Commit be1a7a6f authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.1.2+dfsg

parent 0bd5483c

clipper/CHANGES→CHANGES

+0 −13
Original line number Diff line number Diff line 
r805:

* fixed fastq-mcf 'start' bug for ubuntu 14.04



r780:

* fixed fastq-mcf output

* added support for fastq-multx reading from headers 

* bundled entire sparsehash library, changed Makefile to include it

* fastq-join corrected quality in overlapped regions

* added a proper test suite. requires perl & Test::More

* fastq-multx minimum distance

* fastq-join allow insert < read-length

* fastq-mcf corrected low-complexity filtering



r181	- CASAVA purity filtering

r154	- fixed major bug in RMN's that would invalidate reads

r152	- allowed short adapters to work at the 'begin' of reads

clipper/Makefile→Makefile

+26 −26
Original line number Diff line number Diff line 
#

# $Id$

# $Id: Makefile 670 2013-12-13 16:47:07Z earonesty $



CC=g++

PREFIX?=/usr

BINDIR?=$(PREFIX)/bin

CFLAGS?=-O3 -I. 

CPPFLAGS?=-O3 -I.

# for debugging:

# CFLAGS?=-g -I. 

# CPPFLAGS?=-g -I.



PKG=ea-utils

REL := $(shell svnversion 2>/dev/null | perl -ne 'print $$1 if /(\d+)/' )

REL := $(shell svnversion 2>/dev/null | perl -ne 'print $$1 if /:(\d+)/' )

VER := $(shell grep '%define ver' ${PKG}.spec | perl -ne 'print $$1 if / (\S+) *$$/')



SRC=fastq-clipper.cpp fastq-mcf.cpp fastq-multx.cpp fastq-join.cpp fastq-stats.cpp gcModel.cpp

SRC=fastq-clipper.c fastq-mcf.c fastq-multx.c fastq-join.c fastq-stats.cpp gcModel.c

BIN=fastq-mcf fastq-multx fastq-join fastq-stats fastq-clipper sam-stats varcall

TOOLS=fastx-graph gtf2bed determine-phred randomFQ alc



all: $(BIN) check

all: $(BIN)



debug: 

	CFLAGS="-g -I." ${MAKE} $(MFLAGS) varcall

	CPPFLAGS=-g ${MAKE} $(MFLAGS) varcall



install: $(BIN) $(BINDIR)/fastq-clipper $(BINDIR)/fastq-mcf $(BINDIR)/fastq-multx $(BINDIR)/fastq-join $(BINDIR)/fastq-stats $(BINDIR)/sam-stats $(BINDIR)/varcall $(BINDIR)/fastx-graph $(BINDIR)/determine-phred $(BINDIR)/randomFQ $(BINDIR)/alc
@@ -37,12 +39,12 @@ dist: getrel $(PKG).${VER}-${REL}.tar.gz 
getrel:

	grep "${REL}" $(PKG).spec || touch $(PKG).spex



.PHONY: getrel debug $(PKG).spec

.PHONY: getrel debug



$(PKG).spec:

$(PKG).spec: $(PKG).spex

	perl -pe 's/%RELEASE%/${REL}/' $(PKG).spex > $(PKG).spec



$(PKG).tar.gz: Makefile $(TOOLS) $(SRC) $(PKG).spec fastq-lib.cpp fastq-lib.h sam-stats.cpp fastq-stats.cpp gcModel.cpp gcModel.h varcall.cpp utils.h README CHANGES sparsehash-2.0.2 samtools/*.c t

$(PKG).tar.gz: Makefile $(TOOLS) $(SRC) $(PKG).spec fastq-lib.cpp fastq-lib.h sam-stats.cpp fastq-stats.cpp gcModel.c gcModel.h varcall.cpp utils.h README CHANGES google sparsehash samtools/*.c 

	rm -rf $(PKG).${VER}-${REL}

	mkdir $(PKG).${VER}-${REL}

	mkdir $(PKG).${VER}-${REL}/tidx
@@ -53,28 +55,29 @@ $(PKG).tar.gz: Makefile $(TOOLS) $(SRC) $(PKG).spec fastq-lib.cpp fastq-lib.h sa 
	tar --exclude=".svn" -cvzf $(PKG).tar.gz $(PKG).${VER}-${REL}

	rm -rf $(PKG).${VER}-${REL}



check: $(BIN)

	prove -j 4 t



disttest: $(PKG).tar.gz

	rm -rf $(PKG).${VER}-${REL}

	tar -xzvf $(PKG).tar.gz

	cd $(PKG).${VER}-${REL} && make check

	cd $(PKG).${VER}-${REL} && make

	rm -rf $(PKG).${VER}-${REL}



$(PKG).${VER}-${REL}.tar.gz: $(PKG).tar.gz

	cp $< $@



%: %.cpp fastq-lib.cpp fastq-lib.h sparsehash

	$(CC) $(CFLAGS) $< fastq-lib.cpp -o $@

%: %.c fastq-lib.cpp fastq-lib.h 

	$(CC) $(CFLAGS) fastq-lib.cpp -o $@ $<



%: %.cpp fastq-lib.cpp fastq-lib.h

	$(CC) $(CFLAGS) fastq-lib.cpp -o $@ $<



sparsehash: sparsehash-2.0.2

	cd sparsehash-2.0.2; ./configure; make

	mkdir sparsehash

	cp -r sparsehash-2.0.2/src/sparsehash/* sparsehash/



%: %.c gcModel.c gcModel.h

	$(CC) $(CFLAGS) gcModel.c -o $@ $<



%: %.cpp gcModel.c gcModel.h

	$(CC) $(CFLAGS) gcModel.c -o $@ $<



# why the libbam.a doesn't work?  not sure... *.o works

sam-stats: sam-stats.cpp samtools/libbam.a samtools/bam.h fastq-lib.h sparsehash

sam-stats: sam-stats.cpp samtools/libbam.a samtools/bam.h fastq-lib.h

ifeq ($(OS),Windows_NT)

	$(CC) $(CFLAGS) samtools/*.o -lz -lpthread -lws2_32 fastq-lib.cpp $< -o $@

else
@@ -84,18 +87,15 @@ endif 
samtools/libbam.a: samtools/*.c samtools/*.h

	cd samtools && make libbam.a



ea-bcl2fastq: ea-bcl2fastq.cpp

	$(CC) $(CFLAGS) $< -lz -o $@



varcall: varcall.cpp fastq-lib.cpp tidx/tidx-lib.cpp sparsehash

varcall: varcall.cpp fastq-lib.cpp tidx/tidx-lib.cpp

ifeq ($(OS),Windows_NT)

	echo varcall: not supported yet

else

	$(CC) $(CFLAGS) fastq-lib.cpp tidx/tidx-lib.cpp -o $@ $< -lgsl -lgslcblas

endif



fastq-stats: fastq-stats.cpp fastq-lib.cpp gcModel.cpp sparsehash

	$(CC) $(CFLAGS) fastq-lib.cpp gcModel.cpp -o $@ $<

fastq-stats: fastq-stats.cpp fastq-lib.cpp gcModel.c

	$(CC) $(CFLAGS) fastq-lib.cpp gcModel.c -o $@ $<



bam-filter:  bam-filter.cpp 

	$(CC) $(CFLAGS) fastq-lib.cpp -o $@  $< -lbamtools

clipper/README→README

+0 −4
Original line number Diff line number Diff line
@@ -22,10 +22,6 @@ Variant caller, takes bam or pileup output and does variant calling with advance 


REQUIRES:



On Ubuntu:



sudo apt-get install subversion zlib1g-dev libgsl0-dev



For building sam-stats, please install this first!



https://github.com/pezmaster31/bamtools/wiki/Building-and-installing

README.md

deleted100644 → 0
+0 −5
Original line number Diff line number Diff line 
# ea-utils

This project was automatically exported from code.google.com/p/ea-utils and will now be maintained in this repository on GitHub.



To build ea-utils, follow these [build instructions](https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/Compiling.md). Please see http://expressionanalysis.github.io/ea-utils/ for further help information.

clipper/alc→alc

+0 −0

File moved.

View file