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commit d727e4ad8379c5379065b0e718bf80e8189a4f78 Author: Dylan Aïssi <[email protected]> Date: Fri Jun 23 21:46:58 2017 +0200 Imported Upstream version 4.1~170608+dfsg --- main/LowMemHapAlleleProbs.java | 5 +--- main/Main.java | 6 ++--- vcf/BrefIt.java | 55 ++++++++++++++++++++++-------------------- 3 files changed, 33 insertions(+), 33 deletions(-) diff --git a/main/LowMemHapAlleleProbs.java b/main/LowMemHapAlleleProbs.java index e1403f7..2001db7 100644 --- a/main/LowMemHapAlleleProbs.java +++ b/main/LowMemHapAlleleProbs.java @@ -72,14 +72,11 @@ public class LowMemHapAlleleProbs implements HapAlleleProbs { int end = markers.sumAlleles(m+1); for (int j=start; j<end; ++j) { float p = alleleProbs[j]; - if (p < 0 || p > 1.01f || Float.isNaN(p)) { + if (p < 0 || p > 1.05f || Float.isNaN(p)) { throw new IllegalArgumentException(String.valueOf(p)); } sum += alleleProbs[j]; } - if (sum > 1.01f) { - throw new IllegalArgumentException(String.valueOf(sum)); - } for (int j=start; j<end - 1; ++j) { nonRefProbs[index++] = convertToByte(alleleProbs[j] / sum); } diff --git a/main/Main.java b/main/Main.java index 64f7d71..397b0c6 100644 --- a/main/Main.java +++ b/main/Main.java @@ -65,8 +65,8 @@ public class Main { /** * The program name and version. */ - public static final String program = "beagle.21Jan17.6cc.jar (version 4.1)"; - public static final String command = "java -jar beagle.21Jan17.6cc.jar"; + public static final String program = "beagle.08Jun17.d8b.jar (version 4.1)"; + public static final String command = "java -jar beagle.08Jun17.d8b.jar"; /** * The copyright string. @@ -78,7 +78,7 @@ public class Main { */ public static final String shortHelp = Main.program + Const.nl + Main.copyright - + Const.nl + "Enter \"java -jar beagle.21Jan17.6cc.jar\" for a " + + Const.nl + "Enter \"java -jar beagle.08Jun17.d8b.jar\" for a " + "summary of command line " + "arguments."; private final Par par; diff --git a/vcf/BrefIt.java b/vcf/BrefIt.java index 9027546..74fe2a7 100644 --- a/vcf/BrefIt.java +++ b/vcf/BrefIt.java @@ -222,35 +222,38 @@ public final class BrefIt implements SampleFileIt<VcfEmission> { private void fillBuffer() { assert emBuffer.isEmpty(); + int nRecords; try { - int nRecords = is.readInt(); - if (nRecords>0) { - String chrom = is.readUTF(); - int chromIndex = ChromIds.instance().getIndex(chrom); - int nSeq = is.readByte() + SHIFT; - IntArray hapToSeq = readHapToSeq(nSeq); - for (int j=0; j<nRecords; ++j) { - Marker marker = readMarker(chromIndex); - byte flag = is.readByte(); - switch (flag) { - case 0: - VcfEmission em = readSeqCodedRecord(marker, - samples, hapToSeq, nSeq); - if (markerFilter.accept(marker)) { - emBuffer.add(em); - } - break; - case 1: - em = readLowMafRecord(marker, samples); - if (markerFilter.accept(marker)) { - emBuffer.add(em); - } - break; - default: - Utilities.exit("Error reading file."); + do { + nRecords = is.readInt(); + if (nRecords>0) { + String chrom = is.readUTF(); + int chromIndex = ChromIds.instance().getIndex(chrom); + int nSeq = is.readByte() + SHIFT; + IntArray hapToSeq = readHapToSeq(nSeq); + for (int j=0; j<nRecords; ++j) { + Marker marker = readMarker(chromIndex); + byte flag = is.readByte(); + switch (flag) { + case 0: + VcfEmission em = readSeqCodedRecord(marker, + samples, hapToSeq, nSeq); + if (markerFilter.accept(marker)) { + emBuffer.add(em); + } + break; + case 1: + em = readLowMafRecord(marker, samples); + if (markerFilter.accept(marker)) { + emBuffer.add(em); + } + break; + default: + Utilities.exit("Error reading file."); + } } } - } + } while (nRecords>0 && emBuffer.isEmpty()); } catch (IOException ex) { Utilities.exit("Error reading file", ex); } -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/beagle.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
