id stringlengths 36 36 | text stringlengths 1 1.25M |
|---|---|
0623ec25-3919-42bc-ba65-c8d330f49e83 | public static void setBothSameOrientated(long bothSameOrientated) {
PairedReadEntry.bothSameOrientated = bothSameOrientated;
} |
5419916c-a4d9-4d80-8b12-cd494bae8b9d | public static long getHighDistance() {
return highDistance;
} |
7dced90f-3100-40ef-b1cb-474f9fbe822c | public static void setHighDistance(long highDistance) {
PairedReadEntry.highDistance = highDistance;
} |
9b6d5822-4ddb-4c86-805a-734cb539f85e | public static int getPairedEndReadCount() {
return pairedEndReadCount;
} |
75dda982-6e53-4f75-8e9b-34d267c0dbce | public static void setPairedEndReadCount(int pairedEndReadCount) {
PairedReadEntry.pairedEndReadCount = pairedEndReadCount;
} |
aa3875e0-d1f8-49c5-b091-a16f0a67f2ac | @Override
public void analyzeCoverage() {
// in this analysis, skip and count the read pair where either read
// or mate are flagged as unmapped
if (this.getSamRecord().getReadUnmappedFlag()
|| this.getSamRecord().getMateUnmappedFlag()) {
readMateUnmappedCount++;
return;
}
// in this analysis, ski... |
8bca6eee-a52c-41cb-8b3f-37ef62392c10 | @Override
public void analyseQuality() {
// TODO Auto-generated method stub
super.analyseQuality();
} |
d2304a6d-14d5-4931-8602-97206837e7b1 | public Interval(String chr, int start, int end, int size) {
this.chr = chr;
this.start = start;
this.end = end;
this.size = size;
System.out.println("FILL");
this.coverage = new ArrayList<Byte>(size);
for (int i = 0; i < size; i++) {
System.out.println("FILL");
this.coverage.add((byte) 0);
}
} |
acaffd73-d927-47dc-abe7-a7f93bde09cb | public Interval(String line) {
this.line = line;
} |
570a1145-7bd9-49fe-bebd-4ffd15ee8a74 | public Interval setInterval() {
String[] lines = this.line.split("\t");
int start = Integer.parseInt(lines[1]);
int end = Integer.parseInt(lines[2]);
return new Interval(lines[0].toString(), start, end, (end - start));
} |
4438c397-b234-4ccb-aec4-d4b77f82ad01 | public int getStart() {
return start;
} |
3134b62f-2eca-4a7c-94c2-7f3e7a8ff633 | public void setStart(int start) {
this.start = start;
} |
0038bc4e-0383-41dd-9431-04592c57c1e8 | public int getEnd() {
return end;
} |
59f10d64-e1cd-409e-b129-ebb5f0797271 | public void setEnd(int end) {
this.end = end;
} |
0c629cd8-25dd-4eb6-a957-157714a4200b | public String getChr() {
return chr;
} |
9c946e66-7896-4ea8-954f-3836b6e08af8 | public void setChr(String chr) {
this.chr = chr;
} |
15638dbb-db7f-4e39-ab6d-566024736c97 | public String getLine() {
return line;
} |
c837a22b-cb3e-498d-973b-073c4dda605e | public void setLine(String line) {
this.line = line;
} |
6c939f67-2993-46ac-82c2-30153c028d0d | public int getSize() {
return size;
} |
4699005d-1926-4277-b900-79a6ae57f302 | public void setSize(int size) {
this.size = size;
} |
77b65cf8-2212-4a94-9f7a-fd039bfd9423 | public ArrayList<Byte> getCoverage() {
return coverage;
} |
a5ac6de0-c1a9-4c5f-8429-e1688a86dc42 | public void setCoverage(ArrayList<Byte> coverage) {
this.coverage = coverage;
} |
c4dafec4-8960-40d9-8b96-9a3ac41995bf | public IntervalAbs(String line) {
this.line = line;
} |
a43c20a4-ff1f-4933-a1e6-03e2e1ab6f26 | public IntervalAbs(short chr, long startAbs, long endAbs, int size,
String geneName) {
this.chr = chr;
this.intervalStartAbs = startAbs;
this.intervalEndAbs = endAbs;
this.intervalSize = size;
this.geneName = geneName;
this.coverage = new ArrayList<Integer>(size);
for (int i = 0; i < size; i++) {
th... |
a281d938-1926-474b-a490-6fcc0666934c | public IntervalAbs setInterval() {
String[] lines = this.line.split("\t");
short chr = ChromosomeOffset.chromosomeNumber(lines[0]);
long startAbs = Long.parseLong(lines[1])
+ ChromosomeOffset.getChromosomeOffsetbyNumber(chr).getOffset() - INTERVAL_THRESHOLD;
long endAbs = Long.parseLong(lines[2])
+ Chro... |
79f82758-6605-426a-adef-3a8a5981e1d7 | public String getLine() {
return line;
} |
4f8aa9be-80d9-4252-a9b7-d364cd5c0e73 | public void setLine(String line) {
this.line = line;
} |
a6b6f6a7-168c-4428-9f48-33946d670b9f | public long getStartAbs() {
return intervalStartAbs;
} |
5942513e-75f9-40b5-986f-c620bbe110a1 | public void setStartAbs(long startAbs) {
this.intervalStartAbs = startAbs;
} |
7592260b-e00c-4232-9179-d04b6c01affe | public long getEndAbs() {
return intervalEndAbs;
} |
3edb1ac0-98d4-41c9-82e8-54bfbb1321f3 | public void setEndAbs(long endAbs) {
this.intervalEndAbs = endAbs;
} |
54db017a-a586-41fb-853c-1808f0ce2fe4 | public int getSize() {
return intervalSize;
} |
b06b173a-e693-457f-9fbb-93e788ab220f | public void setSize(int size) {
this.intervalSize = size;
} |
4dd2f1d6-88c4-437f-8ef6-dcd0f772bcd8 | public short getChr() {
return chr;
} |
86ed4edd-7897-4de6-8277-e2418b97b884 | public void setChr(short chr) {
this.chr = chr;
} |
a9ebfaff-f0a4-471c-bf60-c2e0a76360a4 | public ArrayList<Integer> getCoverage() {
return coverage;
} |
9ae49b4f-db57-46ed-a958-bca024fa5eac | public void setCoverage(ArrayList<Integer> coverage) {
this.coverage = coverage;
} |
0953110c-f9f0-45e1-a4b7-dfc9268d1e09 | public String getGeneName() {
return geneName;
} |
373875b4-a5e5-431c-be81-eb099b9c295b | public void setGeneName(String geneName) {
this.geneName = geneName;
} |
514bd689-9a15-4538-a2f2-91c44a408f19 | @Override
public int compareTo(IntervalAbs o) {
if (this.equals(o))
return 0;
// the range is from ~3E9 which is to much for an int, /10 maximizes
// values
return (int) (this.intervalStartAbs / 10 - o.intervalStartAbs / 10);
} |
cda64888-562a-429b-bc9d-8ce7885c95db | @Override
public boolean equals(Object obj) {
// equals in terms of absolute intervals means same start and end,
// ToDo: What is about overlaps ??
if (obj instanceof IntervalAbs) {
IntervalAbs new_name = (IntervalAbs) obj;
if (this.intervalStartAbs == new_name.intervalStartAbs)
return true;
}
retu... |
f27a8e92-6d43-45ef-b46d-461f629d5689 | public boolean readHitsAbsInterval(long readAbsStart, long readAbsEnd) {
boolean hitted = false;
ArrayList<Integer> cov = this.getCoverage();
for (long i = this.intervalStartAbs; i < this.intervalEndAbs; i++) {
if (i >= readAbsStart && i < readAbsEnd) {
cov.set((int) (i - this.intervalStartAbs),
cov.... |
1e2af3c5-7936-4df6-8a3d-2e3457e11370 | @Override
public String toString() {
// TODO Auto-generated method stub
return String.format("%s%d:%,d-%,d (%,d bp)", "chr",
this.getChr(),
(this.getStartAbs() - ChromosomeOffset.offset(getChr())),
(this.getEndAbs() - ChromosomeOffset.offset(getChr())),
this.getSize());
} |
6ed51dbe-fdd7-4db9-8752-3cfa31b1337a | public TargetNucleotidePositionEntry(short chr, long posInAbsGenome,
AlterationType alterationTypeAtPosition, char refAllel,
char altAllel, ReferenceReadPosition referenceReadPostion) {
this.chr = chr;
this.posInAbsGenome = posInAbsGenome;
this.alterationTypeAtPosition = alterationTypeAtPosition;
this.ref... |
54c4a78d-a686-40ae-81a2-6fd9ecea4a68 | public Integer getCoverage() {
return coverage;
} |
68ac2d34-a4a6-4217-854c-5ff6fe18a6af | public void setCoverage(Integer coverage) {
this.coverage = coverage;
} |
abb529ff-50bf-41af-a8b9-0ede43d266fd | public Integer getAltAllelReadCount() {
return altAllelReadCount;
} |
cccf1762-7d22-46e2-b91a-b948ccbf1d9a | public void setAltAllelReadCount(Integer altAllelReadCount) {
this.altAllelReadCount = altAllelReadCount;
} |
2be1e1e4-9be4-4fda-a8f9-7c129a5d3152 | public AlterationType getAlterationTypeAtPosition() {
return alterationTypeAtPosition;
} |
a7c49786-f186-4022-b14e-fb0d3c33a5c5 | public void setAlterationTypeAtPosition(
AlterationType alterationTypeAtPosition) {
this.alterationTypeAtPosition = alterationTypeAtPosition;
} |
2dab6f00-e137-47ee-bd46-7f77f822fb45 | public Integer getHomoPolymerLength() {
return homoPolymerLength;
} |
ae8c85cc-3267-4781-8fab-9656d92214cb | public void setHomoPolymerLength(Integer homoPolymerLength) {
this.homoPolymerLength = homoPolymerLength;
} |
5daa6332-0083-4855-a6b2-bc4f91224431 | public Long getPosInAbsGenome() {
return posInAbsGenome;
} |
b5e64b5b-08a2-4561-87ba-e68361176b86 | public void setPosInAbsGenome(Long posInAbsGenome) {
this.posInAbsGenome = posInAbsGenome;
} |
17914aa4-b0e2-4b67-b118-3d93ac3f78e6 | public Integer getRefAllelReadCount() {
return refAllelReadCount;
} |
ec98f9d5-555f-41ef-ab36-fda5b88ab0b6 | public void setRefAllelReadCount(Integer refAllelReadCount) {
this.refAllelReadCount = refAllelReadCount;
} |
f775612b-eb5e-46d5-aace-a556f9eb47f0 | public char getRefAllel() {
return refAllel;
} |
13cb447a-9742-4bd2-8655-42c59810b66e | public void setRefAllel(char refAllel) {
this.refAllel = refAllel;
} |
75eaff1a-cc56-4eb9-8457-92fecef2171a | public char getAltAllel() {
return altAllel;
} |
ba362a01-d17f-468d-b71a-1a9cb01c4692 | public void setAltAllel(char altAllel) {
this.altAllel = altAllel;
} |
ce164d4f-7fe0-4197-b5f8-9f882a9d873f | public ReferenceReadPosition getReferenceReadPostion() {
return referenceReadPostion;
} |
17a88e74-5fa5-44a3-bfb7-0305b247d74a | public void setReferenceReadPostion(
ReferenceReadPosition referenceReadPostion) {
this.referenceReadPostion = referenceReadPostion;
} |
1a3e0ae7-3e9a-437c-8646-aac4a1d9c2e9 | @Override
public boolean equals(Object obj) {
if (obj instanceof TargetNucleotidePositionEntry) {
TargetNucleotidePositionEntry temp = (TargetNucleotidePositionEntry) obj;
return (temp.posInAbsGenome == this.posInAbsGenome);
}
return false;
} |
f5dfe3da-7d0d-4ed4-9ee5-bb5375feb7ee | @Override
public int compareTo(TargetNucleotidePositionEntry o) {
if (this.equals(o))
return 0;
/*
* the range is from ~3E9 which is to much for an int, /10 maximizes
* values
*/
return (int) (this.posInAbsGenome / 10 - o.posInAbsGenome / 10);
} |
231aeebe-9f1e-4af3-92ca-34b4e014232e | public int calculateHomoPolymerLength() {
return altAllel;
} |
7b4308af-bf95-4c34-aeb9-a6b3671f667e | public short getChr() {
return chr;
} |
2324fb70-ec6c-4a9e-8898-f6ce05da7961 | public void setChr(short chr) {
this.chr = chr;
} |
0172d12a-8d1d-460b-9b6c-78d89579726d | @Override
public String toString() {
// TODO Auto-generated method stub
return String.format(
"%s%d\t%d\t%d\t%c/%c;%d/%d;%d%c;%s;%.2f",
"chr",
this.getChr(),
(this.getPosInAbsGenome() - ChromosomeOffset.offset(getChr()))-1,
(this.getPosInAbsGenome() - ChromosomeOffset.offset(getChr())),
thi... |
9c8e46fe-a1fe-4dd8-ae68-eff83688d181 | public ProtonFileHeader(SAMFileHeader sfh) {
this.sfh = sfh;
Set<Entry<String, String>> attributes = sfh.getAttributes();
System.out.println(attributes);
System.out.println(sfh.getAttribute(CURRENT_VERSION));
System.out.println(sfh.getAttribute(GROUP_ORDER_TAG));
System.out.println(sfh.getAttribute(SORT_ORD... |
c37a1a98-8905-42ab-b896-e719fb06de95 | public GATK_SNV_entry(String chr, Long genomPosition,
Long absGenomPosition, Short chr_nr) {
this.chr = chr;
this.genomPosition = genomPosition;
this.absGenomPosition = absGenomPosition;
this.chr_nr = chr_nr;
} |
cd2f0fb1-3220-4a8c-b9ce-333c38ecb152 | public GATK_SNV_entry(String chr, Long genomPosition,
Long absGenomPosition, Short chr_nr, String dbSNP_entry, String refAllel,
String altAllel, Double qual_SNV,
String filterInfo, String gatkInfo, String gatkFormat,
String gatkGenotype) {
this(chr, genomPosition, absGenomPosition,chr_nr);
this.dbSNP_en... |
6b85e5f0-be27-4235-819d-97357c348f56 | public String getChr() {
return chr;
} |
8dcc6e80-2d48-4d77-b4b9-029475ba8a78 | public Long getGenomPosition() {
return genomPosition;
} |
b1a63ac0-ebab-48c9-87f1-e1d04642fdba | public Long getAbsGenomPosition() {
return absGenomPosition;
} |
c42fc38d-15ba-42bd-aa17-65e60aca71d9 | public Short getChr_nr() {
return chr_nr;
} |
8fb9d9c9-2908-4dc9-89a9-c8cc4c655c11 | public String getRefAllel() {
return refAllel;
} |
b38324d9-b641-491f-b9f6-f59d6c597f97 | public String getAltAllel() {
return altAllel;
} |
2e9b35e2-6ef9-47bb-b1a7-30b42f004254 | public String getDbSNP_entry() {
return dbSNP_entry;
} |
2dbb295c-48ad-4795-9b25-9fd4323f2755 | public Double getQual_SNV() {
return qual_SNV;
} |
9f65e613-241d-40b0-8af2-3958c5fa8862 | public String getFilterInfo() {
return filterInfo;
} |
49b27d39-a54e-454c-b3bd-bd00434190e1 | public String getGatkInfo() {
return gatkInfo;
} |
fe745058-2be6-48e0-b763-66138059b876 | public String getGatkFormat() {
return gatkFormat;
} |
ad7931bf-b827-420a-979b-5dddb8cf2959 | public String getGatkGenotype() {
return gatkGenotype;
} |
7136ffc6-00e3-45fc-a1af-06cbdea7b816 | public SAMRecord getSamRecord() {
return samRecord;
} |
103a6217-084b-42b7-aa13-6f96bcc2e50f | public void setSamRecord(SAMRecord samRecord) {
this.samRecord = samRecord;
} |
b940c360-ea28-4691-8c02-8faddaf0d3af | public abstract void analyzeCoverage(); |
1bb105db-a649-4571-b72f-827ba72b5c0c | public abstract void analyseQuality(); |
df4a09b5-4c5a-4c2b-b78a-f0fd4932fe93 | public int getHardClippedBases() {
return hardClippedBases;
} |
77b5c8f7-3159-46a2-8447-bac14efef116 | public void setHardClippedBases(int hardClippedBases) {
this.hardClippedBases = hardClippedBases;
} |
2f0aedf6-6a2b-4b21-83b6-74dcaeacefdf | public int getSoftClippedBases() {
return softClippedBases;
} |
6d85bfcf-876b-42a5-a391-93e49af226d8 | public void setSoftClippedBases(int softClippedBases) {
this.softClippedBases = softClippedBases;
} |
f1a2b82a-003a-4c91-9ada-390be8412b76 | public int getRawReadLength() {
return rawReadLength;
} |
2a5f39d7-3139-41de-a3f3-ad63f38c867a | public void setRawReadLength(int rawReadLength) {
this.rawReadLength = rawReadLength;
} |
8df20289-f960-4544-b205-17b072fc9edb | public static int getReadCount() {
return readCount;
} |
87308fbe-c7ae-4c3a-b9ca-939e492d82ba | public static void setReadCount(int readCount) {
ReadEntry.readCount = readCount;
} |
c8770659-88ea-4b38-a01e-0cdcb4ceee4c | public int getDeletedTaggedBases() {
return deletedTaggedBases;
} |
907a9c66-95b6-4bce-8f14-1df07ca09196 | public void setDeletedTaggedBases(int deletedTaggedBases) {
this.deletedTaggedBases = deletedTaggedBases;
} |
d0232e5a-950a-441c-b92e-53100e37aa7e | public int getInsertedTaggedBases() {
return insertedTaggedBases;
} |
9a31089a-d933-475e-821a-91cf39dcaf7a | public void setInsertedTaggedBases(int insertedTaggedBases) {
this.insertedTaggedBases = insertedTaggedBases;
} |
31218ac9-38a7-4ba9-a1d9-02805927c931 | public int getEffReadLength() {
return effReadLength;
} |
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