Hi Craig,
I was trying to compile this program and am having some issues with the compilation.
I have no errors up to the point where I make all for the copyNumberDiff program, but once I try to compile it, the first error that comes out is "copyNumberDiff.c:18:17: error: sam.h: No such file or directory" and then a string of errors follow that might hopefully be resolved from solving this first one.
Is sam.h a file that it should be finding in one of the linked libraries, and I actually have an earlier problem, or is it a header file missing somehow? The second error also arises from searching for sam.h in "kent/src/htslib/" and when I navigate to this directory it is indeed absent, but there is a sam.5, sam.c, and sam.o
Should there be a sam.h here and this is a sign that my kent compilation did not work? In the previous step it seemed successful since as you mentioned, this file was present after doing the "make libs" step: kent/src/lib/x86_64/jkweb.a
If it helps to have the full list of compilation errors I will paste below.
Many thanks for any help you have!
Kim
[hiltbrunner@submit01 copyNumberDiff]$ make all
gcc -O -g -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I/home/ubelix/iee/hiltbrunner/progr/kent/src/hg/inc -I/home/ubelix/iee/hiltbrunner/progr/kent/src/inc -I/home/ubelix/iee/hiltbrunner/progr/gsl-1.16/gsl-1.16_install/include -I/home/ubelix/iee/hiltbrunner/progr/R-3.2.3/include -o copyNumberDiff.o -c copyNumberDiff.c
copyNumberDiff.c:18:17: error: sam.h: No such file or directory
In file included from copyNumberDiff.c:19:
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:14:24: error: htslib/sam.h: No such file or directory
In file included from copyNumberDiff.c:19:
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘samfile_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:16: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘bam_index_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:17: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘bam_header_t’
cc1: warnings being treated as errors
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:18: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:18: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:39: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:42: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:53: error: expected ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:60: error: expected declaration specifiers or ‘...’ before ‘bam_fetch_f’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:61: error: expected declaration specifiers or ‘...’ before ‘samfile_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:70: error: expected declaration specifiers or ‘...’ before ‘bam_fetch_f’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:71: error: expected declaration specifiers or ‘...’ before ‘samfile_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:80: error: expected declaration specifiers or ‘...’ before ‘bam_fetch_f’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:81: error: expected declaration specifiers or ‘...’ before ‘samfile_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:88: error: expected ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:91: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:91: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h: In function ‘bamUnpackCigarElement’:
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:101: error: ‘BAM_CIGAR_SHIFT’ undeclared (first use in this function)
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:101: error: (Each undeclared identifier is reported only once
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:101: error: for each function it appears in.)
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:102: error: ‘BAM_CIGAR_MASK’ undeclared (first use in this function)
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h: At top level:
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:112: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:112: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:118: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:118: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:124: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:124: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:130: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:130: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:133: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:133: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:136: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:136: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:139: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:139: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:142: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:142: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:145: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:145: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:149: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:152: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:152: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:155: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:155: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:160: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:160: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:169: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:169: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
copyNumberDiff.c: In function ‘addReadCounts’:
copyNumberDiff.c:381: error: ‘samfile_t’ undeclared (first use in this function)
copyNumberDiff.c:381: error: ‘samFp’ undeclared (first use in this function)
copyNumberDiff.c:382: error: implicit declaration of function ‘sam_open’
copyNumberDiff.c:383: error: ‘bam1_t’ undeclared (first use in this function)
copyNumberDiff.c:383: error: ‘b’ undeclared (first use in this function)
copyNumberDiff.c:383: error: implicit declaration of function ‘bam_init1’
copyNumberDiff.c:384: error: ‘bam1_core_t’ undeclared (first use in this function)
copyNumberDiff.c:384: error: ‘c’ undeclared (first use in this function)
copyNumberDiff.c:394: error: ‘uint8_t’ undeclared (first use in this function)
copyNumberDiff.c:394: error: ‘seq’ undeclared (first use in this function)
copyNumberDiff.c:395: error: ‘uint32_t’ undeclared (first use in this function)
copyNumberDiff.c:395: error: expected ‘;’ before ‘base’
copyNumberDiff.c:398: error: implicit declaration of function ‘samread’
copyNumberDiff.c:403: error: ‘BAM_FSECONDARY’ undeclared (first use in this function)
copyNumberDiff.c:403: error: ‘BAM_FQCFAIL’ undeclared (first use in this function)
copyNumberDiff.c:403: error: ‘BAM_FDUP’ undeclared (first use in this function)
copyNumberDiff.c:403: error: ‘BAM_FUNMAP’ undeclared (first use in this function)
copyNumberDiff.c:424: error: implicit declaration of function ‘bam_get_seq’
copyNumberDiff.c:427: error: ‘base’ undeclared (first use in this function)
copyNumberDiff.c:427: error: implicit declaration of function ‘bam_seqi’
copyNumberDiff.c:442: error: implicit declaration of function ‘bam_get_cigar’
copyNumberDiff.c:498: error: implicit declaration of function ‘sam_close’
copyNumberDiff.c:499: error: implicit declaration of function ‘bam_destroy1’
make: *** [copyNumberDiff.o] Error 1
Hi Craig,
I was trying to compile this program and am having some issues with the compilation.
I have no errors up to the point where I make all for the copyNumberDiff program, but once I try to compile it, the first error that comes out is "copyNumberDiff.c:18:17: error: sam.h: No such file or directory" and then a string of errors follow that might hopefully be resolved from solving this first one.
Is sam.h a file that it should be finding in one of the linked libraries, and I actually have an earlier problem, or is it a header file missing somehow? The second error also arises from searching for sam.h in "kent/src/htslib/" and when I navigate to this directory it is indeed absent, but there is a sam.5, sam.c, and sam.o
Should there be a sam.h here and this is a sign that my kent compilation did not work? In the previous step it seemed successful since as you mentioned, this file was present after doing the "make libs" step: kent/src/lib/x86_64/jkweb.a
If it helps to have the full list of compilation errors I will paste below.
Many thanks for any help you have!
Kim
[hiltbrunner@submit01 copyNumberDiff]$ make all
gcc -O -g -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I/home/ubelix/iee/hiltbrunner/progr/kent/src/hg/inc -I/home/ubelix/iee/hiltbrunner/progr/kent/src/inc -I/home/ubelix/iee/hiltbrunner/progr/gsl-1.16/gsl-1.16_install/include -I/home/ubelix/iee/hiltbrunner/progr/R-3.2.3/include -o copyNumberDiff.o -c copyNumberDiff.c
copyNumberDiff.c:18:17: error: sam.h: No such file or directory
In file included from copyNumberDiff.c:19:
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:14:24: error: htslib/sam.h: No such file or directory
In file included from copyNumberDiff.c:19:
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘samfile_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:16: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘bam_index_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:17: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘bam_header_t’
cc1: warnings being treated as errors
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:18: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:18: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:39: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:42: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:53: error: expected ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:60: error: expected declaration specifiers or ‘...’ before ‘bam_fetch_f’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:61: error: expected declaration specifiers or ‘...’ before ‘samfile_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:70: error: expected declaration specifiers or ‘...’ before ‘bam_fetch_f’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:71: error: expected declaration specifiers or ‘...’ before ‘samfile_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:80: error: expected declaration specifiers or ‘...’ before ‘bam_fetch_f’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:81: error: expected declaration specifiers or ‘...’ before ‘samfile_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:88: error: expected ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:91: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:91: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h: In function ‘bamUnpackCigarElement’:
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:101: error: ‘BAM_CIGAR_SHIFT’ undeclared (first use in this function)
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:101: error: (Each undeclared identifier is reported only once
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:101: error: for each function it appears in.)
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:102: error: ‘BAM_CIGAR_MASK’ undeclared (first use in this function)
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h: At top level:
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:112: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:112: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:118: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:118: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:124: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:124: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:130: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:130: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:133: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:133: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:136: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:136: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:139: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:139: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:142: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:142: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:145: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:145: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:149: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:152: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:152: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:155: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:155: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:160: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:160: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:169: error: type defaults to ‘int’ in declaration of ‘bam1_t’
/home/ubelix/iee/hiltbrunner/progr/kent/src/inc/bamFile.h:169: error: expected ‘;’, ‘,’ or ‘)’ before ‘’ token
copyNumberDiff.c: In function ‘addReadCounts’:
copyNumberDiff.c:381: error: ‘samfile_t’ undeclared (first use in this function)
copyNumberDiff.c:381: error: ‘samFp’ undeclared (first use in this function)
copyNumberDiff.c:382: error: implicit declaration of function ‘sam_open’
copyNumberDiff.c:383: error: ‘bam1_t’ undeclared (first use in this function)
copyNumberDiff.c:383: error: ‘b’ undeclared (first use in this function)
copyNumberDiff.c:383: error: implicit declaration of function ‘bam_init1’
copyNumberDiff.c:384: error: ‘bam1_core_t’ undeclared (first use in this function)
copyNumberDiff.c:384: error: ‘c’ undeclared (first use in this function)
copyNumberDiff.c:394: error: ‘uint8_t’ undeclared (first use in this function)
copyNumberDiff.c:394: error: ‘seq’ undeclared (first use in this function)
copyNumberDiff.c:395: error: ‘uint32_t’ undeclared (first use in this function)
copyNumberDiff.c:395: error: expected ‘;’ before ‘base’
copyNumberDiff.c:398: error: implicit declaration of function ‘samread’
copyNumberDiff.c:403: error: ‘BAM_FSECONDARY’ undeclared (first use in this function)
copyNumberDiff.c:403: error: ‘BAM_FQCFAIL’ undeclared (first use in this function)
copyNumberDiff.c:403: error: ‘BAM_FDUP’ undeclared (first use in this function)
copyNumberDiff.c:403: error: ‘BAM_FUNMAP’ undeclared (first use in this function)
copyNumberDiff.c:424: error: implicit declaration of function ‘bam_get_seq’
copyNumberDiff.c:427: error: ‘base’ undeclared (first use in this function)
copyNumberDiff.c:427: error: implicit declaration of function ‘bam_seqi’
copyNumberDiff.c:442: error: implicit declaration of function ‘bam_get_cigar’
copyNumberDiff.c:498: error: implicit declaration of function ‘sam_close’
copyNumberDiff.c:499: error: implicit declaration of function ‘bam_destroy1’
make: *** [copyNumberDiff.o] Error 1