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Add Blocked GZip Format (BGZF) #19

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Add Blocked GZip Format (BGZF) #19

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1d4c9c3
got most of the code for BGZF compliance entered, not working yet
robegan21 Nov 2, 2014
d4591b8
now --bgzf compresses gzip compliant files
robegan21 Nov 2, 2014
42b4335
reworked indent to be 4 spaces, not tab
robegan21 Nov 3, 2014
c65384f
refactor put_bgzf_trailer_and_header
robegan21 Nov 3, 2014
2f6b003
added support for --bgzf in single threaded mode
robegan21 Nov 3, 2014
35727f2
added support for parallel decompress of --bgzf input files
robegan21 Nov 15, 2014
c0885f8
got decompress on --bgzf working and tested
robegan21 Nov 16, 2014
ea56a0a
added comments and removed debugging printf statements
robegan21 Nov 16, 2014
6623284
fixed some comments
robegan21 Nov 16, 2014
9278884
fixed -t when archive is a BGZF
robegan21 Nov 16, 2014
a9c6e3a
fixed spacing
robegan21 Nov 16, 2014
82cc340
fixed -t to wait for last BGZF block to be processed
robegan21 Nov 16, 2014
83cb87c
added extra checks for eof while reading and parsing gzip header stru…
robegan21 Nov 17, 2014
8c92aa3
fixed 0 byte input file and -p 1 compress
robegan21 Nov 18, 2014
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75 changes: 72 additions & 3 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,68 @@ pigzn: pigzn.o zopfli/deflate.o zopfli/blocksplitter.o zopfli/tree.o zopfli/lz77
pigzn.o: pigz.c
$(CC) $(CFLAGS) -DDEBUG -DNOTHREAD -g -c -o pigzn.o pigz.c

test: pigz
#
# set up pattern rules for tests
#

LONG_NAME = VeryLongNameVeryLongNameVeryLongNameVeryLongNameVeryLongNameVeryLongNameVeryLongNameVeryLongNameVeryLongNameVeryLongNameVeryLongNameVeryLongNameVeryLongNameVeryLongNameVeryLongNameVeryLongNameVeryLongNameVeryLongName

TESTFILES = $(addprefix .testfile-, empty pigz.c largefile $(LONG_NAME) )

.testfile-empty:
cat /dev/null > $@

.testfile-pigz.c: pigz.c
cp pigz.c $@

.testfile-largefile: pigz.c
number=1 ; while [[ $$number -le 100 ]] ; do cat pigz.c >> $@ ; ((number = number + 1)) ; done

.testfile-$(LONG_NAME): .testfile-largefile
cp $< $@

TEST_OPTIONS = .gz .b32.gz .1.gz .B.gz .B1.gz .gz2.gz .B-gz2.gz

.testfile-%.gz : .testfile-% pigz
./pigz -kf $< && touch $@

.testfile-%.b32.gz : .testfile-% pigz
./pigz -kfb 32 $< && mv $<.gz $@ && touch $@

.testfile-%.1.gz : .testfile-% pigz
./pigz -kfp 1 $< && mv $<.gz $@ && touch $@

.testfile-%.B.gz : .testfile-% pigz
./pigz -kfB $< && mv $<.gz $@ && touch $@

.testfile-%.B1.gz : .testfile-% pigz
./pigz -kfBp 1 $< && mv $<.gz $@ && touch $@

.testfile-%.gz2.gz : .testfile-% pigz
./pigz -kf $< && ./pigz -kf $<.gz && mv $<.gz.gz $@ && touch $@

.testfile-%.B-gz2.gz : .testfile-% pigz
./pigz -kfB $< && ./pigz -kfB $<.gz && mv $<.gz.gz $@ && touch $@

.test% : %.gz pigz
./pigz -t $<
./pigz -tp 1 $<
gzip -t $<
./pigz -dc $< > [email protected] && diff -q [email protected] $*
./pigz -dcp 1 $< > [email protected] && diff -q [email protected] $*
gzip -dc $< > [email protected] && diff -q [email protected] $*

TESTFILES_GZ = $(foreach option, $(TEST_OPTIONS), $(addsuffix $(option), $(TESTFILES)) )

testfiles : $(TESTFILES) $(TESTFILES_GZ)

TESTS = $(addprefix .test, $(TESTFILES_GZ))

.SECONDARY : $(TESTFILES) $(TESTFILES_GZ) $(TESTS)

moretests : pigz $(TESTS)

test: pigz moretests
./pigz -kf pigz.c ; ./pigz -t pigz.c.gz
./pigz -kfb 32 pigz.c ; ./pigz -t pigz.c.gz
./pigz -kfp 1 pigz.c ; ./pigz -t pigz.c.gz
Expand All @@ -62,7 +123,15 @@ test: pigz
echo 'compress -f < pigz.c | ./unpigz | cmp - pigz.c' ;\
compress -f < pigz.c | ./unpigz | cmp - pigz.c ;\
fi
@rm -f pigz.c.gz pigz.c.zz pigz.c.zip
./pigz -cp 1 < /dev/null | ./pigz -t -
./pigz -c < /dev/null | ./pigz -t -
./pigz -kfB -p 1 pigz.c \
&& ./pigz -d -c -p 1 pigz.c.gz | diff -q - pigz.c \
&& ./pigz -d -c -p 2 pigz.c.gz | diff -q - pigz.c
./pigz -kfB pigz.c \
&& ./pigz -d -c -p 1 pigz.c.gz | diff -q - pigz.c \
&& ./pigz -d -c -p 2 pigz.c.gz | diff -q - pigz.c
@rm -f pigz.c.gz pigz.c.zz pigz.c.zip .test*

tests: dev test
./pigzn -kf pigz.c ; ./pigz -t pigz.c.gz
Expand All @@ -74,4 +143,4 @@ pigz.pdf: pigz.1
groff -mandoc -f H -T ps pigz.1 | ps2pdf - pigz.pdf

clean:
@rm -f *.o zopfli/*.o pigz unpigz pigzn pigzt pigz.c.gz pigz.c.zz pigz.c.zip
@rm -f *.o zopfli/*.o pigz unpigz pigzn pigzt pigz.c.gz pigz.c.zz pigz.c.zip .test*
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