compile error of assignment of read-only location

[genetalks-fred]

Hello! I‘m using bwtool for analysis, encountered this error when i install libbeato. gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -fno-strict-aliasing -g -O2 -MT metaBigBam.o -MD -MP -MF .deps/metaBigBam.Tpo -c -o metaBigBam.o metaBigBam.c metaBigBam.c: In function ‘mate_endpos’: metaBigBam.c:485:5: warning: ‘cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations] if (h->cigar_tab == 0) ^~ In file included from ../beato/metaBig.h:20:0, from metaBigBam.c:16: /usr/local/include/htslib/sam.h:74:19: note: declared here const int8_t cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead"); ^~~~~ metaBigBam.c:487:2: warning: ‘cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations] h->cigar_tab = (int8_t)calloc(128, sizeof(int8_t)); ^ In file included from ../beato/metaBig.h:20:0, from metaBigBam.c:16: /usr/local/include/htslib/sam.h:74:19: note: declared here const int8_t cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead"); ^~~~~ metaBigBam.c:489:6: warning: ‘cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations] h->cigar_tab[(int)BAM_CIGAR_STR[i]] = i; ^ In file included from ../beato/metaBig.h:20:0, from metaBigBam.c:16: /usr/local/include/htslib/sam.h:74:19: note: declared here const int8_t cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead"); ^~~~~ metaBigBam.c:489:42: error: assignment of read-only location ‘(h->cigar_tab + (sizetype)"MIDNSHP=XB"[i])’ h->cigar_tab[(int)BAM_CIGAR_STR[i]] = i; ^ metaBigBam.c:502:2: warning: ‘cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations] op = (uint8_t)q >= 128? -1 : h->cigar_tab[(int)q]; ^~ In file included from ../beato/metaBig.h:20:0, from metaBigBam.c:16: /usr/local/include/htslib/sam.h:74:19: note: declared here const int8_t cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");

error: assignment of read-only location ‘*(h->cigar_tab + (sizetype)"MIDNSHP=XB"[i])’ Any advice or help is apreciated, Thanks!

[dfermin]

I have the same issue. Did you get a resolution to it?

[mark-liddell]

Same issue for me when trying the workaround mentioned in #6

[phancanhtrinh]

I have the same issue. Does anyone solve this issue? Could you please help me? Thank you very much!

gcc -DHAVE_CONFIG_H -I. -I..    -I.. -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -fno-strict-aliasing -g -O2 -MT metaBigBam.o -MD -MP -MF .deps/metaBigBam.Tpo -c -o metaBigBam.o metaBigBam.c
metaBigBam.c: In function ‘mate_endpos’:
metaBigBam.c:485:5: warning: ‘cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations]
  485 |     if (h->cigar_tab == 0)
      |     ^~
In file included from ../beato/metaBig.h:20,
                 from metaBigBam.c:16:
/usr/local/include/htslib/sam.h:84:19: note: declared here
   84 |     const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
      |                   ^~~~~~~~~
metaBigBam.c:487:2: warning: ‘cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations]
  487 |  h->cigar_tab = (int8_t*)calloc(128, sizeof(int8_t));
      |  ^
In file included from ../beato/metaBig.h:20,
                 from metaBigBam.c:16:
/usr/local/include/htslib/sam.h:84:19: note: declared here
   84 |     const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
      |                   ^~~~~~~~~
metaBigBam.c:489:6: warning: ‘cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations]
  489 |      h->cigar_tab[(int)BAM_CIGAR_STR[i]] = i;
      |      ^
In file included from ../beato/metaBig.h:20,
                 from metaBigBam.c:16:
/usr/local/include/htslib/sam.h:84:19: note: declared here
   84 |     const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
      |                   ^~~~~~~~~
metaBigBam.c:489:42: error: assignment of read-only location ‘*(h->cigar_tab + (sizetype)"MIDNSHP=XB"[i])’
  489 |      h->cigar_tab[(int)BAM_CIGAR_STR[i]] = i;
      |                                          ^
metaBigBam.c:502:2: warning: ‘cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations]
  502 |  op = (uint8_t)*q >= 128? -1 : h->cigar_tab[(int)*q];
      |  ^~
In file included from ../beato/metaBig.h:20,
                 from metaBigBam.c:16:
/usr/local/include/htslib/sam.h:84:19: note: declared here
   84 |     const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
      |                   ^~~~~~~~~
make[2]: *** [Makefile:419: metaBigBam.o] Error 1
make[2]: Leaving directory '/home/trinh/opt/libbeato/beato'
make[1]: *** [Makefile:634: all-recursive] Error 1
make[1]: Leaving directory '/home/trinh/opt/libbeato'
make: *** [Makefile:551: all] Error 2