| /dports/biology/pbbam/pbbam-0.18.0/tests/src/ |
| H A D | test_BamRecordImplVariableData.cpp | 60 BamRecordImpl bam; in TEST() local
81 bam.Tags(tags); in TEST()
109 bam.Tags(tags); in TEST()
138 bam.Tags(tags); in TEST()
158 bam.Tags(tags); in TEST()
248 bam.Tags(tags); in TEST()
278 bam.Tags(tags); in TEST()
322 bam.Tags(tags); in TEST()
353 bam.Tags(tags); in TEST()
384 bam.Tags(tags); in TEST()
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| H A D | test_BamRecordImplTags.cpp | 26 BamRecordImpl bam; in TEST() local
27 bam.Tags(tags); in TEST()
34 EXPECT_FALSE(bam.HasTag("")); in TEST()
53 BamRecordImpl bam; in TEST() local
54 bam.Tags(tags); in TEST()
90 BamRecordImpl bam; in TEST() local
91 bam.Tags(tags); in TEST()
126 BamRecordImpl bam; in TEST() local
127 bam.Tags(tags); in TEST()
161 BamRecordImpl bam; in TEST() local
[all …]
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| H A D | test_BamRecordBuilder.cpp | 43 static void CheckRawData(const BamRecord& bam) { CheckRawData(bam.Impl()); } in CheckRawData() argument
50 BamRecord bam = builder.Build(); in TEST() local
77 EXPECT_EQ(0, bam.Impl().Bin()); in TEST()
78 EXPECT_EQ(0, bam.Impl().Flag()); in TEST()
79 EXPECT_EQ(0, bam.Impl().InsertSize()); in TEST()
83 EXPECT_EQ(0, bam.Impl().Position()); in TEST()
90 EXPECT_TRUE(bam.Impl().IsMapped()); in TEST()
93 EXPECT_FALSE(bam.Impl().IsPaired()); in TEST()
128 BamRecord bam = builder.Build(); in TEST() local
159 EXPECT_EQ(42, bam.Impl().Bin()); in TEST()
[all …]
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| H A D | test_BamRecordImplCore.cpp | 37 BamRecordImpl bam; in CreateBamImpl() local
38 bam.Bin(42); in CreateBamImpl()
39 bam.Flag(42); in CreateBamImpl()
40 bam.InsertSize(42); in CreateBamImpl()
41 bam.MapQuality(42); in CreateBamImpl()
44 bam.Position(42); in CreateBamImpl()
45 bam.ReferenceId(42); in CreateBamImpl()
52 bam.Tags(tags); in CreateBamImpl()
54 return bam; in CreateBamImpl()
178 bam.Bin(42); in TEST()
[all …]
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| /dports/emulators/libretro-vice/vice-libretro-5725415/vice/src/vdrive/ |
| H A D | vdrive-bam.c | 316 uint8_t *bam = vdrive->bam; in vdrive_bam_get_track_entry() local
345 if (track >= bam[(i * 0x100) + 4] && track < bam[(i * 0x100) + 5]) { in vdrive_bam_get_track_entry()
356 if (track >= bam[(i * 0x100) + 4] && track < bam[(i * 0x100) + 5]) { in vdrive_bam_get_track_entry()
443 uint8_t *bam = vdrive->bam; in vdrive_bam_clear_all() local
498 vdrive->bam[2] = 65; in vdrive_bam_create_empty_bam()
501 vdrive->bam[3] = 0x80; in vdrive_bam_create_empty_bam()
523 vdrive->bam[0x02] = 68; in vdrive_bam_create_empty_bam()
527 vdrive->bam[0x200] = 0; in vdrive_bam_create_empty_bam()
549 vdrive->bam[0] = 38; in vdrive_bam_create_empty_bam()
550 vdrive->bam[1] = 0; in vdrive_bam_create_empty_bam()
[all …]
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| /dports/biology/bamutil/bamUtil-1.0.15/test/ |
| H A D | testRevert.sh | 5 …bam revert --in testFiles/testRevert.sam --out results/revertSam.bam --cigar --qual --noph 2> resu…
11 …bam revert --in testFiles/testRevert.sam --out results/revertCigarSam.bam --cigar --noph 2> result…
17 …bam revert --in testFiles/testRevert.sam --out results/revertQualSam.bam --qual --noph 2> results/…
23 …bam revert --in testFiles/testRevert.sam --out results/revertKeepTagsSam.bam --qual --cigar --keep…
29 …bam revert --in testFiles/testRevert.bam --out results/revertBam.bam --cigar --qual --noph 2> resu…
35 …bam revert --in testFiles/testRevert.bam --out results/revertCigarBam.bam --cigar --noph 2> result…
41 …bam revert --in testFiles/testRevert.bam --out results/revertQualBam.bam --qual --noph 2> results/…
47 …bam revert --in testFiles/testRevert.bam --out results/revertKeepTagsBam.bam --qual --cigar --keep…
57 …bam revert --in testFiles/testRevert.sam --out results/revertRmBQSam.bam --qual --cigar --rmBQ --n…
60 …bam revert --in testFiles/testRevert.bam --out results/revertRmBQBam.bam --qual --cigar --rmBQ --n…
[all …]
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| H A D | testSeq.sh | 13 ../bin/bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.bam --out re…
15 ../bin/bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.bam --out re…
17 ../bin/bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.bam --out re…
22 …bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.sam --out results/…
24 …bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.sam --out results/…
26 …bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.sam --out results/…
28 …bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.sam --out results/…
31 …bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.bam --out results/…
33 …bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.bam --out results/…
35 …bam convert --refFile testFilesLibBam/chr1_partial.fa --in testFiles/testFilter.bam --out results/…
[all …]
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| H A D | samTests.sh | 10 ../bin/bam validate --in testFiles/testInvalid1.sam --v --noph 2> results/validateInvalid1.txt
17 ../bin/bam validate --in testFiles/testInvalid2.sam --v --noph 2> results/validateInvalid2.txt
24 ../bin/bam validate --in testFiles/testInvalid2.bam --v --noph 2> results/validateInvalid2Bam.txt
44 ../bin/bam convert --params --in testFilesLibBam/testBam.bam --out results/convertBam.sam --noph 2>…
51 ../bin/bam convert --in testFilesLibBam/testBam.bam --out - --noph > results/convertBamStdout.sam 2…
58 …bam convert --in testFilesLibBam/testSam.sam --out results/convertSam.bam --noph 2> results/conver…
65 …bam convert --in testFilesLibBam/testSam.sam --out -.bam --noph > results/convertSamStdout.bam 2> …
72 …bam convert --in testFilesLibBam/testSam.sam --out -.bam --noph > results/convertSamStdout.bam 2> …
79 ../bin/bam convert --in testFilesLibBam/testSam.sam --out -.bam --noph 2> results/convertSamStdout…
86 …bam convert --in testFilesLibBam/testBam.bam --out -.sam --noph 2> results/convertBamStdoutSamPip…
[all …]
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| H A D | testStats.sh | 15 ../bin/bam stats --basic --in testFilesLibBam/testBam.bam --qual --noph 2> results/qualStats2.txt \
18 ../bin/bam stats --basic --in testFilesLibBam/sortedBam.bam --noph 2> results/sortedStats.txt \
21 ../bin/bam stats --in testFilesLibBam/sortedBam.bam --qual --noph 2> results/sortedQualStats.txt \
24 ../bin/bam stats --basic --in testFilesLibBam/sortedBam.bam --unmapped --noph 2> results/unmappedSt…
27 ../bin/bam stats --basic --in testFilesLibBam/sortedBam.bam --unmapped --qual --noph 2> results/unm…
30 ../bin/bam stats --basic --in testFilesLibBam/sortedBam.bam --unmapped --qual --bamIndex testFilesL…
36 ../bin/bam stats --in testFilesLibBam/sortedBam.bam --unmapped --qual --maxNumReads 1 --noph 2> res…
39 ../bin/bam stats --basic --in testFiles/testStatsQual.bam --qual --noph 2> results/qualStatsQual.tx…
54 ../bin/bam stats --basic --in testFiles/testStatsQual.bam --excludeFlags 12 --qual --noph 2> result…
57 ../bin/bam stats --basic --in testFiles/testStatsQual.bam --requiredFlags 12 --qual --noph 2> resul…
[all …]
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| H A D | writeRegion.sh | 3 ../bin/bam writeRegion --noph --in testFilesLibBam/sortedBam.bam --out results/regionNeg1.bam --re…
4 && diff results/regionNeg1.bam expected/regionNeg1.bam && diff results/regionNeg1.txt expected/regi…
6 ../bin/bam writeRegion --noph --in testFilesLibBam/sortedBam.bam --out results/regionRead.sam --rea…
15 ../bin/bam writeRegion --noph --in testFilesLibBam/sortedBam.bam --out results/regionRead4.sam --re…
21 ../bin/bam writeRegion --noph --in testFilesLibBam/sortedBam.bam --out results/regionRead6.sam --re…
27 ../bin/bam writeRegion --noph --in testFilesLibBam/sortedBam.bam --out results/regionRead8.sam --be…
30 ../bin/bam writeRegion --noph --in testFilesLibBam/sortedBam.bam --out results/regionRead9.sam --be…
36 ../bin/bam writeRegion --noph --in testFilesLibBam/sortedBam.bam --out results/regionRead11.sam --b…
42 ../bin/bam writeRegion --noph --in testFilesLibBam/sortedBam.bam --out results/regionReadRnFile.sam…
45 ../bin/bam writeRegion --noph --in testFilesLibBam/sortedBam.bam --out results/regionReadRnFile1.sa…
[all …]
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| H A D | testSqueeze.sh | 4 ../bin/bam squeeze --in testFiles/squeeze.sam --out results/squeezeSam.sam --noph 2> results/squeez…
12 ../bin/bam squeeze --in testFiles/squeeze.bam --out results/squeezeBam.bam --noph 2> results/squeez…
13 diff results/squeezeBam.bam expected/squeeze.bam && diff results/squeezeBam2Bam.log expected/squeez…
21 ../bin/bam squeeze --in testFiles/squeeze.sam --out results/squeezeSam.bam --noph 2> results/squeez…
22 diff results/squeezeSam.bam expected/squeeze.bam && diff results/squeezeSam2Bam.log expected/squeez…
29 ../bin/bam squeeze --in testFiles/squeeze.bam --out results/squeezeBam.sam --noph 2> results/squeez…
86 ../bin/bam squeeze --in testFilesLibBam/testBam.bam --out results/squeezeReadName.bam --readName re…
87 diff results/squeezeReadName.bam expected/squeezeReadName.bam && diff results/squeezeReadNameBam.lo…
102 ../bin/bam squeeze --in testFilesLibBam/testBam.bam --out results/squeezeReadNameUnsorted.sam --sre…
110 ../bin/bam squeeze --in testFiles/sortedReadName.bam --out results/squeezeReadNameSorted.bam --srea…
[all …]
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| /dports/games/edge/Edge-1.35-source/epi/ |
| H A D | math_angle.h | 33 u32_t bam;
41 angle_c(const angle_c& rhs) : bam(rhs.bam) { } in angle_c()
171 return angle_c(bam + rhs.bam, false);
176 return angle_c(bam - rhs.bam, false);
196 return (bam >= other.bam) ? angle_c(bam - other.bam, false) : in Dist()
197 angle_c(other.bam - bam, false); in Dist()
202 bam += rhs.bam;
208 bam -= rhs.bam;
214 bam *= factor;
220 bam /= factor;
[all …]
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| /dports/emulators/vice/vice-3.5/src/vdrive/ |
| H A D | vdrive-bam.c | 501 uint8_t *bam = vdrive->bam; in vdrive_bam_get_track_entry() local
531 if (track >= bam[(i * 0x100) + 4] && track < bam[(i * 0x100) + 5]) { in vdrive_bam_get_track_entry()
542 if (track >= bam[(i * 0x100) + 4] && track < bam[(i * 0x100) + 5]) { in vdrive_bam_get_track_entry()
557 if (track >= bam[(i * 0x100) + 4] && track < bam[(i * 0x100) + 5]) { in vdrive_bam_get_track_entry()
679 uint8_t *bam = vdrive->bam; in vdrive_bam_clear_all() local
753 vdrive->bam[2] = 65; in vdrive_bam_create_empty_bam()
756 vdrive->bam[3] = 0x80; in vdrive_bam_create_empty_bam()
778 vdrive->bam[0x02] = 68; in vdrive_bam_create_empty_bam()
782 vdrive->bam[0x200] = 0; in vdrive_bam_create_empty_bam()
806 vdrive->bam[2] = 67; in vdrive_bam_create_empty_bam()
[all …]
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| /dports/biology/seqan1/seqan-1.3.1/lib/samtools/examples/ |
| H A D | Makefile | 2 ex1.glf ex1.pileup.gz ex1.bam.bai ex1f-rmduppe.bam ex1f-rmdupse.bam ex1.glfview.gz ex1.bcf calDepth
7 ex1.bam:ex1.sam.gz ex1.fa.fai
9 ex1.bam.bai:ex1.bam
10 ../samtools index ex1.bam
13 ex1.glf:ex1.bam ex1.fa
17 ex1a.bam:ex1.bam
19 ex1b.bam:ex1.bam
23 ex1f.bam:ex1.bam ex1a.bam ex1b.bam ex1f.rg
24 ../samtools merge -rh ex1f.rg $@ ex1.bam ex1a.bam ex1b.bam
25 ex1f-rmduppe.bam:ex1f.bam
[all …]
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| /dports/biology/bamutil/bamUtil-1.0.15/libStatGen/bam/test/ |
| H A D | test.sh | 10 diff $expected/testEqWithBases.bam results/outSamEqBases.bam && \
11 diff $expected/testEqWithEq.bam results/outSamEqEquals.bam && \
12 diff $expected/testEqWithOrig.bam results/outSamEqOrig.bam && \
14 diff $expected/updateTag.bam results/updateTagFromSam.bam && \
16 diff $expected/addedTagToSam.bam results/addedTagToSam.bam && \
19 diff $expected/testShift.bam results/testShiftFromSam.bam && \
27 diff $expected/testEqWithEq.bam results/outSamEqEquals.bam && \
28 diff $expected/testEqWithOrig.bam results/outSamEqOrig.bam && \
37 diff $expected/updateTag.bam results/updateTagFromBam.bam && \
38 diff $expected/updateTag.bam results/updateTagFromSam.bam && \
[all …]
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| /dports/biology/bedtools/bedtools2-2.30.0/src/bamToBed/ |
| H A D | bamToBed.cpp | 297 BamAlignment bam; in ConvertBamToBed() local
384 if (bam.GetTag(tag, uTagValue)) in PrintTag()
408 string name = bam.Name; in PrintBed()
469 if (!bam.GetTag("X0", x0) && !bam.GetTag("X1", x1)) { in PrintBed()
540 string name = bam.Name; in PrintBed12()
556 << bam.Position << "\t" in PrintBed12()
564 << bam.Position << "\t" in PrintBed12()
696 if ( (bam.RefID == bam.MateRefID) && (bam.InsertSize > 0) ) { in bamtobed_IsCorrectMappingForBEDPE()
699 else if ( (bam.RefID == bam.MateRefID) && in bamtobed_IsCorrectMappingForBEDPE()
701 bam.IsFirstMate() ) in bamtobed_IsCorrectMappingForBEDPE()
[all …]
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| /dports/biology/samtools/samtools-1.14/test/mpileup/ |
| H A D | depth.reg | 17 INIT x $samtools index xx#depth1.bam
18 INIT x $samtools index xx#depth2.bam
27 P d1_12.out $samtools depth -r xx:5-16 xx#depth1.bam xx#depth2.bam
29 P d2_12r.out $samtools depth -r xx:8-13 xx#depth1.bam xx#depth2.bam
33 P d3_12r1a.out $samtools depth -a -r xx:5-16 xx#depth1.bam xx#depth2.bam
34 P d3_12r1a.out $samtools depth -a -b xx.bed xx#depth1.bam xx#depth2.bam
35 P d3_12r2a.out $samtools depth -a -r xx:8-13 xx#depth1.bam xx#depth2.bam
36 P d3_12r2a.out $samtools depth -a -b xx.bed2 xx#depth1.bam xx#depth2.bam
40 P d4_12.out $samtools depth -a -a xx#depth1.bam xx#depth2.bam
41 P d4_12r.out $samtools depth -a -a -r xx:5-16 xx#depth1.bam xx#depth2.bam
[all …]
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| /dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-bam/ |
| H A D | Makefile.libs | 36 ngs-bam \
37 ngs-bam-c++
52 ngs-bam: $(LIBDIR) $(OBJDIR) $(LIBDIR)/$(LPFX)ngs-bam.$(SHLX)
54 ngs-bam-c++: $(LIBDIR) $(LIBDIR)/$(LPFX)ngs-bam-c++-static.$(LIBX)
56 $(LIBDIR)/$(LPFX)ngs-bam-c++-static.$(LIBX): $(LIBDIR)/$(LPFX)ngs-bam-c++.$(LIBX)
60 runtests: ngs-bam ngs-bam-c++
70 bam \
71 ngs-bam
92 $(LIBDIR)/$(LPFX)ngs-bam.$(MAJVERS_SHLX): $(LIBDIR)/$(LPFX)ngs-bam.$(VERSION_SHLX)
96 $(LIBDIR)/$(LPFX)ngs-bam.$(SHLX): $(LIBDIR)/$(LPFX)ngs-bam.$(MAJVERS_SHLX)
[all …]
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| /dports/biology/ncbi-vdb/ngs-2.11.0/ngs-bam/ |
| H A D | Makefile.libs | 36 ngs-bam \
37 ngs-bam-c++
52 ngs-bam: $(LIBDIR) $(OBJDIR) $(LIBDIR)/$(LPFX)ngs-bam.$(SHLX)
54 ngs-bam-c++: $(LIBDIR) $(LIBDIR)/$(LPFX)ngs-bam-c++-static.$(LIBX)
56 $(LIBDIR)/$(LPFX)ngs-bam-c++-static.$(LIBX): $(LIBDIR)/$(LPFX)ngs-bam-c++.$(LIBX)
60 runtests: ngs-bam ngs-bam-c++
70 bam \
71 ngs-bam
92 $(LIBDIR)/$(LPFX)ngs-bam.$(MAJVERS_SHLX): $(LIBDIR)/$(LPFX)ngs-bam.$(VERSION_SHLX)
96 $(LIBDIR)/$(LPFX)ngs-bam.$(SHLX): $(LIBDIR)/$(LPFX)ngs-bam.$(MAJVERS_SHLX)
[all …]
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| /dports/biology/ngs-sdk/ngs-2.11.1/ngs-bam/ |
| H A D | Makefile.libs | 36 ngs-bam \
37 ngs-bam-c++
52 ngs-bam: $(LIBDIR) $(OBJDIR) $(LIBDIR)/$(LPFX)ngs-bam.$(SHLX)
54 ngs-bam-c++: $(LIBDIR) $(LIBDIR)/$(LPFX)ngs-bam-c++-static.$(LIBX)
56 $(LIBDIR)/$(LPFX)ngs-bam-c++-static.$(LIBX): $(LIBDIR)/$(LPFX)ngs-bam-c++.$(LIBX)
60 runtests: ngs-bam ngs-bam-c++
70 bam \
71 ngs-bam
92 $(LIBDIR)/$(LPFX)ngs-bam.$(MAJVERS_SHLX): $(LIBDIR)/$(LPFX)ngs-bam.$(VERSION_SHLX)
96 $(LIBDIR)/$(LPFX)ngs-bam.$(SHLX): $(LIBDIR)/$(LPFX)ngs-bam.$(MAJVERS_SHLX)
[all …]
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| /dports/textproc/p5-CSS-Sass/CSS-Sass-3.6.4/t/sass-spec/spec/libsass/parent-selector/ |
| H A D | outer-combinator.hrx | 4 bam: true;
7 bam: true;
13 bam: true;
40 bam: true;
43 bam: true;
47 bam: true;
50 bam: true;
54 bam: true;
57 bam: true;
61 bam: true;
[all …]
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| H A D | inner-combinator.hrx | 4 bam: true;
7 bam: true;
13 bam: true;
40 bam: true;
43 bam: true;
47 bam: true;
50 bam: true;
54 bam: true;
57 bam: true;
61 bam: true;
[all …]
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| /dports/biology/bedtools/bedtools2-2.30.0/test/genomecov/ |
| H A D | test-genomecov.sh | 22 $htsutil samtobam one_block.sam one_block.bam
23 $htsutil samtobam two_blocks.sam two_blocks.bam
25 $htsutil samtobam sam-w-del.sam sam-w-del.bam
26 $htsutil samtobam pair-chip.sam pair-chip.bam
27 $htsutil samtobam chip.sam chip.bam
150 $BT genomecov -ibam sam-w-del.bam -bg > obs
167 $BT genomecov -ibam y.bam > obs
179 $BT genomecov -ibam y.bam -bg > obs
195 $BT genomecov -ibam y.bam -bga > obs
265 rm one_block.bam two_blocks.bam three_blocks.bam sam-w-del.bam pair-chip.bam chip.bam merged.bam
[all …]
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| /dports/biology/py-deeptools/deepTools-3.5.1/deeptools/ |
| H A D | bamHandler.py | 9 bam = openBam(fname)
12 for b in bam.fetch(chrom, start, end):
25 def getMappingStats(bam, nThreads): argument
31 header = [(x, y) for x, y in zip(bam.references, bam.lengths)]
42 unmapped += bam.count("*")
84 if bam.is_cram and returnStats:
86 elif bam.is_bam:
87 mapped = bam.mapped
88 unmapped = bam.unmapped
94 if bam.is_bam or (bam.is_cram and returnStats):
[all …]
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| /dports/biology/bedtools/bedtools2-2.30.0/test/bamtobed/ |
| H A D | test-bamtobed.sh | 22 $htsutil samtobam one_block.sam one_block.bam
23 $htsutil samtobam two_blocks.sam two_blocks.bam
27 $htsutil samtobam numeric_tag.sam numeric_tag.bam
37 $BT bamtobed -i one_block.bam > obs
48 $BT bamtobed -i one_block.bam -split > obs
59 $BT bamtobed -i two_blocks.bam > obs
71 $BT bamtobed -i two_blocks.bam -split > obs
82 $BT bamtobed -i three_blocks.bam > obs
95 $BT bamtobed -i three_blocks.bam -split > obs
106 $BT bamtobed -i three_blocks.bam -bed12 > obs
[all …]
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