[med-svn] [fastqc] 04/05: Fix line endings in patch
Andreas Tille
tille at debian.org
Tue Nov 22 14:16:59 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository fastqc.
commit 8a90a6c594d7cd550e2df9acb7345a138e44721d
Author: Andreas Tille <tille at debian.org>
Date: Tue Nov 22 14:47:55 2016 +0100
Fix line endings in patch
---
debian/patches/drop-fast5.patch | 210 ++++++++++++++++++++--------------------
1 file changed, 103 insertions(+), 107 deletions(-)
diff --git a/debian/patches/drop-fast5.patch b/debian/patches/drop-fast5.patch
index 294f3bc..6b1b0ad 100644
--- a/debian/patches/drop-fast5.patch
+++ b/debian/patches/drop-fast5.patch
@@ -13,8 +13,8 @@ Description: HDF5 1.10 is about to transition into unstable, and unfortunately
poretools, I propose to temporarily drop fast5 support from FastQC
to avoid a removal from testing.
---- fastqc.orig/fastqc
-+++ fastqc/fastqc
+--- a/fastqc
++++ b/fastqc
@@ -74,7 +74,6 @@ my $quiet;
my $nogroup;
my $expgroup;
@@ -54,111 +54,107 @@ Description: HDF5 1.10 is about to transition into unstable, and unfortunately
--nofilter If running with --casava then don't remove read flagged by
casava as poor quality when performing the QC analysis.
-Index: fastqc/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
-===================================================================
---- fastqc.orig/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
-+++ fastqc/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
+--- a/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
++++ b/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
@@ -99,9 +99,6 @@ public class SequenceFactory {
- // We default to using all reads
- return new BAMFile(file,false);
- }
-- else if (file.getName().toLowerCase().endsWith(".fast5")) {
-- return new Fast5File(file);
-- }
- else {
- return new FastQFile(config,file);
- }
-Index: fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java
-===================================================================
---- fastqc.orig/uk/ac/babraham/FastQC/Sequence/Fast5File.java
+ // We default to using all reads
+ return new BAMFile(file,false);
+ }
+- else if (file.getName().toLowerCase().endsWith(".fast5")) {
+- return new Fast5File(file);
+- }
+ else {
+ return new FastQFile(config,file);
+ }
+--- a/uk/ac/babraham/FastQC/Sequence/Fast5File.java
+++ /dev/null
@@ -1,89 +0,0 @@
--/**
-- * Copyright Copyright 2010-15 Simon Andrews
-- *
-- * This file is part of FastQC.
-- *
-- * FastQC is free software; you can redistribute it and/or modify
-- * it under the terms of the GNU General Public License as published by
-- * the Free Software Foundation; either version 3 of the License, or
-- * (at your option) any later version.
-- *
-- * FastQC 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 for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with FastQC; if not, write to the Free Software
-- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-- */
--package uk.ac.babraham.FastQC.Sequence;
--
--import java.io.File;
--import java.io.IOException;
--
--import ch.systemsx.cisd.hdf5.HDF5Factory;
--import ch.systemsx.cisd.hdf5.IHDF5SimpleReader;
--
--public class Fast5File implements SequenceFile {
--
-- private Sequence nextSequence = null;
-- private File file;
--
-- private String name;
--
-- protected Fast5File(File file) throws SequenceFormatException, IOException {
-- this.file = file;
-- name = file.getName();
--
-- IHDF5SimpleReader reader = HDF5Factory.openForReading(file);
--
-- if (reader.exists("Analyses/Basecall_2D_000/BaseCalled_template/Fastq")) {
--
-- String fastq = reader.readString("Analyses/Basecall_2D_000/BaseCalled_template/Fastq");
--
-- String [] sections = fastq.split("\\n");
--
-- if (sections.length != 4) {
-- throw new SequenceFormatException("Didn't get 4 sections from "+fastq);
-- }
--
-- nextSequence = new Sequence(this, sections[1].toUpperCase(),sections[3], sections[0]);
-- }
-- reader.close();
--
-- }
--
-- public String name() {
-- return name;
-- }
--
-- public int getPercentComplete() {
-- if (! hasNext()) return 100;
--
-- return 0;
-- }
--
-- public boolean isColorspace() {
-- return false;
-- }
--
-- public boolean hasNext() {
-- return nextSequence != null;
-- }
--
-- public Sequence next() throws SequenceFormatException {
-- Sequence seq = nextSequence;
-- nextSequence = null;
-- return seq;
-- }
--
-- public void remove() {
-- // No action here
-- }
--
-- public File getFile() {
-- return file;
-- }
--
--}
+-/**
+- * Copyright Copyright 2010-15 Simon Andrews
+- *
+- * This file is part of FastQC.
+- *
+- * FastQC is free software; you can redistribute it and/or modify
+- * it under the terms of the GNU General Public License as published by
+- * the Free Software Foundation; either version 3 of the License, or
+- * (at your option) any later version.
+- *
+- * FastQC 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 for more details.
+- *
+- * You should have received a copy of the GNU General Public License
+- * along with FastQC; if not, write to the Free Software
+- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+- */
+-package uk.ac.babraham.FastQC.Sequence;
+-
+-import java.io.File;
+-import java.io.IOException;
+-
+-import ch.systemsx.cisd.hdf5.HDF5Factory;
+-import ch.systemsx.cisd.hdf5.IHDF5SimpleReader;
+-
+-public class Fast5File implements SequenceFile {
+-
+- private Sequence nextSequence = null;
+- private File file;
+-
+- private String name;
+-
+- protected Fast5File(File file) throws SequenceFormatException, IOException {
+- this.file = file;
+- name = file.getName();
+-
+- IHDF5SimpleReader reader = HDF5Factory.openForReading(file);
+-
+- if (reader.exists("Analyses/Basecall_2D_000/BaseCalled_template/Fastq")) {
+-
+- String fastq = reader.readString("Analyses/Basecall_2D_000/BaseCalled_template/Fastq");
+-
+- String [] sections = fastq.split("\\n");
+-
+- if (sections.length != 4) {
+- throw new SequenceFormatException("Didn't get 4 sections from "+fastq);
+- }
+-
+- nextSequence = new Sequence(this, sections[1].toUpperCase(),sections[3], sections[0]);
+- }
+- reader.close();
+-
+- }
+-
+- public String name() {
+- return name;
+- }
+-
+- public int getPercentComplete() {
+- if (! hasNext()) return 100;
+-
+- return 0;
+- }
+-
+- public boolean isColorspace() {
+- return false;
+- }
+-
+- public boolean hasNext() {
+- return nextSequence != null;
+- }
+-
+- public Sequence next() throws SequenceFormatException {
+- Sequence seq = nextSequence;
+- nextSequence = null;
+- return seq;
+- }
+-
+- public void remove() {
+- // No action here
+- }
+-
+- public File getFile() {
+- return file;
+- }
+-
+-}
--
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