1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
|
Description: using the correct SamReader api
Author: Pierre Gruet <pgt@debian.org>
Origin: https://sources.debian.org/src/fastqc/0.11.9+dfsg-4/debian/patches/htsjdk-api.patch
Forwarded: not-needed
Last-Update: 2020-11-06
--- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMComparisonMode.java
+++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMComparisonMode.java
@@ -32,9 +32,7 @@
import org.campagnelab.goby.util.dynoptions.RegisterThis;
import htsjdk.samtools.ValidationStringency;
import it.unimi.dsi.logging.ProgressLogger;
-import htsjdk.samtools.SAMFileReader;
-import htsjdk.samtools.SAMRecord;
-import htsjdk.samtools.SAMRecordIterator;
+import htsjdk.samtools.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -284,12 +282,15 @@
}
System.out.println("Comparing source bam and destination bam");
- final SAMFileReader sourceParser = new SAMFileReader(new FileInputStream(sourceBamFile));
- final SAMFileReader destParser = new SAMFileReader(new FileInputStream(destBamFile));
+ final SamInputResource sirSource = SamInputResource.of(new FileInputStream(sourceBamFile));
+ final SamReaderFactory srfSource = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+ final SamInputResource sirDest = SamInputResource.of(new FileInputStream(destBamFile));
+ final SamReaderFactory srfDest = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+
+ final SamReader sourceParser = srfSource.open(sirSource);
+ final SamReader destParser = srfDest.open(sirDest);
// We need to set the validation to silent because an incomplete file (if the source isn't the entire file)
// we can see errors that wouldn't exist in a real conversion.
- sourceParser.setValidationStringency(ValidationStringency.SILENT);
- destParser.setValidationStringency(ValidationStringency.SILENT);
final SAMRecordIterator sourceIterator = sourceParser.iterator();
final SAMRecordIterator destIterator = destParser.iterator();
AlignmentReaderImpl gobyReader = null;
--- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMToCompactMode.java
+++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMToCompactMode.java
@@ -242,10 +242,11 @@
final ProgressLogger progress = new ProgressLogger(LOG);
progress.displayFreeMemory = true;
// the following is required to set validation to SILENT before loading the header (done in the SAMFileReader constructor)
- SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
-
final InputStream stream = "-".equals(inputFile) ? System.in : new FileInputStream(inputFile);
- final SAMFileReader parser = new SAMFileReader(stream);
+ final SamInputResource sir = SamInputResource.of(stream);
+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+
+ final SamReader parser = srf.open(sir);
// transfer read groups to Goby header:
final SAMFileHeader samHeader = parser.getFileHeader();
final IndexedIdentifier readGroups = new IndexedIdentifier();
--- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMToCompactOldMode.java
+++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMToCompactOldMode.java
@@ -128,8 +128,10 @@
final int[] readLengths = createReadLengthArray();
final ProgressLogger progress = new ProgressLogger(LOG);
- final SAMFileReader parser = new SAMFileReader(new File(inputFile));
- parser.setValidationStringency(ValidationStringency.SILENT);
+ final SamInputResource sir = SamInputResource.of(new File(inputFile));
+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+
+ final SamReader parser = srf.open(sir);
progress.start();
--- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMToCompactSamHelperMode.java
+++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMToCompactSamHelperMode.java
@@ -231,10 +231,11 @@
final ProgressLogger progress = new ProgressLogger(LOG);
progress.displayFreeMemory = true;
// the following is required to set validation to SILENT before loading the header (done in the SAMFileReader constructor)
- SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
-
final InputStream stream = "-".equals(inputFile) ? System.in : new FileInputStream(inputFile);
- final SAMFileReader parser = new SAMFileReader(stream);
+ final SamInputResource sir = SamInputResource.of(stream);
+ SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+
+ final SamReader parser = srf.open(sir);
// transfer read groups to Goby header:
final SAMFileHeader samHeader = parser.getFileHeader();
final IndexedIdentifier readGroups = new IndexedIdentifier();
@@ -827,4 +828,4 @@
}
-}
\ No newline at end of file
+}
--- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/SamExtractReadsMode.java
+++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/SamExtractReadsMode.java
@@ -30,8 +30,7 @@
import htsjdk.samtools.ValidationStringency;
import it.unimi.dsi.lang.MutableString;
import it.unimi.dsi.logging.ProgressLogger;
-import htsjdk.samtools.SAMFileReader;
-import htsjdk.samtools.SAMRecord;
+import htsjdk.samtools.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -142,8 +141,10 @@
try {
final ProgressLogger progress = new ProgressLogger(LOG);
// the following is required to set validation to SILENT before loading the header (done in the SAMFileReader constructor)
- SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
- final SAMFileReader parser = new SAMFileReader(new File(inputFilename), null);
+ final SamInputResource sir = SamInputResource.of(new File(inputFilename));
+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+
+ final SamReader parser = srf.open(sir);
progress.start();
--- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/SampleQualityScoresMode.java
+++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/SampleQualityScoresMode.java
@@ -29,8 +29,7 @@
import it.unimi.dsi.fastutil.ints.IntArrayList;
import it.unimi.dsi.fastutil.ints.IntList;
import it.unimi.dsi.lang.MutableString;
-import htsjdk.samtools.SAMFileReader;
-import htsjdk.samtools.SAMRecord;
+import htsjdk.samtools.*;
import org.apache.commons.lang.ArrayUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@@ -350,8 +349,10 @@
private int processSamReadsFile(final String inputFilename) throws IOException {
// Create directory for output file if it doesn't already exist
int i = 0;
- SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFilename));
+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFilename));
+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+
+ final SamReader parser = srf.open(sir);
for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {
final String quality = samRecord.getBaseQualityString();
if (quality != null && quality.length() != 0) {
--- a/goby-distribution/src/test/java/org/campagnelab/goby/readers/sam/RoundTripAlignment.java
+++ b/goby-distribution/src/test/java/org/campagnelab/goby/readers/sam/RoundTripAlignment.java
@@ -32,9 +32,7 @@
import org.campagnelab.goby.reads.RandomAccessSequenceTestSupport;
import htsjdk.samtools.ValidationStringency;
import it.unimi.dsi.logging.ProgressLogger;
-import htsjdk.samtools.SAMFileReader;
-import htsjdk.samtools.SAMRecord;
-import htsjdk.samtools.SAMRecordIterator;
+import htsjdk.samtools.*;
import org.apache.commons.io.FilenameUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -172,12 +170,15 @@
}
LOG.info("Comparing source bam and destination bam");
- final SAMFileReader sourceParser = new SAMFileReader(new FileInputStream(sourceBamFilename));
- final SAMFileReader destParser = new SAMFileReader(new FileInputStream(destBamFilename));
+ final SamInputResource sirSource = SamInputResource.of(new FileInputStream(sourceBamFilename));
+ final SamReaderFactory srfSource = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+ final SamInputResource sirDest = SamInputResource.of(new FileInputStream(destBamFilename));
+ final SamReaderFactory srfDest = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+
+ final SamReader sourceParser = srfSource.open(sirSource);
+ final SamReader destParser = srfDest.open(sirDest);
// We need to set the validation to silent because an incomplete file (if the source isn't the entire file)
// we can see errors that wouldn't exist in a real conversion.
- sourceParser.setValidationStringency(ValidationStringency.SILENT);
- destParser.setValidationStringency(ValidationStringency.SILENT);
final SAMRecordIterator sourceIterator = sourceParser.iterator();
final SAMRecordIterator destIterator = destParser.iterator();
AlignmentReaderImpl gobyReader = null;
--- a/goby-distribution/src/test/java/org/campagnelab/goby/readers/sam/TestSamRecordParser.java
+++ b/goby-distribution/src/test/java/org/campagnelab/goby/readers/sam/TestSamRecordParser.java
@@ -25,8 +25,7 @@
import htsjdk.samtools.ValidationStringency;
import it.unimi.dsi.lang.MutableString;
import junit.framework.Assert;
-import htsjdk.samtools.SAMFileReader;
-import htsjdk.samtools.SAMRecord;
+import htsjdk.samtools.*;
import org.apache.commons.io.FilenameUtils;
import org.slf4j.Logger;
import org.junit.BeforeClass;
@@ -65,8 +64,10 @@
// like 9 no genome
public void testSamToCompactTrickCase9NoGenome() throws IOException {
final String inputFile = "test-data/splicedsamhelper/tricky-spliced-9.sam";
- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));
- parser.setValidationStringency(ValidationStringency.SILENT);
+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));
+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+
+ final SamReader parser = srf.open(sir);
final SamRecordParser recordParser = new SamRecordParser();
for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {
@@ -84,8 +85,10 @@
public void testSamToCompactTrickCase10NoGenome() throws IOException {
final String inputFile = "test-data/splicedsamhelper/tricky-spliced-10.sam";
- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));
- parser.setValidationStringency(ValidationStringency.SILENT);
+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));
+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+
+ final SamReader parser = srf.open(sir);
final SamRecordParser recordParser = new SamRecordParser();
for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {
@@ -103,8 +106,10 @@
@Test
public void testSamToCompactTrickCase11() throws IOException {
final String inputFile = "test-data/splicedsamhelper/tricky-spliced-11.sam";
- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));
- parser.setValidationStringency(ValidationStringency.SILENT);
+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));
+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+
+ final SamReader parser = srf.open(sir);
final SamRecordParser recordParser = new SamRecordParser();
for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {
@@ -121,8 +126,11 @@
public void testSamToCompactTrickCase12NoGenome() throws IOException {
final String inputFile = "test-data/splicedsamhelper/tricky-spliced-12.sam";
- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));
final SamRecordParser recordParser = new SamRecordParser();
+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));
+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+
+ final SamReader parser = srf.open(sir);
for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {
final GobySamRecord gobySamRecord = recordParser.processRead(samRecord);
@@ -146,7 +154,10 @@
public void testSamToCompactTrickCase13NoGenomeSoftClips() throws IOException {
final String inputFile = "test-data/splicedsamhelper/tricky-spliced-13.sam";
- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));
+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));
+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+
+ final SamReader parser = srf.open(sir);
final SamRecordParser recordParser = new SamRecordParser();
for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {
@@ -179,8 +190,10 @@
public void testSamToCompactTrickCase13SoftClipsWithGenome() throws IOException {
final String inputFile = "test-data/splicedsamhelper/tricky-spliced-14.sam";
- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));
- parser.setValidationStringency(ValidationStringency.SILENT);
+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));
+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+
+ final SamReader parser = srf.open(sir);
final SamRecordParser recordParser = new SamRecordParser();
@@ -209,7 +222,10 @@
public void testSamToCompactTrickCase15NoGenomeThreeSplice() throws IOException {
final String inputFile = "test-data/splicedsamhelper/tricky-spliced-15.sam";
- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));
+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));
+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+
+ final SamReader parser = srf.open(sir);
final SamRecordParser recordParser = new SamRecordParser();
for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {
final GobySamRecord gobySamRecord = recordParser.processRead(samRecord);
@@ -247,8 +263,10 @@
public void testSamToCompactTrickCase16() throws IOException {
final String inputFile = "test-data/splicedsamhelper/tricky-spliced-16.sam";
- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));
- parser.setValidationStringency(ValidationStringency.SILENT);
+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));
+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+
+ final SamReader parser = srf.open(sir);
final SamRecordParser recordParser = new SamRecordParser();
for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {
final GobySamRecord gobySamRecord = recordParser.processRead(samRecord);
@@ -337,8 +355,10 @@
@Test
public void testSamToCompactTrickCase17() throws IOException {
final String inputFile = "test-data/splicedsamhelper/tricky-spliced-17.sam";
- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));
- parser.setValidationStringency(ValidationStringency.SILENT);
+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));
+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+
+ final SamReader parser = srf.open(sir);
final SamRecordParser recordParser = new SamRecordParser();
for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {
final GobySamRecord gobySamRecord = recordParser.processRead(samRecord);
@@ -422,8 +442,10 @@
@Test
public void testDelNonSplice1() throws IOException {
final String inputFile = "test-data/splicedsamhelper/del-nonsplice-1.sam";
- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));
- parser.setValidationStringency(ValidationStringency.SILENT);
+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));
+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+
+ final SamReader parser = srf.open(sir);
final SamRecordParser recordParser = new SamRecordParser();
for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {
final GobySamRecord gobySamRecord = recordParser.processRead(samRecord);
@@ -453,8 +475,10 @@
@Test
public void testLeftPadding1() throws IOException {
final String inputFile = "test-data/splicedsamhelper/leftpad-nosplice-1.sam";
- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));
- parser.setValidationStringency(ValidationStringency.SILENT);
+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));
+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+
+ final SamReader parser = srf.open(sir);
final SamRecordParser recordParser = new SamRecordParser();
for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {
final GobySamRecord gobySamRecord = recordParser.processRead(samRecord);
@@ -491,8 +515,10 @@
@Test
public void testSeqVarReads() throws IOException {
final String inputFile = "test-data/seq-var-test/seq-var-reads-gsnap.sam";
- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));
- parser.setValidationStringency(ValidationStringency.SILENT);
+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));
+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+
+ final SamReader parser = srf.open(sir);
final SamRecordParser recordParser = new SamRecordParser();
final PositionToBasesMap<PerQueryAlignmentData> seqvarDataMap = TestIteratedSortedAlignment2.readSeqVarFile(
"test-data/seq-var-test/seq-var-reads-gsnap.seqvar");
|
