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|
Author: Andreas Tille <tille@debian.org>
Last-Update: 2020-04-11
Description: getline belongs to libc - no need to have a copy here
Forwarded: yes
# email sent to twu@gene.com on 2021-02-26
--- gmap.orig/src/Makefile.am
+++ gmap/src/Makefile.am
@@ -259,7 +259,7 @@
request.c request.h result.c result.h outputtype.h output.c output.h \
inbuffer.c inbuffer.h samheader.c samheader.h printbuffer.c printbuffer.h outbuffer.c outbuffer.h \
chimera.c chimera.h datadir.c datadir.h parserange.c parserange.h \
- getline.c getline.h getopt.c getopt1.c getopt.h gmap.c
+ getline.c getline.h gmap.c
# Note: dist_ commands get read by bootstrap, and don't follow the flags
@@ -357,7 +357,7 @@
request.c request.h result.c result.h outputtype.h output.c output.h \
inbuffer.c inbuffer.h samheader.c samheader.h printbuffer.c printbuffer.h outbuffer.c outbuffer.h \
chimera.c chimera.h datadir.c datadir.h parserange.c parserange.h \
- getline.c getline.h getopt.c getopt1.c getopt.h gmap.c
+ getline.c getline.h gmap.c
# Note: dist_ commands get read by bootstrap, and don't follow the flags
@@ -496,7 +496,7 @@
inbuffer.c inbuffer.h samheader.c samheader.h printbuffer.c printbuffer.h outbuffer.c outbuffer.h \
uintpairtable.c uintpairtable.h splice-count.c splice-count.h support.c support.h \
datadir.c datadir.h pass.h mode.h parserange.c parserange.h \
- getline.c getline.h getopt.c getopt1.c getopt.h gsnap.c
+ getline.c getline.h gsnap.c
# Note: dist_ commands get read by bootstrap, and don't follow the flags
@@ -643,7 +643,7 @@
inbuffer.c inbuffer.h samheader.c samheader.h printbuffer.c printbuffer.h outbuffer.c outbuffer.h \
uint8pairtable.c uint8pairtable.h splice-count.c splice-count.h support.c support.h \
datadir.c datadir.h pass.h mode.h parserange.c parserange.h \
- getline.c getline.h getopt.c getopt1.c getopt.h gsnap.c
+ getline.c getline.h gsnap.c
# Note: dist_ commands get read by bootstrap, and don't follow the flags
@@ -727,7 +727,7 @@
request.c request.h \
inbuffer.c inbuffer.h samheader.c samheader.h printbuffer.c printbuffer.h outbuffer.c outbuffer.h \
datadir.c datadir.h mode.h parserange.c parserange.h \
- getline.c getline.h getopt.c getopt1.c getopt.h gexact.c
+ getline.c getline.h gexact.c
gexact_nosimd_CC = $(PTHREAD_CC)
gexact_nosimd_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DGEXACT=1
@@ -801,7 +801,7 @@
request.c request.h \
inbuffer.c inbuffer.h printbuffer.c printbuffer.h outbuffer.c outbuffer.h \
datadir.c datadir.h \
- getline.c getline.h getopt.c getopt1.c getopt.h gfilter.c
+ getline.c getline.h gfilter.c
gfilter_nosimd_CC = $(PTHREAD_CC)
gfilter_nosimd_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DGFILTER=1
@@ -861,7 +861,7 @@
COMPARE2TRUTH_FILES = bool.h \
except.c except.h assert.c assert.h mem.c mem.h \
intlist.c intlist.h uintlist.c uintlist.h list.c list.h \
- getopt.c getopt1.c getopt.h compare2truth.c
+ compare2truth.c
compare2truth_CC = $(PTHREAD_CC)
compare2truth_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"
@@ -918,7 +918,7 @@
indexdbdef.h indexdb.c indexdb.h indexdb-write.c indexdb-write.h \
complement.h compress-write.c compress-write.h bzip2.c bzip2.h fopen.c fopen.h \
datadir.c datadir.h parserange.c parserange.h \
- getline.c getline.h getopt.c getopt1.c getopt.h indexdb-cat.c
+ getline.c getline.h indexdb-cat.c
indexdb_cat_CC = $(PTHREAD_CC)
indexdb_cat_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
@@ -946,7 +946,7 @@
chrom.c chrom.h \
complement.h md5.c md5.h bzip2.c bzip2.h fopen.c fopen.h sequence.c sequence.h genome.c genome.h \
datadir.c datadir.h parserange.c parserange.h \
- getline.c getline.h getopt.c getopt1.c getopt.h snpindex.c
+ getline.c getline.h snpindex.c
snpindex_CC = $(PTHREAD_CC)
snpindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
@@ -974,7 +974,7 @@
uintlist.c uintlist.h intlist.c intlist.h \
uint8list.c uint8list.h \
list.c list.h datadir.c datadir.h parserange.c parserange.h \
- getline.c getline.h getopt.c getopt1.c getopt.h cmetindex.c
+ getline.c getline.h cmetindex.c
cmetindex_CC = $(PTHREAD_CC)
cmetindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
@@ -1002,7 +1002,7 @@
uintlist.c uintlist.h intlist.c intlist.h \
uint8list.c uint8list.h \
list.c list.h datadir.c datadir.h parserange.c parserange.h \
- getline.c getline.h getopt.c getopt1.c getopt.h atoiindex.c
+ getline.c getline.h atoiindex.c
atoiindex_CC = $(PTHREAD_CC)
atoiindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
@@ -1027,7 +1027,7 @@
bitpack64-readtwo.c bitpack64-readtwo.h transcriptome.c transcriptome.h \
datadir.c datadir.h \
bzip2.c bzip2.h getline.c getline.h \
- getopt.c getopt1.c getopt.h trindex.c
+ trindex.c
trindex_CC = $(PTHREAD_CC)
trindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
@@ -1051,7 +1051,7 @@
chrnum.c chrnum.h \
datadir.c datadir.h parserange.c parserange.h \
getline.c getline.h \
- getopt.c getopt1.c getopt.h get-genome.c
+ get-genome.c
get_genome_CC = $(PTHREAD_CC)
get_genome_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
@@ -1071,7 +1071,7 @@
iit-write-univ.c iit-write-univ.h iitdef.h iit-write.c iit-write.h \
tableint.c tableint.h table.c table.h chrom.c chrom.h \
bzip2.c bzip2.h getline.c getline.h \
- getopt.c getopt1.c getopt.h iit_store.c
+ iit_store.c
iit_store_CC = $(PTHREAD_CC)
iit_store_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DUTILITYP=1
@@ -1091,7 +1091,7 @@
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
complement.h parserange.c parserange.h \
bzip2.c bzip2.h getline.c getline.h \
- getopt.c getopt1.c getopt.h iit_get.c
+ iit_get.c
iit_get_CC = $(PTHREAD_CC)
iit_get_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DUTILITYP=1
@@ -1107,7 +1107,7 @@
stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h parserange.c parserange.h \
- getopt.c getopt1.c getopt.h iit_dump.c
+ iit_dump.c
iit_dump_CC = $(PTHREAD_CC)
iit_dump_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DUTILITYP=1
@@ -1123,7 +1123,7 @@
genomicpos.h interval.c interval.h \
intlist.c intlist.h uintlist.c uintlist.h iitdef.h iit-read.c iit-read.h \
univinterval.c univinterval.h iit-read-univ.c iit-read-univ.h parserange.c parserange.h \
- getopt.c getopt1.c getopt.h iit_pileup.c
+ iit_pileup.c
iit_pileup_CC = $(PTHREAD_CC)
iit_pileup_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DUTILITYP=1
@@ -1145,7 +1145,7 @@
parserange.c parserange.h iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
samflags.h samheader.c samheader.h samread.c samread.h \
bzip2.c bzip2.h getline.c getline.h datadir.c datadir.h \
- getopt.c getopt1.c getopt.h sam_sort.c
+ sam_sort.c
sam_sort_CC = $(PTHREAD_CC)
sam_sort_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
@@ -1163,7 +1163,7 @@
bzip2.c bzip2.h getline.c getline.h \
stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
list.c list.h datadir.c datadir.h \
- getopt.c getopt1.c getopt.h umi-correct.c
+ umi-correct.c
umi_correct_CC = $(PTHREAD_CC)
umi_correct_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
@@ -1182,7 +1182,7 @@
bzip2.c bzip2.h getline.c getline.h \
stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
list.c list.h datadir.c datadir.h \
- getopt.c getopt1.c getopt.h velocity-counts.c
+ velocity-counts.c
velocity_counts_CC = $(PTHREAD_CC)
velocity_counts_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1 $(POPCNT_CFLAGS)
@@ -1207,7 +1207,7 @@
bzip2.c bzip2.h getline.c getline.h \
stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
list.c list.h datadir.c datadir.h \
- getopt.c getopt1.c getopt.h gcount-bulk.c
+ gcount-bulk.c
gcount_bulk_CC = $(PTHREAD_CC)
gcount_bulk_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1 $(POPCNT_CFLAGS)
@@ -1233,7 +1233,7 @@
bzip2.c bzip2.h getline.c getline.h \
stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
list.c list.h datadir.c datadir.h \
- getopt.c getopt1.c getopt.h gcount-sc.c
+ gcount-sc.c
gcount_sc_CC = $(PTHREAD_CC)
gcount_sc_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1 $(POPCNT_CFLAGS)
@@ -1256,7 +1256,7 @@
# chrnum.c chrnum.h \
# maxent.c maxent.h maxent_hr.c maxent_hr.h \
# branchpoint.c branchpoint.h \
-# parserange.c parserange.h datadir.c datadir.h getopt.c getopt1.c getopt.h splicing-score.c
+# parserange.c parserange.h datadir.c datadir.h splicing-score.c
#
#splicing_score_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\"
#splicing_score_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(PTHREAD_CFLAGS)
|
