Burrows-Wheeler Aligner

Excellent software - essential for many genomics applications.

Great software, thank you.

Error with make in the latest version. angelinadaniel@ubuntu:/media/angelinadaniel/linux/bwa-0.7.3a$ make gcc -c -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD ksw.c -o ksw.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o bwt.c: In function ‘bwt_restore_bwt’: bwt.c:408:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwt.c:409:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwt.c:410:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwt.c: In function ‘bwt_restore_sa’: bwt.c:382:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwt.c:384:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwt.c:385:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwt.c:386:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwt.c:393:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o bntseq.c: In function ‘bns_restore_core’: bntseq.c:98:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] bntseq.c:106:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] bntseq.c:114:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] bntseq.c:123:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] bntseq.c:129:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwa.c -o bwa.o bwa.c: In function ‘bwa_idx_load’: bwa.c:261:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwamem.c -o bwamem.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwamem_pair.c -o bwamem_pair.o ar -csru libbwa.a utils.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o bwt_gen.c: In function ‘BWTIncBuildRelativeRank’: bwt_gen.c:873:10: warning: variable ‘oldInverseSa0RelativeRank’ set but not used [-Wunused-but-set-variable] bwt_gen.c: In function ‘BWTIncMergeBwt’: bwt_gen.c:947:15: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable] bwt_gen.c: In function ‘BWTIncConstructFromPacked’: bwt_gen.c:1452:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwt_gen.c:1468:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwt_gen.c:1483:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwase.c -o bwase.o bwase.c: In function ‘bwa_sai2sam_se_core’: bwase.c:516:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwase.c:530:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwase.c:535:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwase.c: In function ‘bwa_refine_gapped’: bwase.c:309:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD is.c -o is.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o bwtindex.c: In function ‘bwt_pac2bwt’: bwtindex.c:73:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwtindex.c: In function ‘bwa_seq_len’: bwtindex.c:52:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwape.c -o bwape.o bwape.c: In function ‘bwa_sai2sam_pe_core’: bwape.c:642:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwape.c:645:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwape.c:653:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwape.c: In function ‘bwa_paired_sw’: bwape.c:497:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwape.c: In function ‘bwa_cal_pac_pos_pe’: bwape.c:278:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwape.c:282:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -g -Wall -O2 -DHAVE_PTHREAD kopen.c -o kopen.o kopen.c: In function ‘kopen’: kopen.c:265:8: warning: ignoring return value of ‘pipe’, declared with attribute warn_unused_result [-Wunused-result] kopen.c: In function ‘http_open’: kopen.c:93:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] kopen.c: In function ‘kftp_send_cmd’: kopen.c:146:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -g -Wall -O2 -DHAVE_PTHREAD pemerge.c -o pemerge.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o bwtsw2_aux.c: In function ‘bsw2_aln’: bwtsw2_aux.c:738:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD fastmap.c -o fastmap.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_pair.c -o bwtsw2_pair.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o gcc -g -Wall -O2 -DHAVE_PTHREAD QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o is.o bwtindex.o bwape.o kopen.o pemerge.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread gcc -c -g -Wall -O2 -DHAVE_PTHREAD example.c -o example.o gcc -g -Wall -O2 -DHAVE_PTHREAD example.o -o bwamem-lite -L. -lbwa -lm -lz -lpthread

HI, I downloaded the latest bwa (already been using bwa ). I tried to do 'make' to install but get an error, In file included from bwtaln.h:6, from bwaseqio.c:4: bwt.h:63: error: expected specifier-qualifier-list before âsize_tâ make: *** [bwaseqio.o] Error 1 Please can you help me here. I know this is a reviews page, but cannot find a way to post the message on any forum. Thanks.

Only consider BWA version 0.6.2 as the latest sufficiently tested and stable version. That said, this is a very good application for aligning short sequencing reads.