g++ -DMAXGAP=0 -DMAXHITS=1000 -DTHREAD -funroll-loops -Lsamtools -Isamtools -O3   -DREAD_144 -c align.cpp -o align.o
align.cpp: In member function ‘void SingleAlign::s_OutHit(int, int, bit8_t, Hit*, int, RefSeq&, std::string&)’:
align.cpp:549:213: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘std::basic_string<char>::size_type {aka long unsigned int}’ [-Wformat]
g++ -DMAXGAP=0 -DMAXHITS=1000 -DTHREAD -funroll-loops -Lsamtools -Isamtools -O3   -DREAD_144 -c dbseq.cpp -o dbseq.o
g++ -DMAXGAP=0 -DMAXHITS=1000 -DTHREAD -funroll-loops -Lsamtools -Isamtools -O3   -DREAD_144 -c main.cpp -o main.o
main.cpp: In function ‘int main(int, char**)’:
main.cpp:434:31: warning: ignoring return value of ‘char* realpath(const char*, char*)’, declared with attribute warn_unused_result [-Wunused-result]
main.cpp:435:49: warning: ignoring return value of ‘char* realpath(const char*, char*)’, declared with attribute warn_unused_result [-Wunused-result]
main.cpp:438:18: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result]
g++ -DMAXGAP=0 -DMAXHITS=1000 -DTHREAD -funroll-loops -Lsamtools -Isamtools -O3   -DREAD_144 -c pairs.cpp -o pairs.o
pairs.cpp: In member function ‘void PairAlign::s_OutHitPair(PairHit, int, RefSeq&, std::string&)’:
pairs.cpp:343:185: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘std::basic_string<char>::size_type {aka long unsigned int}’ [-Wformat]
pairs.cpp:395:185: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘std::basic_string<char>::size_type {aka long unsigned int}’ [-Wformat]
pairs.cpp: In member function ‘void PairAlign::s_OutHitUnpair(int, int, int, int, int, Hit, int, Hit, RefSeq&, std::string&)’:
pairs.cpp:461:177: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘std::basic_string<char>::size_type {aka long unsigned int}’ [-Wformat]
pairs.cpp:466:217: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘std::basic_string<char>::size_type {aka long unsigned int}’ [-Wformat]
g++ -DMAXGAP=0 -DMAXHITS=1000 -DTHREAD -funroll-loops -Lsamtools -Isamtools -O3   -DREAD_144 -c param.cpp -o param.o
g++ -DMAXGAP=0 -DMAXHITS=1000 -DTHREAD -funroll-loops -Lsamtools -Isamtools -O3   -DREAD_144 -c reads.cpp -o reads.o
g++ -DMAXGAP=0 -DMAXHITS=1000 -DTHREAD -funroll-loops -Lsamtools -Isamtools -O3   -DREAD_144 -c utilities.cpp -o utilities.o
(cd samtools; make)
make[1]: Entering directory `/home/kpasumar/scripts/bsmap-2.2/samtools'
make[2]: Entering directory `/home/kpasumar/scripts/bsmap-2.2/samtools'
make[3]: Entering directory `/home/kpasumar/scripts/bsmap-2.2/samtools'
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function ‘bgzf_close’:
bgzf.c:630:8: warning: variable ‘count’ set but not used [-Wunused-but-set-variable]
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
bam_index.c: In function ‘bam_index_load_core’:
bam_index.c:330:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:337:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:350:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:353:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:357:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:361:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:371:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:375:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
bam_pileup.c: In function ‘resolve_cigar2’:
bam_pileup.c:75:9: warning: variable ‘is_head’ set but not used [-Wunused-but-set-variable]
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
razf.c: In function ‘razf_close’:
razf.c:804:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c:805:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c:808:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c:810:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c: In function ‘razf_end_flush’:
razf.c:258:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c: In function ‘_razf_write’:
razf.c:201:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c: In function ‘save_zindex’:
razf.c:96:17: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c:99:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c:106:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c:107:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c: In function ‘razf_flush’:
razf.c:221:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c:234:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
knetfile.c: In function ‘khttp_connect_file’:
knetfile.c:415:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
knetfile.c: In function ‘kftp_send_cmd’:
knetfile.c:236:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
bam_reheader.c: In function ‘bam_reheader’:
bam_reheader.c:11:16: warning: variable ‘old’ set but not used [-Wunused-but-set-variable]
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
kprobaln.c: In function ‘kpa_glocal’:
kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
make[3]: Leaving directory `/home/kpasumar/scripts/bsmap-2.2/samtools'
make[3]: Entering directory `/home/kpasumar/scripts/bsmap-2.2/samtools/bcftools'
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function ‘bcf_em1’:
em.c:175:12: warning: variable ‘n2’ set but not used [-Wunused-but-set-variable]
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
make[3]: Leaving directory `/home/kpasumar/scripts/bsmap-2.2/samtools/bcftools'
make[3]: Entering directory `/home/kpasumar/scripts/bsmap-2.2/samtools/misc'
make[3]: Nothing to be done for `lib'.
make[3]: Leaving directory `/home/kpasumar/scripts/bsmap-2.2/samtools/misc'
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
cut_target.c: In function ‘main_cut_target’:
cut_target.c:137:36: warning: variable ‘lastpos’ set but not used [-Wunused-but-set-variable]
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -Wall -O2  -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools  libbam.a -lbcf -lcurses  -lm -lz
make[2]: Leaving directory `/home/kpasumar/scripts/bsmap-2.2/samtools'
make[2]: Entering directory `/home/kpasumar/scripts/bsmap-2.2/samtools/bcftools'
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -Wall -O2  -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L.  -lbcf -lm -lz
make[2]: Leaving directory `/home/kpasumar/scripts/bsmap-2.2/samtools/bcftools'
make[2]: Entering directory `/home/kpasumar/scripts/bsmap-2.2/samtools/misc'
gcc -c -g -Wall -O2  -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -Wall -O2  -o md5sum-lite md5sum-lite.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
gcc -g -Wall -O2  -c -I.. -o md5fa.o md5fa.c
gcc -g -Wall -O2  -o md5fa md5.o md5fa.o -lz
gcc -g -Wall -O2  -o maq2sam-short maq2sam.c -lz
gcc -g -Wall -O2  -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -Wall -O2  -o wgsim wgsim.o -lm
make[2]: Leaving directory `/home/kpasumar/scripts/bsmap-2.2/samtools/misc'
make[1]: Leaving directory `/home/kpasumar/scripts/bsmap-2.2/samtools'
g++ -DMAXGAP=0 -DMAXHITS=1000 -DTHREAD -funroll-loops -Lsamtools -Isamtools -O3   -DREAD_144 align.o dbseq.o main.o pairs.o param.o reads.o utilities.o -o bsmap -lpthread -lz -lbam
samtools/libbam.a(bam_import.o): In function `ks_getuntil':
/home/kpasumar/scripts/bsmap-2.2/samtools/bam_import.c:17: undefined reference to `gzread'
samtools/libbam.a(bam_import.o): In function `__bam_get_lines':
/home/kpasumar/scripts/bsmap-2.2/samtools/bam_import.c:76: undefined reference to `gzdopen'
/home/kpasumar/scripts/bsmap-2.2/samtools/bam_import.c:92: undefined reference to `gzclose'
/home/kpasumar/scripts/bsmap-2.2/samtools/bam_import.c:76: undefined reference to `gzopen64'
samtools/libbam.a(bam_import.o): In function `sam_header_read2':
/home/kpasumar/scripts/bsmap-2.2/samtools/bam_import.c:126: undefined reference to `gzdopen'
samtools/libbam.a(bam_import.o): In function `ks_getc':
/home/kpasumar/scripts/bsmap-2.2/samtools/bam_import.c:17: undefined reference to `gzread'
samtools/libbam.a(bam_import.o): In function `sam_header_read2':
/home/kpasumar/scripts/bsmap-2.2/samtools/bam_import.c:147: undefined reference to `gzclose'
/home/kpasumar/scripts/bsmap-2.2/samtools/bam_import.c:126: undefined reference to `gzopen64'
samtools/libbam.a(bam_import.o): In function `sam_open':
/home/kpasumar/scripts/bsmap-2.2/samtools/bam_import.c:463: undefined reference to `gzdopen'
/home/kpasumar/scripts/bsmap-2.2/samtools/bam_import.c:463: undefined reference to `gzopen64'
samtools/libbam.a(bam_import.o): In function `sam_close':
/home/kpasumar/scripts/bsmap-2.2/samtools/bam_import.c:476: undefined reference to `gzclose'
samtools/libbam.a(bgzf.o): In function `deflate_block':
/home/kpasumar/scripts/bsmap-2.2/samtools/bgzf.c:311: undefined reference to `deflate'
/home/kpasumar/scripts/bsmap-2.2/samtools/bgzf.c:313: undefined reference to `deflateEnd'
/home/kpasumar/scripts/bsmap-2.2/samtools/bgzf.c:305: undefined reference to `deflateInit2_'
/home/kpasumar/scripts/bsmap-2.2/samtools/bgzf.c:329: undefined reference to `deflateEnd'
/home/kpasumar/scripts/bsmap-2.2/samtools/bgzf.c:345: undefined reference to `crc32'
/home/kpasumar/scripts/bsmap-2.2/samtools/bgzf.c:346: undefined reference to `crc32'
samtools/libbam.a(bgzf.o): In function `inflate_block':
/home/kpasumar/scripts/bsmap-2.2/samtools/bgzf.c:380: undefined reference to `inflateInit2_'
/home/kpasumar/scripts/bsmap-2.2/samtools/bgzf.c:385: undefined reference to `inflate'
/home/kpasumar/scripts/bsmap-2.2/samtools/bgzf.c:391: undefined reference to `inflateEnd'
/home/kpasumar/scripts/bsmap-2.2/samtools/bgzf.c:387: undefined reference to `inflateEnd'
samtools/libbam.a(razf.o): In function `_razf_write':
/home/kpasumar/scripts/bsmap-2.2/samtools/razf.c:197: undefined reference to `deflate'
samtools/libbam.a(razf.o): In function `razf_open_w':
/home/kpasumar/scripts/bsmap-2.2/samtools/razf.c:170: undefined reference to `deflateInit2_'
/home/kpasumar/scripts/bsmap-2.2/samtools/razf.c:186: undefined reference to `deflateSetHeader'
samtools/libbam.a(razf.o): In function `razf_open_r':
/home/kpasumar/scripts/bsmap-2.2/samtools/razf.c:389: undefined reference to `inflateInit2_'
/home/kpasumar/scripts/bsmap-2.2/samtools/razf.c:390: undefined reference to `inflateEnd'
samtools/libbam.a(razf.o): In function `_razf_read':
/home/kpasumar/scripts/bsmap-2.2/samtools/razf.c:602: undefined reference to `inflate'
samtools/libbam.a(razf.o): In function `razf_flush':
/home/kpasumar/scripts/bsmap-2.2/samtools/razf.c:230: undefined reference to `deflate'
samtools/libbam.a(razf.o): In function `_razf_reset_read':
/home/kpasumar/scripts/bsmap-2.2/samtools/razf.c:709: undefined reference to `inflateReset'
/home/kpasumar/scripts/bsmap-2.2/samtools/razf.c:709: undefined reference to `inflateReset'
samtools/libbam.a(razf.o): In function `razf_close':
/home/kpasumar/scripts/bsmap-2.2/samtools/razf.c:826: undefined reference to `inflateEnd'
samtools/libbam.a(razf.o): In function `razf_end_flush':
/home/kpasumar/scripts/bsmap-2.2/samtools/razf.c:254: undefined reference to `deflate'
samtools/libbam.a(razf.o): In function `razf_close':
/home/kpasumar/scripts/bsmap-2.2/samtools/razf.c:800: undefined reference to `deflateEnd'
collect2: ld returned 1 exit status
make: *** [bsmap] Error 1