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Old 01-14-2014, 03:18 AM   #21
maivantan
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Location: Vietnam

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Posts: 51
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Dear GenoMax
I tried bellow commands, i think it worked.

USER-no-MacBook-Pro-4:bowtie2-2.1.0 user$ samtools mpileup -uf example/reference/lambda_virus.fa eg2.sorted.bam | ~/tan_analysis/samtools-0.1.19/bcftools/bcftools view -bvcg - > eg2.raw.bcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[afs] 0:4254.406 1:3.562 2:113.032
USER-no-MacBook-Pro-4:bowtie2-2.1.0 user$ ~/tan_analysis/samtools-0.1.19/bcftools/bcftools view eg2.raw.bcf
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT eg2.sorted.bam
gi|9626243|ref|NC_001416.1| 2 . GGCG GGCGCGGGGGCG 5.08 . INDEL;IS=1,0.500000;DP=2;AF1=1;AC1=2;DP4=0,0,1,0;MQ=42;FQ=-37.5 GT:PL:GQ 1/1:41,3,0:3
gi|9626243|ref|NC_001416.1| 244 . CA C 30.6 . INDEL;IS=1,0.028571;DP=35;VDB=1.039505e-01;AF1=1;AC1=2;DP4=0,0,4,2;MQ=37;FQ=-52.5 GT:PL:GQ 1/1:71,18,0:33
gi|9626243|ref|NC_001416.1| 245 . ATT AT 194 . INDEL;IS=33,0.942857;DP=34;VDB=2.115336e-01;AF1=1;AC1=2;DP4=0,0,13,12;MQ=37;FQ=-110 GT:PL:GQ 1/1:235,75,0:99
gi|

is it correct? can you check it?

Thank you very much
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Old 01-14-2014, 03:22 AM   #22
GenoMax
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It does look like the command worked this time. You should be set to go to the next step.
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Old 01-14-2014, 03:24 AM   #23
maivantan
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yes,
I am looking how go to next steps.
Do you have any suggestion?
Thank you very much again
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Old 01-14-2014, 03:26 AM   #24
GenoMax
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I though you were following the guide on multisample SNP calling on this page: http://samtools.sourceforge.net/mpileup.shtml
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Old 01-14-2014, 03:29 AM   #25
maivantan
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i am going to try it.
Thank you very much GenoMax,
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Old 03-18-2014, 06:28 AM   #26
Hamid
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Default installing samtools on mac

Hi,

Does anyone have a guide on how to properly install samtools version 0.1.19 on a macbook pro with osx 10.9.2.
I would greatly appreciate your help.

Thank you.

Hamid
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Old 03-18-2014, 09:21 AM   #27
GenoMax
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Quote:
Originally Posted by Hamid View Post
Hi,

Does anyone have a guide on how to properly install samtools version 0.1.19 on a macbook pro with osx 10.9.2.
I would greatly appreciate your help.

Thank you.

Hamid
1. Download and install Xcode 5.1 from app store if you have not done so already.
2. Download samtools source from: http://sourceforge.net/projects/samt...d?source=files
3. Change to the directory where you downloaded the source file.

Code:
$ bunzip2 samtools*.bz2
$ tar -xvf samtools-0.1.19.tar
$ cd samtools-0.1.19
$ make
If all goes well there should be an executable produced that you can test run

Code:
$ ./samtools
You strictly do not have to "install", but if you want you could copy the executable to a directory that is in your $PATH in case you do not want to provide full path to the samtools executable when you run it.

Last edited by GenoMax; 03-18-2014 at 09:25 AM.
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Old 03-20-2014, 12:33 PM   #28
Hamid
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Thank you very much GenoMax...It worked great.

Is it possible to have the commands be universally available from any directory without having to specify the path?

Thank you

hamid
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Old 03-20-2014, 04:35 PM   #29
GenoMax
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You can copy the samtools executable to a directory in your $PATH.

Code:
$ echo $PATH
Following assumes that you have a /usr/local/bin and it is in your $PATH. If this directory does not exist then you could choose to use /bin.

Go to the directory containing the samtools executable and do the following:

Code:
$ sudo cp samtools /usr/local/bin
That should allow you to run samtools (or other executables) without having to provide full path each time.
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Old 03-22-2014, 02:03 PM   #30
beline
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Default Error installing samtools to my Mac

Quote:
Originally Posted by GenoMax View Post
1. Download and install Xcode 5.1 from app store if you have not done so already.
2. Download samtools source from: http://sourceforge.net/projects/samt...d?source=files
3. Change to the directory where you downloaded the source file.

Code:
$ bunzip2 samtools*.bz2
$ tar -xvf samtools-0.1.19.tar
$ cd samtools-0.1.19
$ make
If all goes well there should be an executable produced that you can test run

Code:
$ ./samtools
You strictly do not have to "install", but if you want you could copy the executable to a directory that is in your $PATH in case you do not want to provide full path to the samtools executable when you run it.
I am having trouble with this exact scenario. After I typing the command "make" I get this error message:

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:44:1: warning: unused function 'kh_clear_cache' [-Wunused-function]
KHASH_MAP_INIT_INT64(cache, cache_t)
^
./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:228:1: note: expanded from here
kh_clear_cache
^
1 warning generated.
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
bam_aux.c:5:1: warning: unused function 'kh_clear_s' [-Wunused-function]
KHASH_MAP_INIT_STR(s, int)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:197:1: note: expanded from here
kh_clear_s
^
bam_aux.c:5:1: warning: unused function 'kh_del_s' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:211:1: note: expanded from here
kh_del_s
^
bam_aux.c:6:1: warning: unused function 'kh_init_r2l' [-Wunused-function]
KHASH_MAP_INIT_STR(r2l, str_p)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:168:23: note: expanded from macro 'KHASH_INIT2'
SCOPE kh_##name##_t *kh_init_##name() { \
^
<scratch space>:218:1: note: expanded from here
kh_init_r2l
^
bam_aux.c:6:1: warning: unused function 'kh_destroy_r2l' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:171:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_destroy_##name(kh_##name##_t *h) \
^
<scratch space>:223:1: note: expanded from here
kh_destroy_r2l
^
bam_aux.c:6:1: warning: unused function 'kh_clear_r2l' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:226:1: note: expanded from here
kh_clear_r2l
^
bam_aux.c:6:1: warning: unused function 'kh_get_r2l' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \
^
<scratch space>:229:1: note: expanded from here
kh_get_r2l
^
bam_aux.c:6:1: warning: unused function 'kh_put_r2l' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:260:16: note: expanded from macro 'KHASH_INIT2'
SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
^
<scratch space>:235:1: note: expanded from here
kh_put_r2l
^
bam_aux.c:6:1: warning: unused function 'kh_del_r2l' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:240:1: note: expanded from here
kh_del_r2l
^
8 warnings generated.
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
bam_import.c:18:1: warning: unused function 'kh_clear_ref' [-Wunused-function]
KHASH_MAP_INIT_STR(ref, uint64_t)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:197:1: note: expanded from here
kh_clear_ref
^
bam_import.c:18:1: warning: unused function 'kh_get_ref' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \
^
<scratch space>:200:1: note: expanded from here
kh_get_ref
^
bam_import.c:18:1: warning: unused function 'kh_del_ref' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:211:1: note: expanded from here
kh_del_ref
^
3 warnings generated.
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:64:1: warning: unused function 'kh_clear_i' [-Wunused-function]
KHASH_MAP_INIT_INT(i, bam_binlist_t)
^
./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:211:1: note: expanded from here
kh_clear_i
^
bam_index.c:64:1: warning: unused function 'kh_del_i' [-Wunused-function]
./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:225:1: note: expanded from here
kh_del_i
^
2 warnings generated.
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
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
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
faidx.c:14:1: warning: unused function 'kh_clear_s' [-Wunused-function]
KHASH_MAP_INIT_STR(s, faidx1_t)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:154:1: note: expanded from here
kh_clear_s
^
faidx.c:14:1: warning: unused function 'kh_del_s' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:168:1: note: expanded from here
kh_del_s
^
2 warnings generated.
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
bedidx.c:24:1: warning: unused function 'kh_clear_reg' [-Wunused-function]
KHASH_MAP_INIT_STR(reg, bed_reglist_t)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:207:1: note: expanded from here
kh_clear_reg
^
bedidx.c:24:1: warning: unused function 'kh_del_reg' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:221:1: note: expanded from here
kh_del_reg
^
2 warnings generated.
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
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
sam_header.c:9:1: warning: unused function 'kh_clear_str' [-Wunused-function]
KHASH_MAP_INIT_STR(str, const char *)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:154:1: note: expanded from here
kh_clear_str
^
sam_header.c:9:1: warning: unused function 'kh_del_str' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:168:1: note: expanded from here
kh_del_str
^
2 warnings generated.
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
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
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
/bin/sh: line 0: cd: /Users/Tiger: No such file or directory
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
vcf.c:238:15: warning: explicitly assigning a variable of type 'int' to itself [-Wself-assign]
endblock: i = i;
~ ^ ~
vcf.c:8:1: warning: unused function 'ks_getc' [-Wunused-function]
KSTREAM_INIT(gzFile, gzread, 4096)
^
../kseq.h:142:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETC(__read, __bufsize) \
^
../kseq.h:66:20: note: expanded from macro '__KS_GETC'
static inline int ks_getc(kstream_t *ks) \
^
2 warnings generated.
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
bcfutils.c:6:1: warning: unused function 'kh_clear_str2id' [-Wunused-function]
KHASH_MAP_INIT_STR(str2id, int)
^
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:37:1: note: expanded from here
kh_clear_str2id
^
bcfutils.c:6:1: warning: unused function 'kh_del_str2id' [-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:51:1: note: expanded from here
kh_del_str2id
^
2 warnings generated.
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
prob1.c:10:1: warning: unused function 'ks_getc' [-Wunused-function]
KSTREAM_INIT(gzFile, gzread, 16384)
^
../kseq.h:142:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETC(__read, __bufsize) \
^
../kseq.h:66:20: note: expanded from macro '__KS_GETC'
static inline int ks_getc(kstream_t *ks) \
^
1 warning generated.
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
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
/bin/sh: line 0: cd: /Users/Tiger: No such file or directory
/bin/sh: line 0: cd: misc: No such file or directory
make[2]: Nothing to be done for `lib'.
/bin/sh: line 0: cd: /Users/Tiger: No such file or directory
make[1]: *** [lib-recur] Error 1
make: *** [all-recur] Error 1

When I attempt the "make" command again I get the abbreviated version:

make[2]: Nothing to be done for `lib'.
/bin/sh: line 0: cd: /Users/Tiger: No such file or directory
make[2]: Nothing to be done for `lib'.
/bin/sh: line 0: cd: /Users/Tiger: No such file or directory
/bin/sh: line 0: cd: misc: No such file or directory
make[2]: Nothing to be done for `lib'.
/bin/sh: line 0: cd: /Users/Tiger: No such file or directory
make[1]: *** [lib-recur] Error 1
make: *** [all-recur] Error 1

I've tried this with both samtools 0.1.18 and 0.1.19. Any thoughts?
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Old 03-22-2014, 07:41 PM   #31
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,049
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What version of OS X and XCode are you running? You are issuing the make command inside the samtools-0.1.19 directory, correct?
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Old 03-22-2014, 10:32 PM   #32
beline
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Location: Vancouver, BC

Join Date: Mar 2014
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I'm using OS X ver 10.9.2 and Xcode 5.1 (5B130a) and yes I'm issuing the command into the samtools-0.1.19 directory.
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Old 03-23-2014, 06:09 AM   #33
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,049
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You have perhaps tried this already but if not can you start with a fresh download of the source and retry the compilation?

I assume your samtools directory is right under /Users/Tiger. I am not sure why you are getting errors for that top level directory.
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Old 03-23-2014, 10:24 AM   #34
beline
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Location: Vancouver, BC

Join Date: Mar 2014
Posts: 3
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That directory is "/Users/Tiger Mac"... and not just "/Users/Tiger". Now that you've pointed it out it must be that space that is giving me trouble.

I created a new user with admin privileges and started from scratch there. Was able to successfully compile Samtools with the resulting executable! Thank you.

I still get a long list of warnings as follows but not that last bit about there being "No such file or directory". I'm assuming the warnings are not serious.

computer-3esktop unixuser$ cd samtools-0.1.19
computer-3:samtools-0.1.19 unixuser$ make
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
bgzf.c:82:1: warning: unused function 'kh_clear_cache' [-Wunused-function]
KHASH_MAP_INIT_INT64(cache, cache_t)
^
./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_i...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h...
^
<scratch space>:91:1: note: expanded from here
kh_clear_cache
^
1 warning generated.
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
bam_aux.c:5:1: warning: unused function 'kh_clear_s' [-Wunused-function]
KHASH_MAP_INIT_STR(s, int)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h...
^
<scratch space>:193:1: note: expanded from here
kh_clear_s
^
bam_aux.c:5:1: warning: unused function 'kh_del_s' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
^
<scratch space>:207:1: note: expanded from here
kh_del_s
^
bam_aux.c:6:1: warning: unused function 'kh_init_r2l' [-Wunused-function]
KHASH_MAP_INIT_STR(r2l, str_p)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:168:23: note: expanded from macro 'KHASH_INIT2'
SCOPE kh_##name##_t *kh_init_##name() ...
^
<scratch space>:214:1: note: expanded from here
kh_init_r2l
^
bam_aux.c:6:1: warning: unused function 'kh_destroy_r2l' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:171:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_destroy_##name(kh_##name##_t *h...
^
<scratch space>:219:1: note: expanded from here
kh_destroy_r2l
^
bam_aux.c:6:1: warning: unused function 'kh_clear_r2l' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h...
^
<scratch space>:222:1: note: expanded from here
kh_clear_r2l
^
bam_aux.c:6:1: warning: unused function 'kh_get_r2l' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key...
^
<scratch space>:225:1: note: expanded from here
kh_get_r2l
^
bam_aux.c:6:1: warning: unused function 'kh_put_r2l' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:260:16: note: expanded from macro 'KHASH_INIT2'
SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
^
<scratch space>:231:1: note: expanded from here
kh_put_r2l
^
bam_aux.c:6:1: warning: unused function 'kh_del_r2l' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
^
<scratch space>:236:1: note: expanded from here
kh_del_r2l
^
8 warnings generated.
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
bam_import.c:18:1: warning: unused function 'kh_clear_ref' [-Wunused-function]
KHASH_MAP_INIT_STR(ref, uint64_t)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h...
^
<scratch space>:193:1: note: expanded from here
kh_clear_ref
^
bam_import.c:18:1: warning: unused function 'kh_get_ref' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key...
^
<scratch space>:196:1: note: expanded from here
kh_get_ref
^
bam_import.c:18:1: warning: unused function 'kh_del_ref' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
^
<scratch space>:207:1: note: expanded from here
kh_del_ref
^
3 warnings generated.
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:64:1: warning: unused function 'kh_clear_i' [-Wunused-function]
KHASH_MAP_INIT_INT(i, bam_binlist_t)
^
./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h...
^
<scratch space>:211:1: note: expanded from here
kh_clear_i
^
bam_index.c:64:1: warning: unused function 'kh_del_i' [-Wunused-function]
./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
^
<scratch space>:225:1: note: expanded from here
kh_del_i
^
2 warnings generated.
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
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
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
faidx.c:14:1: warning: unused function 'kh_clear_s' [-Wunused-function]
KHASH_MAP_INIT_STR(s, faidx1_t)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h...
^
<scratch space>:154:1: note: expanded from here
kh_clear_s
^
faidx.c:14:1: warning: unused function 'kh_del_s' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
^
<scratch space>:168:1: note: expanded from here
kh_del_s
^
2 warnings generated.
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
bedidx.c:24:1: warning: unused function 'kh_clear_reg' [-Wunused-function]
KHASH_MAP_INIT_STR(reg, bed_reglist_t)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h...
^
<scratch space>:207:1: note: expanded from here
kh_clear_reg
^
bedidx.c:24:1: warning: unused function 'kh_del_reg' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
^
<scratch space>:221:1: note: expanded from here
kh_del_reg
^
2 warnings generated.
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
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
sam_header.c:9:1: warning: unused function 'kh_clear_str' [-Wunused-function]
KHASH_MAP_INIT_STR(str, const char *)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h...
^
<scratch space>:154:1: note: expanded from here
kh_clear_str
^
sam_header.c:9:1: warning: unused function 'kh_del_str' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
^
<scratch space>:168:1: note: expanded from here
kh_del_str
^
2 warnings generated.
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
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
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
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
vcf.c:243:15: warning: explicitly assigning a variable of type 'int' to itself
[-Wself-assign]
endblock: i = i;
~ ^ ~
vcf.c:8:1: warning: unused function 'ks_getc' [-Wunused-function]
KSTREAM_INIT(gzFile, gzread, 4096)
^
../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETC(__read, __bufsize) \
^
../kseq.h:67:20: note: expanded from macro '__KS_GETC'
static inline int ks_getc(kstream_t *ks...
^
2 warnings generated.
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
bcfutils.c:7:1: warning: unused function 'kh_clear_str2id' [-Wunused-function]
KHASH_MAP_INIT_STR(str2id, int)
^
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h...
^
<scratch space>:34:1: note: expanded from here
kh_clear_str2id
^
bcfutils.c:7:1: warning: unused function 'kh_del_str2id' [-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
^
<scratch space>:48:1: note: expanded from here
kh_del_str2id
^
2 warnings generated.
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
prob1.c:13:1: warning: unused function 'ks_getc' [-Wunused-function]
KSTREAM_INIT(gzFile, gzread, 16384)
^
../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETC(__read, __bufsize) \
^
../kseq.h:67:20: note: expanded from macro '__KS_GETC'
static inline int ks_getc(kstream_t *ks...
^
1 warning generated.
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
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[2]: Nothing to be done for `lib'.
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
sam_view.c:12:1: warning: unused function 'kh_clear_rg' [-Wunused-function]
KHASH_SET_INIT_STR(rg)
^
./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'
KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_ha...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h...
^
<scratch space>:34:1: note: expanded from here
kh_clear_rg
^
sam_view.c:12:1: warning: unused function 'kh_del_rg' [-Wunused-function]
./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'
KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_ha...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
^
<scratch space>:48:1: note: expanded from here
kh_del_rg
^
2 warnings generated.
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
bam_rmdup.c:12:1: warning: unused function 'kh_get_pos' [-Wunused-function]
KHASH_MAP_INIT_INT64(pos, bam1_p)
^
./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_i...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key...
^
<scratch space>:225:1: note: expanded from here
kh_get_pos
^
bam_rmdup.c:12:1: warning: unused function 'kh_del_pos' [-Wunused-function]
./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_i...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
^
<scratch space>:236:1: note: expanded from here
kh_del_pos
^
bam_rmdup.c:20:1: warning: unused function 'kh_clear_lib' [-Wunused-function]
KHASH_MAP_INIT_STR(lib, lib_aux_t)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h...
^
<scratch space>:253:1: note: expanded from here
kh_clear_lib
^
bam_rmdup.c:20:1: warning: unused function 'kh_del_lib' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
^
<scratch space>:267:1: note: expanded from here
kh_del_lib
^
4 warnings generated.
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
bam_rmdupse.c:18:1: warning: unused function 'kh_clear_best' [-Wunused-function]
KHASH_MAP_INIT_INT(best, elem_p)
^
./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h...
^
<scratch space>:95:1: note: expanded from here
kh_clear_best
^
bam_rmdupse.c:18:1: warning: unused function 'kh_get_best' [-Wunused-function]
./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key...
^
<scratch space>:98:1: note: expanded from here
kh_get_best
^
bam_rmdupse.c:25:1: warning: unused function 'kh_clear_lib' [-Wunused-function]
KHASH_MAP_INIT_STR(lib, lib_aux_t)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h...
^
<scratch space>:126:1: note: expanded from here
kh_clear_lib
^
bam_rmdupse.c:25:1: warning: unused function 'kh_del_lib' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
^
<scratch space>:140:1: note: expanded from here
kh_del_lib
^
4 warnings generated.
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
bam2bcf_indel.c:32:52: warning: for loop has empty body [-Wempty-body]
...for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p;
^
bam2bcf_indel.c:32:52: note: put the semicolon on a separate line to silence
this warning
bam2bcf_indel.c:33:52: warning: for loop has empty body [-Wempty-body]
...for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q;
^
bam2bcf_indel.c:33:52: note: put the semicolon on a separate line to silence
this warning
bam2bcf_indel.c:9:1: warning: unused function 'kh_clear_rg' [-Wunused-function]
KHASH_SET_INIT_STR(rg)
^
./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'
KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_ha...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h...
^
<scratch space>:193:1: note: expanded from here
kh_clear_rg
^
bam2bcf_indel.c:9:1: warning: unused function 'kh_del_rg' [-Wunused-function]
./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'
KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_ha...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
^
<scratch space>:207:1: note: expanded from here
kh_del_rg
^
4 warnings generated.
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
errmod.c:79:8: warning: self-comparison always evaluates to false
[-Wtautological-compare]
if (m > m) return -1;
^
1 warning generated.
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
sample.c:5:1: warning: unused function 'kh_clear_sm' [-Wunused-function]
KHASH_MAP_INIT_STR(sm, int)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h...
^
<scratch space>:136:1: note: expanded from here
kh_clear_sm
^
sample.c:5:1: warning: unused function 'kh_del_sm' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
^
<scratch space>:150:1: note: expanded from here
kh_del_sm
^
2 warnings generated.
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
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
phase.c:45:1: warning: unused function 'kh_clear_set64' [-Wunused-function]
KHASH_SET_INIT_INT64(set64)
^
./khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64'
KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int6...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h...
^
<scratch space>:40:1: note: expanded from here
kh_clear_set64
^
phase.c:45:1: warning: unused function 'kh_del_set64' [-Wunused-function]
./khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64'
KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int6...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
^
<scratch space>:54:1: note: expanded from here
kh_del_set64
^
phase.c:46:1: warning: unused function 'kh_clear_64' [-Wunused-function]
KHASH_MAP_INIT_INT64(64, frag_t)
^
./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_i...
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h...
^
<scratch space>:69:1: note: expanded from here
kh_clear_64
^
3 warnings generated.
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 -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
bedcov.c:12:1: warning: unused function 'ks_getc' [-Wunused-function]
KSTREAM_INIT(gzFile, gzread, 16384)
^
./kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETC(__read, __bufsize) \
^
./kseq.h:67:20: note: expanded from macro '__KS_GETC'
static inline int ks_getc(kstream_t *ks...
^
1 warning generated.
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
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
call1.c:17:1: warning: unused function 'ks_getc' [-Wunused-function]
KSTREAM_INIT(gzFile, gzread, 16384)
^
../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETC(__read, __bufsize) \
^
../kseq.h:67:20: note: expanded from macro '__KS_GETC'
static inline int ks_getc(kstream_t *ks...
^
1 warning generated.
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
main.c:9:1: warning: unused function 'ks_getc' [-Wunused-function]
KSTREAM_INIT(gzFile, gzread, 0x10000)
^
../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETC(__read, __bufsize) \
^
../kseq.h:67:20: note: expanded from macro '__KS_GETC'
static inline int ks_getc(kstream_t *ks...
^
1 warning generated.
gcc -g -Wall -O2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
gcc -c -g -Wall -O2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
md5.c:155:27: warning: 'memset' call operates on objects of type
'struct MD5Context' while the size is based on a different type
'struct MD5Context *' [-Wsizeof-pointer-memaccess]
memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */
~~~ ^~~
md5.c:155:27: note: did you mean to dereference the argument to 'sizeof' (and
multiply it by the number of elements)?
memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */
^~~
1 warning generated.
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
md5.c:155:27: warning: 'memset' call operates on objects of type
'struct MD5Context' while the size is based on a different type
'struct MD5Context *' [-Wsizeof-pointer-memaccess]
memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */
~~~ ^~~
md5.c:155:27: note: did you mean to dereference the argument to 'sizeof' (and
multiply it by the number of elements)?
memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */
^~~
1 warning generated.
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 -g -Wall -O2 -c -I.. -o ace2sam.o ace2sam.c
ace2sam.c:33:1: warning: unused function 'ks_getc' [-Wunused-function]
KSTREAM_INIT(gzFile, gzread, 16384)
^
../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETC(__read, __bufsize) \
^
../kseq.h:67:20: note: expanded from macro '__KS_GETC'
static inline int ks_getc(kstream_t *ks...
^
1 warning generated.
gcc -g -Wall -O2 -o ace2sam ace2sam.o -lz
gcc -g -Wall -O2 -c -I.. -o wgsim.o wgsim.c
gcc -g -Wall -O2 -o wgsim wgsim.o -lm -lz
gcc -g -Wall -O2 -c -I.. -o bamcheck.o bamcheck.c
bamcheck.c:52:1: warning: unused function 'kh_init_kh_faidx' [-Wunused-function]
KHASH_MAP_INIT_STR(kh_faidx, faidx1_t)
^
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
../khash.h:168:23: note: expanded from macro 'KHASH_INIT2'
SCOPE kh_##name##_t *kh_init_##name() ...
^
<scratch space>:35:1: note: expanded from here
kh_init_kh_faidx
^
bamcheck.c:52:1: warning: unused function 'kh_destroy_kh_faidx'
[-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
../khash.h:171:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_destroy_##name(kh_##name##_t *h...
^
<scratch space>:40:1: note: expanded from here
kh_destroy_kh_faidx
^
bamcheck.c:52:1: warning: unused function 'kh_clear_kh_faidx'
[-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h...
^
<scratch space>:43:1: note: expanded from here
kh_clear_kh_faidx
^
bamcheck.c:52:1: warning: unused function 'kh_put_kh_faidx' [-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
../khash.h:260:16: note: expanded from macro 'KHASH_INIT2'
SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
^
<scratch space>:52:1: note: expanded from here
kh_put_kh_faidx
^
bamcheck.c:52:1: warning: unused function 'kh_del_kh_faidx' [-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
^
<scratch space>:57:1: note: expanded from here
kh_del_kh_faidx
^
bamcheck.c:53:1: warning: unused function 'kh_init_kh_bam_tid'
[-Wunused-function]
KHASH_MAP_INIT_STR(kh_bam_tid, int)
^
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
../khash.h:168:23: note: expanded from macro 'KHASH_INIT2'
SCOPE kh_##name##_t *kh_init_##name() ...
^
<scratch space>:64:1: note: expanded from here
kh_init_kh_bam_tid
^
bamcheck.c:53:1: warning: unused function 'kh_destroy_kh_bam_tid'
[-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
../khash.h:171:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_destroy_##name(kh_##name##_t *h...
^
<scratch space>:69:1: note: expanded from here
kh_destroy_kh_bam_tid
^
bamcheck.c:53:1: warning: unused function 'kh_clear_kh_bam_tid'
[-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h...
^
<scratch space>:72:1: note: expanded from here
kh_clear_kh_bam_tid
^
bamcheck.c:53:1: warning: unused function 'kh_put_kh_bam_tid'
[-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
../khash.h:260:16: note: expanded from macro 'KHASH_INIT2'
SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
^
<scratch space>:81:1: note: expanded from here
kh_put_kh_bam_tid
^
bamcheck.c:53:1: warning: unused function 'kh_del_kh_bam_tid'
[-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
^
<scratch space>:86:1: note: expanded from here
kh_del_kh_bam_tid
^
bamcheck.c:54:1: warning: unused function 'kh_clear_kh_rg' [-Wunused-function]
KHASH_MAP_INIT_STR(kh_rg, const char *)
^
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h...
^
<scratch space>:101:1: note: expanded from here
kh_clear_kh_rg
^
bamcheck.c:54:1: warning: unused function 'kh_del_kh_rg' [-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
^
../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
^
<scratch space>:115:1: note: expanded from here
kh_del_kh_rg
^
12 warnings generated.
gcc -g -Wall -O2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
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Old 03-23-2014, 11:18 AM   #35
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,049
Default

Spaces in file/directory names will result in unforeseen consequences. If you are coming to Unix from PC/Mac it is a good idea to get into the habit of putting "_" in names when you feel like using a space.

I am little surprised that you are seeing so many warnings but as long as the executable was made and you are able to run it I think it should be fine to go forward.
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Old 05-09-2014, 08:52 AM   #36
SOLiD J
Junior Member
 
Location: State College, PA

Join Date: Jul 2009
Posts: 4
Smile

I had basically the same problem as many on this thread. I have a mac and recently "upgraded" to Mavericks. What ended up working was deleting every version of samtools I have from my laptop. Then following the post I'm quoting here exactly. I didn't even move samtools after I downloaded it, I left it in the Downloads folder just to be safe and now it works. Thank you to all of those that contributed to this thread. I then used another post to place samtools in my PATH and that worked too.



Quote:
Originally Posted by GenoMax View Post
1. Download and install Xcode 5.1 from app store if you have not done so already.
2. Download samtools source from: http://sourceforge.net/projects/samt...d?source=files
3. Change to the directory where you downloaded the source file.

Code:
$ bunzip2 samtools*.bz2
$ tar -xvf samtools-0.1.19.tar
$ cd samtools-0.1.19
$ make
If all goes well there should be an executable produced that you can test run

Code:
$ ./samtools
You strictly do not have to "install", but if you want you could copy the executable to a directory that is in your $PATH in case you do not want to provide full path to the samtools executable when you run it.
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