testdata/net/sf/picard/sam/fastq2bam/ok-paired/s_1_sequence.txt
@@ -0,0 +1,40 @@
+ at SL-XAP:1:1:0:1171#0/1
+NTGAGGAGGAATCAGATGAAGTGGAGGATAACGACAATGACTCTGAAATGGAGAGGCCTGTAAATAGAGGAGGCAG
++SL-XAP:1:1:0:1171#0/1
+DNUYUPUNUXXYWYSYYSVYVRNSWUUYYYYVTSYYXWPWYVYVYPSRTRNPLTQLUYSFSVXXBBBBBBBBBBBB
+ at SL-XAP:1:1:0:1477#0/1
+NCACTCGTTTATCCATCCTCTCGTTACTGGGTCATGTCATAAGACTGCAGCCATCTTGGAATCATAAGCTCTATCA
++SL-XAP:1:1:0:1477#0/1
+DMWYUSUWVWYUQRSUSUWSWYWVWSYYVVVWNRTWROQUWBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XAP:1:1:0:1733#0/1
+NAGAACGAGCAGTTTGGAAGTTGCTACCAATTTAATACTCAGACTGCTCTTTCTTGTAAAGAAGCTTATGTTTCAT
++SL-XAP:1:1:0:1733#0/1
+DOTWZVRUNUVQV[VQNVRNUTKTZZZXVVY[YTQVXXZZRJQODEOYYYYZBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XAP:1:1:0:1384#0/1
+NAAATTTATACTTTAAATTACCTTCACTGTTCCATCAAATGACCAAGAAAGCAGTCTTGAATTTTTCAATATTCTA
++SL-XAP:1:1:0:1384#0/1
+DP[[[[[[Z[[[[[YZZ[[[Z[[[Z[[XRX[[ZZ[ZXXUVOV[[XTPWUUMXXIXZYTOTQVYYYY[WBBBBBBBB
+ at SL-XAP:1:1:0:528#0/1
+NAGAAATAATATATATCCTATTTCTTAGTAAGCCACCTAGAACAGCAAGAGTGGCTAAAATGAGATGGTGTTCCTT
++SL-XAP:1:1:0:528#0/1
+DOUVXXXXYZ[[[YXY[[YXY[[[[YSLVXURXZZ[[[TBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XAP:1:1:1:408#0/1
+NGCCACTACGCCATGAAGATCCTCAACAAGCAGAAGGTGGTGAATATGAAGCATGTCTAGCACATACTTAACTAGA
++SL-XAP:1:1:1:408#0/1
+DMWYVYWUUQUYYTLSWSVYYYYWVWYWVPBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XAP:1:1:2:1424#0/1
+NTCAAGTTTCATTACTTTCTTAATTTATTTCCTAAATAGGCTGCCATGATGTCTTATGATCTTAAGAATTAACATT
++SL-XAP:1:1:2:1424#0/1
+DO[[VLV[[[[[[[[[[[[[[[[[[[[[[[Y[[ZZZZBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XAP:1:1:2:1419#0/1
+NGATCATAGGCAAGAGCCACCACATCGACCTAGCACTGCTTTNTAACCTGTGCTCTGACCTGCCCCTCCCAAGCAT
++SL-XAP:1:1:2:1419#0/1
+DMWWXWXWURWWURWUUWWWWWXVWSKSWWWWUWWWUKSWXNDPUWWWNEMPSWWUOPVWTOTXWVWBBBBBBBBB
+ at SL-XAP:1:1:2:1872#0/1
+NTATGTACGTAGTCTAGGCCATATGTGTTGGAGATTGAGACTAGTAGGGCTAGTCCCACCGCTGCTTCGCAGGCGG
++SL-XAP:1:1:2:1872#0/1
+DPWWUWXWRWTPUWWSPPTWUWVWSTNUUONUPTWBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XAP:1:1:2:472#0/1
+NATGACTTGTGGGACATCACAGTAGAAGTTGTCCAGTTCATTGGGCCCACAGAAAGGCAGCTGTATGACTAGTATG
++SL-XAP:1:1:2:472#0/1
+DNWVWYYWRVTSSVWVWYYYYVWUUUVSVTRTYWTRVYWVWUNFLTYWBBBBBBBBBBBBBBBBBBBBBBBBBBBB
\ No newline at end of file
diff --git a/testdata/net/sf/picard/sam/fastq2bam/ok-paired/pair1.txt b/testdata/net/sf/picard/sam/fastq2bam/permissive-format/pair1.txt
similarity index 97%
copy from testdata/net/sf/picard/sam/fastq2bam/ok-paired/pair1.txt
copy to testdata/net/sf/picard/sam/fastq2bam/permissive-format/pair1.txt
index 2842b77..6e11bc1 100644
--- a/testdata/net/sf/picard/sam/fastq2bam/ok-paired/pair1.txt
+++ b/testdata/net/sf/picard/sam/fastq2bam/permissive-format/pair1.txt
@@ -2,19 +2,24 @@
AAAAAAAAAAAAA
+
1111111111111
+
@record:2/1
AAAAAAAAAAAAA
+
1111111111111
@record:3/1
+
AAAAAAAAAAAAA
+
1111111111111
@record:4/1
AAAAAAAAAAAAA
+
+
1111111111111
@record:5/1
AAAAAAAAAAAAA
+
+
1111111111111
+
diff --git a/testdata/net/sf/picard/sam/fastq2bam/permissive-format/pair2.txt b/testdata/net/sf/picard/sam/fastq2bam/permissive-format/pair2.txt
new file mode 100644
index 0000000..e384167
--- /dev/null
+++ b/testdata/net/sf/picard/sam/fastq2bam/permissive-format/pair2.txt
@@ -0,0 +1,28 @@
+ at record:1/2
+CCCCCCCCCCCCC
++
+2222222222222
+ at record:2/2
+CCCCCCCCCCCCC
++
+2222222222222
+
+
+
+
+ at record:3/2
+CCCCCCCCCCCCC
++
+2222222222222
+ at record:4/2
+
+
+
+
+CCCCCCCCCCCCC
++
+2222222222222
+ at record:5/2
+CCCCCCCCCCCCC
++
+2222222222222
diff --git a/testdata/net/sf/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt b/testdata/net/sf/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt
new file mode 100644
index 0000000..c562875
--- /dev/null
+++ b/testdata/net/sf/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt
@@ -0,0 +1,51 @@
+ at SL-XBG:1:1:4:1663#0/1
+TGGTCTTTCTGATCACAAGAANTATGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:1663#0/1
+abbaabbbbbbaaaabb\BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+
+ at SL-XBG:1:1:4:661#0/1
+TAAAGAAACAATTGAGAAGTGNGATANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:661#0/1
+Z[^b````aaabbaU^VBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+
+ at SL-XBG:1:1:4:33#0/1
+GTGGGCAGTCCGTAGATGTGGNGGGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:33#0/1
+`_aaaaaa_a`aaa`\`aBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+
+ at SL-XBG:1:1:4:548#0/1
+ATAGAGAGGTAGAGTTTTTTTNGTGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:548#0/1
+`bbbbbabb_bbbb_bab`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+
+ at SL-XBG:1:1:4:1390#0/1
+CATGTCTGCCTCTTCTGCCAGNGGTCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:1390#0/1
+aa_`^`babaaaa^baabBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+
+ at SL-XBG:1:1:4:1529#0/1
+CAGTTCAGGGCCAGGCACTCCNGGCCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:1529#0/1
+``a^`a_^TS]aaaaaaaaBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+
+ at SL-XBG:1:1:4:1223#0/1
+CCTGGTGTTTGCCATTCTCTCNCCTGCNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
++SL-XBG:1:1:4:1223#0/1
+abbaa^b`babaaaba_bbaBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:972#0/1
+
+TGGAACCACTGAATGGAGTCGNTCTCANGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:972#0/1
+Tbbabbbbbbbabab_[V_bBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:1877#0/1
+GCACCTGTAATCCCAGCTACTNTGGAGNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
++SL-XBG:1:1:4:1877#0/1
+abbbababaabaaa^aabaaBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:2003#0/1
+GGCAGATGGACAACGCCTAATNATCACNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
+
++SL-XBG:1:1:4:2003#0/1
+aaa_abbb_Za^abbbba[`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
diff --git a/testdata/net/sf/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt b/testdata/net/sf/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt
new file mode 100644
index 0000000..a9733bb
--- /dev/null
+++ b/testdata/net/sf/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt
@@ -0,0 +1,41 @@
+
+ at SL-XBG:1:1:4:1663#0/2
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:1663#0/2
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:661#0/2
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:661#0/2
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:33#0/2
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:33#0/2
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:548#0/2
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:548#0/2
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:1390#0/2
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:1390#0/2
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:1529#0/2
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:1529#0/2
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:1223#0/2
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:1223#0/2
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:972#0/2
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:972#0/2
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:1877#0/2
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:1877#0/2
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XBG:1:1:4:2003#0/2
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++SL-XBG:1:1:4:2003#0/2
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
diff --git a/testdata/net/sf/picard/sam/fastq2bam/permissive-format/s_1_sequence.txt b/testdata/net/sf/picard/sam/fastq2bam/permissive-format/s_1_sequence.txt
new file mode 100644
index 0000000..092c393
--- /dev/null
+++ b/testdata/net/sf/picard/sam/fastq2bam/permissive-format/s_1_sequence.txt
@@ -0,0 +1,62 @@
+ at SL-XAP:1:1:0:1171#0/1
+NTGAGGAGGAATCAGATGAAGTGGAGGATAACGACAATGACTCTGAAATGGAGAGGCCTGTAAATAGAGGAGGCAG
++SL-XAP:1:1:0:1171#0/1
+DNUYUPUNUXXYWYSYYSVYVRNSWUUYYYYVTSYYXWPWYVYVYPSRTRNPLTQLUYSFSVXXBBBBBBBBBBBB
+
+
+
+ at SL-XAP:1:1:0:1477#0/1
+NCACTCGTTTATCCATCCTCTCGTTACTGGGTCATGTCATAAGACTGCAGCCATCTTGGAATCATAAGCTCTATCA
++SL-XAP:1:1:0:1477#0/1
+DMWYUSUWVWYUQRSUSUWSWYWVWSYYVVVWNRTWROQUWBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+
+ at SL-XAP:1:1:0:1733#0/1
+NAGAACGAGCAGTTTGGAAGTTGCTACCAATTTAATACTCAGACTGCTCTTTCTTGTAAAGAAGCTTATGTTTCAT
++SL-XAP:1:1:0:1733#0/1
+DOTWZVRUNUVQV[VQNVRNUTKTZZZXVVY[YTQVXXZZRJQODEOYYYYZBBBBBBBBBBBBBBBBBBBBBBBB
+
+
+
+
+
+
+
+ at SL-XAP:1:1:0:1384#0/1
+NAAATTTATACTTTAAATTACCTTCACTGTTCCATCAAATGACCAAGAAAGCAGTCTTGAATTTTTCAATATTCTA
++SL-XAP:1:1:0:1384#0/1
+
+
+DP[[[[[[Z[[[[[YZZ[[[Z[[[Z[[XRX[[ZZ[ZXXUVOV[[XTPWUUMXXIXZYTOTQVYYYY[WBBBBBBBB
+ at SL-XAP:1:1:0:528#0/1
+NAGAAATAATATATATCCTATTTCTTAGTAAGCCACCTAGAACAGCAAGAGTGGCTAAAATGAGATGGTGTTCCTT
++SL-XAP:1:1:0:528#0/1
+
+
+DOUVXXXXYZ[[[YXY[[YXY[[[[YSLVXURXZZ[[[TBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XAP:1:1:1:408#0/1
+NGCCACTACGCCATGAAGATCCTCAACAAGCAGAAGGTGGTGAATATGAAGCATGTCTAGCACATACTTAACTAGA
++SL-XAP:1:1:1:408#0/1
+
+
+
+
+DMWYVYWUUQUYYTLSWSVYYYYWVWYWVPBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XAP:1:1:2:1424#0/1
+NTCAAGTTTCATTACTTTCTTAATTTATTTCCTAAATAGGCTGCCATGATGTCTTATGATCTTAAGAATTAACATT
++SL-XAP:1:1:2:1424#0/1
+DO[[VLV[[[[[[[[[[[[[[[[[[[[[[[Y[[ZZZZBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XAP:1:1:2:1419#0/1
+NGATCATAGGCAAGAGCCACCACATCGACCTAGCACTGCTTTNTAACCTGTGCTCTGACCTGCCCCTCCCAAGCAT
++SL-XAP:1:1:2:1419#0/1
+
+
+
+DMWWXWXWURWWURWUUWWWWWXVWSKSWWWWUWWWUKSWXNDPUWWWNEMPSWWUOPVWTOTXWVWBBBBBBBBB
+ at SL-XAP:1:1:2:1872#0/1
+NTATGTACGTAGTCTAGGCCATATGTGTTGGAGATTGAGACTAGTAGGGCTAGTCCCACCGCTGCTTCGCAGGCGG
++SL-XAP:1:1:2:1872#0/1
+DPWWUWXWRWTPUWWSPPTWUWVWSTNUUONUPTWBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ at SL-XAP:1:1:2:472#0/1
+NATGACTTGTGGGACATCACAGTAGAAGTTGTCCAGTTCATTGGGCCCACAGAAAGGCAGCTGTATGACTAGTATG
++SL-XAP:1:1:2:472#0/1
+DNWVWYYWRVTSSVWVWYYYYVWUUUVSVTRTYWTRVYWVWUNFLTYWBBBBBBBBBBBBBBBBBBBBBBBBBBBB
--
Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/picard-tools.git
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