search

vibansal / crisp

Code for multi-sample variant calling from sequence data of pooled or unpooled DNA samples
MIT License
19 stars 8 forks source link

Installation error. does not seem to compile right #25

Closed tvdwbar closed 2 years ago

tvdwbar commented 2 years ago

After download from github, execute make all in crisp directory does not make an executable file CRISP. Compilation not going correct, but i am not seeing the error. Full log below, please advice?

Ubuntu@server:/home/administrator/Documents/Software/crisp/crisp$ make all make -C samtools all make[1]: Entering directory '/home/administrator/Documents/Software/crisp/crisp/samtools' make[2]: Entering directory '/home/administrator/Documents/Software/crisp/crisp/samtools' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o bgzf.c: In function ‘bgzf_close’: bgzf.c:630:8: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] int count, block_length = deflate_block(fp, 0); ^~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o bam_index.c: In function ‘bam_index_load_core’: bam_index.c:330:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(magic, 1, 4, fp); ^~~~~~ bam_index.c:337:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&idx->n, 4, 1, fp); ^~~~~~~~ bam_index.c:350:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&size, 4, 1, fp); ^~~~~~ bam_index.c:353:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&key, 4, 1, fp); ^~~~~ bam_index.c:357:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&p->n, 4, 1, fp); ^~~~~~ bam_index.c:361:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p->list, 16, p->n, fp); ^~~~~~~~ bam_index.c:371:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&index2->n, 4, 1, fp); ^~~~~~~ bam_index.c:375:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(index2->offset, index2->n, 8, fp); ^~~~~~~~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o bam_pileup.c: In function ‘resolve_cigar2’: bam_pileup.c:75:9: warning: variable ‘is_head’ set but not used [-Wunused-but-set-variable] int k, is_head = 0; ^~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o razf.c: In function ‘razf_flush’: razf.c:221:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~ razf.c:234:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~ razf.c: In function ‘_razf_write’: razf.c:201:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~ razf.c: In function ‘razf_close’: razf.c:804:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &rz->in, sizeof(int64_t)); ^~~~~~~~~~ razf.c:805:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &rz->out, sizeof(int64_t)); ^~~~~~~~~~~ razf.c:808:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &v64, sizeof(int64_t)); ^~~~~~~~~~~ razf.c:810:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &v64, sizeof(int64_t)); ^~~~~~~~~~~ razf.c: In function ‘razf_end_flush’: razf.c:258:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~ razf.c: In function ‘save_zindex’: razf.c:96:12: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] if(is_be) write(fd, &rz->index->size, sizeof(int)); ^~~~~~~~~~~~ razf.c:99:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd, &v32, sizeof(uint32_t)); ^~~~~~~~~ razf.c:106:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd, rz->index->bin_offsets, sizeof(int64_t) v32); ^~~~~~~~~~~~ razf.c:107:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd, rz->index->cell_offsets, sizeof(int32_t) rz->index->size); ^~~~~~~~~~~~~~~~~ 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: In function ‘fai_load’: faidx.c:277:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ faidx.c:280:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ if (fp == 0) { ^~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o In file included from knetfile.c:46:0: knetfile.c: In function ‘kftp_send_cmd’: knetfile.h:9:32: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]

define netwrite(fd, ptr, len) write(fd, ptr, len)

                            ^~~~~~~~~~~~~~~~~~~

knetfile.c:236:2: note: in expansion of macro ‘netwrite’ netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); ^~~~ knetfile.c: In function ‘khttp_connect_file’: knetfile.h:9:32: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]

define netwrite(fd, ptr, len) write(fd, ptr, len)

                            ^~~~~~~~~~~~~~~~~~~

knetfile.c:415:2: note: in expansion of macro ‘netwrite’ netwrite(fp->fd, buf, l); ^~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o bam_reheader.c: In function ‘bam_reheader’: bam_reheader.c:11:16: warning: variable ‘old’ set but not used [-Wunused-but-set-variable] bam_header_t old; ^~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o kprobaln.c: In function ‘kpa_glocal’: kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable] int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; ^~~ 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 ar: u' modifier ignored sinceD' is the default (see U') make[2]: Leaving directory '/home/administrator/Documents/Software/crisp/crisp/samtools' make[2]: Entering directory '/home/administrator/Documents/Software/crisp/crisp/samtools/bcftools' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o em.c: In function ‘bcf_em1’: em.c:174:12: warning: variable ‘n2’ set but not used [-Wunused-but-set-variable] int i, n, n2; ^~ 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 ar:u' modifier ignored since D' is the default (seeU') make[2]: Leaving directory '/home/administrator/Documents/Software/crisp/crisp/samtools/bcftools' make[2]: Entering directory '/home/administrator/Documents/Software/crisp/crisp/samtools/misc' make[2]: Nothing to be done for 'lib'. make[2]: Leaving directory '/home/administrator/Documents/Software/crisp/crisp/samtools/misc' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o bam2bcf_indel.c: In function ‘bcf_call_add_rg’: bam2bcf_indel.c:32:4: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (r = p; r && r != '\t' && r != '\n'; ++r); lp = r - p; ^~~ bam2bcf_indel.c:32:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ for (r = p; r && r != '\t' && r != '\n'; ++r); lp = r - p; ^~ bam2bcf_indel.c:33:4: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (r = q; r && r != '\t' && r != '\n'; ++r); lq = r - q; ^~~ bam2bcf_indel.c:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ for (r = q; r && r != '\t' && *r != '\n'; ++r); lq = r - q; ^~ 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: In function ‘errmod_cal’: errmod.c:79:8: warning: self-comparison always evaluates to false [-Wtautological-compare] if (m > m) return -1; ^ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o cut_target.c: In function ‘main_cut_target’: cut_target.c:137:36: warning: variable ‘lastpos’ set but not used [-Wunused-but-set-variable] int c, tid, pos, n, lasttid = -1, lastpos = -1, l, max_l; ^~~ cut_target.c: In function ‘process_cns.isra.1’: cut_target.c:96:2: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow] for (i = 0, s = -1; i <= l; ++i) { ^~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o gcc -g -Wall -O2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz make[1]: Leaving directory '/home/administrator/Documents/Software/crisp/crisp/samtools' mkdir -p include bin; make -C . new make[1]: Entering directory '/home/administrator/Documents/Software/crisp/crisp' gcc -Wall -D_GNU_SOURCE -c parsebam/readfasta.c -o include/readfasta.o parsebam/readfasta.c: In function ‘read_fastaheader’: parsebam/readfasta.c:88:3: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while (buffer[c] == ' ' || buffer[c] == '\t') c++; j= c; ^~~~~ parsebam/readfasta.c:88:55: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ while (buffer[c] == ' ' || buffer[c] == '\t') c++; j= c; ^ parsebam/readfasta.c:89:3: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while (buffer[c] != ' ' && buffer[c] != '\t') c++; reflist->lengths[i] = 0; ^~~~~ parsebam/readfasta.c:89:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ while (buffer[c] != ' ' && buffer[c] != '\t') c++; reflist->lengths[i] = 0; ^~~ parsebam/readfasta.c:95:3: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while (buffer[c] == ' ' || buffer[c] == '\t') c++; j=c; // move to next character that is not space or tab ^~~~~ parsebam/readfasta.c:95:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ while (buffer[c] == ' ' || buffer[c] == '\t') c++; j=c; // move to next character that is not space or tab ^ parsebam/readfasta.c:96:3: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while (buffer[c] != ' ' && buffer[c] != '\t') c++; reflist->offsets[i] = 0; ^~~~~ parsebam/readfasta.c:96:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ while (buffer[c] != ' ' && buffer[c] != '\t') c++; reflist->offsets[i] = 0; ^~~ parsebam/readfasta.c:62:33: warning: unused variable ‘length’ [-Wunused-variable] int i=0,j=0,c=0,c1=0,k=0; char length[64]; ^~ parsebam/readfasta.c: In function ‘read_bedfile’: parsebam/readfasta.c:257:3: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while(buffer[c] == ' ' || buffer[c] == '\t') c++; s = c; while (buffer[c] != ' ' && buffer[c] != '\t') c++; e = c; ^~~~~ parsebam/readfasta.c:257:53: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ while(buffer[c] == ' ' || buffer[c] == '\t') c++; s = c; while (buffer[c] != ' ' && buffer[c] != '\t') c++; e = c; ^ parsebam/readfasta.c:258:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (i=s;i<e;i++) chrom[i-s] = buffer[i]; chrom[i-s] = '\0'; ^~~ parsebam/readfasta.c:258:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ for (i=s;i<e;i++) chrom[i-s] = buffer[i]; chrom[i-s] = '\0'; ^~~~~ parsebam/readfasta.c:260:3: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while(buffer[c] == ' ' || buffer[c] == '\t') c++; s = c; while (buffer[c] != ' ' && buffer[c] != '\t') c++; e = c; ^~~~~ parsebam/readfasta.c:260:53: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ while(buffer[c] == ' ' || buffer[c] == '\t') c++; s = c; while (buffer[c] != ' ' && buffer[c] != '\t') c++; e = c; ^ parsebam/readfasta.c:263:3: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while(buffer[c] == ' ' || buffer[c] == '\t') c++; s = c; ^~~~~ parsebam/readfasta.c:263:53: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ while(buffer[c] == ' ' || buffer[c] == '\t') c++; s = c; ^ parsebam/readfasta.c:264:3: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while (buffer[c] != ' ' && buffer[c] != '\t' && buffer[c] != '\n' && isdigit(buffer[c])) c++; e = c; ^~~~~ parsebam/readfasta.c:264:97: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ while (buffer[c] != ' ' && buffer[c] != '\t' && buffer[c] != '\n' && isdigit(buffer[c])) c++; e = c; ^ parsebam/readfasta.c:270:4: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while(buffer[c] == ' ' || buffer[c] == '\t') c++; s = c; ^~~~~ parsebam/readfasta.c:270:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ while(buffer[c] == ' ' || buffer[c] == '\t') c++; s = c; ^ parsebam/readfasta.c:271:4: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while (buffer[c] != ' ' && buffer[c] != '\t' && buffer[c] != '\n') c++; e = c; ^~~~~ parsebam/readfasta.c:271:76: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ while (buffer[c] != ' ' && buffer[c] != '\t' && buffer[c] != '\n') c++; e = c; ^ parsebam/readfasta.c:274:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (i=s;i<e;i++) annotation[i-s] = buffer[i]; annotation[i-s] = '\0'; ^~~ parsebam/readfasta.c:274:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ for (i=s;i<e;i++) annotation[i-s] = buffer[i]; annotation[i-s] = '\0'; ^~~~~~ gcc -Wall -D_GNU_SOURCE -Isamtools -c parsebam/bamsreader.c -o include/bamsreader.o parsebam/bamsreader.c: In function ‘free_read_queue’: parsebam/bamsreader.c:97:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ parsebam/bamsreader.c: In function ‘allocate_mem_heap’: parsebam/bamsreader.c:121:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ gcc -Wall -D_GNU_SOURCE -Isamtools -c parsebam/variant.c -o include/variant.o In file included from parsebam/variant.c:29:0: parsebam/process_indel_variant.c: In function ‘identify_indelalleles’: parsebam/process_indel_variant.c:155:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (i=0;i<alleles;i++) free(indelalleles[i].bases); free(indelalleles); ^~~ parsebam/process_indel_variant.c:155:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ for (i=0;i<alleles;i++) free(indelalleles[i].bases); free(indelalleles); ^~~~ parsebam/process_indel_variant.c:198:2: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (i=0;i<alleles;i++) free(indelalleles[i].bases); free(indelalleles); ^~~ parsebam/process_indel_variant.c:198:55: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ for (i=0;i<alleles;i++) free(indelalleles[i].bases); free(indelalleles); ^~~~ parsebam/process_indel_variant.c: In function ‘print_indel_haplotypes’: parsebam/process_indel_variant.c:215:53: warning: unused variable ‘ol’ [-Wunused-variable] int base; int offset=0; double ep; int op = 0; int ol=0; int i=0; ^~ parsebam/process_indel_variant.c:215:41: warning: unused variable ‘op’ [-Wunused-variable] int base; int offset=0; double ep; int op = 0; int ol=0; int i=0; ^~ parsebam/process_indel_variant.c:215:33: warning: unused variable ‘ep’ [-Wunused-variable] int base; int offset=0; double ep; int op = 0; int ol=0; int i=0; ^~ parsebam/process_indel_variant.c:215:16: warning: unused variable ‘offset’ [-Wunused-variable] int base; int offset=0; double ep; int op = 0; int ol=0; int i=0; ^~ parsebam/process_indel_variant.c:215:6: warning: unused variable ‘base’ [-Wunused-variable] int base; int offset=0; double ep; int op = 0; int ol=0; int i=0; ^~~~ In file included from parsebam/variant.c:30:0: parsebam/init_variant.c: In function ‘initialize_variant’: parsebam/init_variant.c:111:24: warning: array subscript has type ‘char’ [-Wchar-subscripts] variant->refbase = BTI[variant->refb]; // what if this is IUPAC ambig. base ^ parsebam/init_variant.c:106:10: warning: unused variable ‘j’ [-Wunused-variable] int i=0,j=0,p=0,q=0; ^ parsebam/init_variant.c: In function ‘init_poolsizes’: parsebam/init_variant.c:140:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (i=0;ibamfiles;i++) variant->ploidy[i] = options->POOLSIZE; variant->varpoolsize = 0; ^~~ parsebam/init_variant.c:140:91: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ for (i=0;ibamfiles;i++) variant->ploidy[i] = options->POOLSIZE; variant->varpoolsize = 0; ^~~ parsebam/init_variant.c:155:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (i=0;ibamfiles;i++) variant->ploidy[i] = 2; variant->varpoolsize =0; ^~~ parsebam/init_variant.c:155:76: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ for (i=0;ibamfiles;i++) variant->ploidy[i] = 2; variant->varpoolsize =0; ^~~ parsebam/variant.c: In function ‘advance_read’: parsebam/variant.c:61:15: warning: unused variable ‘i’ [-Wunused-variable] int op=0,l=0,i=0; ^ parsebam/variant.c: In function ‘calculate_allelecounts’: parsebam/variant.c:248:80: warning: implicit declaration of function ‘realign_read’; did you mean ‘print_read’? [-Wimplicit-function-declaration] if (INDEL_REALIGNMENT ==2 && bcall->realigned ==0 && bcall->mismatches > 0) realign_read(bamfiles_data,j,bcall,reflist); ^~~~ print_read parsebam/variant.c:304:17: warning: array subscript has type ‘char’ [-Wchar-subscripts] ibase = BTI[base]; bcall->allele = ibase+offset; ^ parsebam/variant.c:233:6: warning: unused variable ‘i’ [-Wunused-variable] int i=0; int reads=0; int j=0; int ar=0; ^ parsebam/variant.c:231:43: warning: unused variable ‘allelematch’ [-Wunused-variable] int offset=0; double ep; int allele; int allelematch=0; int bin=0; ^~~ parsebam/variant.c:231:31: warning: unused variable ‘allele’ [-Wunused-variable] int offset=0; double ep; int allele; int allelematch=0; int bin=0; ^~ parsebam/variant.c:228:12: warning: unused variable ‘base_m’ [-Wunused-variable] char base,base_m; uint8_t strand,randomstrand=0; ^~ parsebam/variant.c:227:33: warning: variable ‘indelalleles’ set but not used [-Wunused-but-set-variable] int insertions =0,deletions =0,indelalleles=0; ^~~~ In file included from parsebam/variant.c:29:0: parsebam/process_indel_variant.c: In function ‘calculate_indel_ambiguity’: parsebam/process_indel_variant.c:92:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ parsebam/process_indel_variant.c: In function ‘print_indel_haplotypes’: parsebam/process_indel_variant.c:230:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ In file included from parsebam/variant.c:30:0: parsebam/init_variant.c: In function ‘initialize_variant’: parsebam/init_variant.c:132:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ parsebam/variant.c: In function ‘calculate_allelecounts’: parsebam/variant.c:276:5: warning: ‘bcall_mate’ may be used uninitialized in this function [-Wmaybe-uninitialized] evaluate_OPE_readpair(bcall,bcall_mate,variant,&strand,&randomstrand,&quality); ^~~~~~~~~~~~~~~~~~ gcc -Wall -D_GNU_SOURCE -Isamtools -c parsebam/allelecounts.c -o include/allelecounts.o In file included from parsebam/allelecounts.c:8:0: parsebam/calculatelikelihoods.c: In function ‘compute_GLLs’: parsebam/calculatelikelihoods.c:46:16: warning: array subscript has type ‘char’ [-Wchar-subscripts] allele = BTI[bcall->sequence[bcall->l1+bcall->delta]]; ^ parsebam/allelecounts.c: In function ‘print_variantreads’: parsebam/allelecounts.c:23:10: warning: unused variable ‘j’ [-Wunused-variable] int i=0,j=0; ^ parsebam/allelecounts.c: In function ‘calculate_uniquereads’: parsebam/allelecounts.c:45:10: warning: unused variable ‘j’ [-Wunused-variable] int i=0,j=0,reads=0; unique =1; middle = 0; ^ parsebam/allelecounts.c:44:6: warning: unused variable ‘UFLAG’ [-Wunused-variable] int UFLAG=1; ^~~~~ gcc -Wall -D_GNU_SOURCE -Isamtools -c FET/chisquare.c -o include/chisquare.o FET/chisquare.c: In function ‘chi2pvalue’: FET/chisquare.c:56:2: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (Ef[0] >=0.999) Ef[0] = 0.999; if (Ef[1] >=0.999) Ef[1] = 0.999; ^~ FET/chisquare.c:56:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (Ef[0] >=0.999) Ef[0] = 0.999; if (Ef[1] >=0.999) Ef[1] = 0.999; ^~ FET/chisquare.c:57:2: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (Er[0] >=0.999) Er[0] = 0.999; if (Er[1] >=0.999) Er[1] = 0.999; ^~ FET/chisquare.c:57:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (Er[0] >=0.999) Er[0] = 0.999; if (Er[1] >=0.999) Er[1] = 0.999; ^~ FET/chisquare.c:21:43: warning: unused variable ‘statistic’ [-Wunused-variable] double statisticjoint[2] = {0,0}; double statistic[2]={0,0}; double statisticf[2]={0,0},statisticr[2]={0,0}; ^~~~~ gcc -Wall -D_GNU_SOURCE -c FET/contables.c -o include/contables.o FET/contables.c: In function ‘fetsided’: FET/contables.c:102:9: warning: unused variable ‘ptable’ [-Wunused-variable] double ptable = ncr(r1,c1) + ncr(r2,c2); double DEN= ncr(r1+r2,c1+c2); ^~ FET/contables.c: In function ‘pvalue_contable_iter_stranded’: FET/contables.c:265:36: warning: variable ‘deltac’ set but not used [-Wunused-but-set-variable] double clra =0, clranew=0; double deltac=0; double DOF = size-1; ^~ gcc -Wall -D_GNU_SOURCE -Iparsebam -Isamtools -c crisp/newcrispcaller.c -o include/newcrispcaller.o In file included from crisp/newcrispcaller.c:17:0: crisp/../FET/chisquare-stratified.c: In function ‘chi2pvalue_stratified’: crisp/../FET/chisquare-stratified.c:40:2: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (Ef[0] >=0.999) Ef[0] = 0.999; if (Er[0] >=0.999) Er[0] = 0.999; if (Eb[0] >=0.999) Eb[0] = 0.999; ^~ crisp/../FET/chisquare-stratified.c:40:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (Ef[0] >=0.999) Ef[0] = 0.999; if (Er[0] >=0.999) Er[0] = 0.999; if (Eb[0] >=0.999) Eb[0] = 0.999; ^~ In file included from crisp/newcrispcaller.c:17:0: crisp/../FET/chisquare-stratified.c:18:9: warning: unused variable ‘statnew’ [-Wunused-variable] double statnew[2]={0,0},pairwisestat[2]={0,0}; ^~~ crisp/../FET/chisquare-stratified.c:16:37: warning: unused variable ‘SF’ [-Wunused-variable] double pvalue[3] = {0,0,0}; double SF,RUGF; ^~ crisp/../FET/chisquare-stratified.c:16:9: warning: unused variable ‘pvalue’ [-Wunused-variable] double pvalue[3] = {0,0,0}; double SF,RUGF; ^~ In file included from crisp/newcrispcaller.c:17:0: crisp/../FET/chisquare-stratified.c: In function ‘chi2pvalue_stratified_pivotsample’: crisp/../FET/chisquare-stratified.c:129:2: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (Ef[0] >=0.999) Ef[0] = 0.999; if (Ef[1] >=0.999) Ef[1] = 0.999; ^~ crisp/../FET/chisquare-stratified.c:129:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (Ef[0] >=0.999) Ef[0] = 0.999; if (Ef[1] >=0.999) Ef[1] = 0.999; ^~ crisp/../FET/chisquare-stratified.c:130:2: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (Er[0] >=0.999) Er[0] = 0.999; if (Er[1] >=0.999) Er[1] = 0.999; ^~ crisp/../FET/chisquare-stratified.c:130:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (Er[0] >=0.999) Er[0] = 0.999; if (Er[1] >=0.999) Er[1] = 0.999; ^~ crisp/../FET/chisquare-stratified.c:131:2: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (Eb[0] >=0.999) Eb[0] = 0.999; if (Eb[1] >=0.999) Eb[1] = 0.999; ^~ crisp/../FET/chisquare-stratified.c:131:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (Eb[0] >=0.999) Eb[0] = 0.999; if (Eb[1] >=0.999) Eb[1] = 0.999; ^~ crisp/../FET/chisquare-stratified.c:90:43: warning: unused variable ‘statistic’ [-Wunused-variable] double statisticjoint[2] = {0,0}; double statistic[2]={0,0}; double statisticf[2]={0,0},statisticr[2]={0,0}; ^~~~~ In file included from crisp/crispEM.c:24:0, from crisp/newcrispcaller.c:18: crisp/../FET/lowcovFET.c: In function ‘pvalue_lowcoverage’: crisp/../FET/lowcovFET.c:47:2: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (i=0;i<maxcoverage+1;i++) bincounts[i] = 0; for (i=0;i<size;i++) bincounts[atable[i].N]++; ^~~ crisp/../FET/lowcovFET.c:47:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ for (i=0;i<maxcoverage+1;i++) bincounts[i] = 0; for (i=0;i<size;i++) bincounts[atable[i].N]++; ^~~ crisp/../FET/lowcovFET.c:25:39: warning: unused variable ‘num’ [-Wunused-variable] int i=0,j=0,offset=0; int den=0; int num=0; ^~~ crisp/../FET/lowcovFET.c:25:28: warning: unused variable ‘den’ [-Wunused-variable] int i=0,j=0,offset=0; int den=0; int num=0; ^~~ crisp/../FET/lowcovFET.c: In function ‘pvalue_lowcoverage_stranded’: crisp/../FET/lowcovFET.c:161:9: warning: unused variable ‘sstat’ [-Wunused-variable] double sstat =0; ^~~~~ crisp/../FET/lowcovFET.c: In function ‘pvalue_lowcoverage_stranded1’: crisp/../FET/lowcovFET.c:312:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (sstat[1] < sstat[0]) sstat[3] +=1; if (sstat[2] < sstat[0]) sstat[4] +=1; ^~ crisp/../FET/lowcovFET.c:312:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (sstat[1] < sstat[0]) sstat[3] +=1; if (sstat[2] < sstat[0]) sstat[4] +=1; ^~ In file included from crisp/crispEM.c:33:0, from crisp/newcrispcaller.c:18: crisp/LRstatistic.c: In function ‘calculate_likelihood_EM’: crisp/LRstatistic.c:39:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (pnew < MINP) pnew= MINP; if (1.0-pnew <=MINP) pnew = 1.0-MINP; ^~ crisp/LRstatistic.c:39:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (pnew < MINP) pnew= MINP; if (1.0-pnew <=MINP) pnew = 1.0-MINP; ^~ crisp/LRstatistic.c:8:14: warning: unused variable ‘k’ [-Wunused-variable] int i=0,j=0,k=0,K=0,iter=0; ^ crisp/LRstatistic.c: In function ‘calculate_LRstatistic’: crisp/LRstatistic.c:60:9: warning: unused variable ‘pcombined1’ [-Wunused-variable] double pcombined1 = calculate_likelihood_EM(variant,allele1,allele2,allele3,p,&dataLL1,E01,E10,5); ^~~~~~ In file included from crisp/newcrispcaller.c:18:0: crisp/crispEM.c: In function ‘calculate_pooled_likelihoods_snp’: crisp/crispEM.c:109:14: warning: array subscript has type ‘char’ [-Wchar-subscripts] base = BTI[bcall->sequence[bcall->l1+bcall->delta]]; ^ crisp/crispEM.c: In function ‘calculate_genotypes’: crisp/crispEM.c:148:22: warning: variable ‘sbgenotype’ set but not used [-Wunused-but-set-variable] int bestgenotype =0,sbgenotype =0; ^~~~~~ crisp/crispEM.c: In function ‘EMmethod’: crisp/crispEM.c:254:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (j==0) LLnull += temp; if (j==0) LLnullf += tempf; if (j==0) LLnullr += tempr; ^~ crisp/crispEM.c:254:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (j==0) LLnull += temp; if (j==0) LLnullf += tempf; if (j==0) LLnullr += tempr; ^~ crisp/crispEM.c:299:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (pnew < MINP) pnew= MINP; if (1.0-pnew <=MINP) pnew = 1.0-MINP; ^~ crisp/crispEM.c:299:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (pnew < MINP) pnew= MINP; if (1.0-pnew <=MINP) pnew = 1.0-MINP; ^~ crisp/crispEM.c:300:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (pnewf < MINP) pnewf= MINP; if (1.0-pnewf <=MINP) pnewf = 1.0-MINP; ^~ crisp/crispEM.c:300:34: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (pnewf < MINP) pnewf= MINP; if (1.0-pnewf <=MINP) pnewf = 1.0-MINP; ^~ crisp/crispEM.c:301:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (pnewr < MINP) pnewr= MINP; if (1.0-pnewr <=MINP) pnewr = 1.0-MINP; ^~ crisp/crispEM.c:301:34: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (pnewr < MINP) pnewr= MINP; if (1.0-pnewr <=MINP) pnewr = 1.0-MINP; ^~ crisp/crispEM.c:302:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (pnewb < MINP) pnewb= MINP; if (1.0-pnewb <=MINP) pnewb = 1.0-MINP; ^~ crisp/crispEM.c:302:34: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (pnewb < MINP) pnewb= MINP; if (1.0-pnewb <=MINP) pnewb = 1.0-MINP; ^~ crisp/crispEM.c:226:29: warning: unused variable ‘convergence_delta’ [-Wunused-variable] int maxiter = 1000; double convergence_delta = 0.01; int exitloop =0; ^~~~~ crisp/crispEM.c:217:9: warning: unused variable ‘LLrefsub’ [-Wunused-variable] double LLrefsub=0,LLrefadd=0; ^~~~ crisp/crispEM.c:215:40: warning: unused variable ‘LLnullb’ [-Wunused-variable] double LLtotal =0,LLnullf=0,LLnullr=0,LLnullb=0; ^~~ crisp/crispEM.c:214:57: warning: unused variable ‘deltar’ [-Wunused-variable] double pnew=0,pnewf=0,pnewr=0,pnewb=0; double deltaf=0,deltar=0; double Lf=0,Lr=0,Lj=0,Lb=0; ^~ crisp/crispEM.c: In function ‘compute_GLL_pooled’: crisp/crispEM.c:381:10: warning: unused variable ‘pvalue’ [-Wunused-variable] double pvalue = calculate_LRstatistic(variant,allele1,allele2,allele3,p_EM,E01,E10); ^~ In file included from crisp/newcrispprint.c:11:0, from crisp/newcrispcaller.c:26: crisp/crisp_header_options.c: In function ‘print_sampleids’: crisp/crisp_header_options.c:9:3: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while (options->bamfilelist[i][s] != '/' && s >0) s--; s++; // go backwards to find first '/' character ^~~~~ crisp/crisp_header_options.c:9:58: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ while (options->bamfilelist[i][s] != '/' && s >0) s--; s++; // go backwards to find first '/' character ^ In file included from crisp/newcrispcaller.c:26:0: crisp/newcrispprint.c: In function ‘print_VCF_first_5cols’: crisp/newcrispprint.c:54:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (j=1;j<longestdel;j++) fprintf(vfile,"%c",variant->itb[variant->alleles[k]][j]); fprintf(vfile,"\t"); ^~~ crisp/newcrispprint.c:54:88: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ for (j=1;j<longestdel;j++) fprintf(vfile,"%c",variant->itb[variant->alleles[k]][j]); fprintf(vfile,"\t"); ^~~ In file included from crisp/newcrispcaller.c:26:0: crisp/newcrispprint.c: In function ‘print_VCF_genotypes_diploid’: crisp/newcrispprint.c:136:18: warning: unused variable ‘coverage’ [-Wunused-variable] int i=0,j=0,k=0,coverage=0,bidir=0; ^~~~ crisp/newcrispprint.c:136:14: warning: unused variable ‘k’ [-Wunused-variable] int i=0,j=0,k=0,coverage=0,bidir=0; ^ crisp/newcrispprint.c: In function ‘print_VCF_genotypes_pooled_full’: crisp/newcrispprint.c:205:4: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (j=0;jploidy[i];j++) fprintf(vfile,"./"); fprintf(vfile,".:0:."); ^~~ crisp/newcrispprint.c:205:60: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ for (j=0;jploidy[i];j++) fprintf(vfile,"./"); fprintf(vfile,".:0:."); ^~~ crisp/newcrispprint.c:221:4: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (j=0;jploidy[i];j++) fprintf(vfile,"./"); fprintf(vfile,".:0:."); ^~~ crisp/newcrispprint.c:221:60: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ for (j=0;jploidy[i];j++) fprintf(vfile,"./"); fprintf(vfile,".:0:."); ^~~ crisp/newcrispprint.c:187:14: warning: unused variable ‘k’ [-Wunused-variable] int i=0,j=0,k=0,coverage=0,bidir=0; ^ crisp/newcrispprint.c: In function ‘print_pooledvariant’: crisp/newcrispprint.c:387:2: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (MQflag >0) filters++; if (variant->strandpass > 0 && EMflag ==0) filters++; else if (lowcoverage ==1) filters++; ^~ crisp/newcrispprint.c:387:28: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (MQflag >0) filters++; if (variant->strandpass > 0 && EMflag ==0) filters++; else if (lowcoverage ==1) filters++; ^~ crisp/newcrispprint.c:434:4: warning: format not a string literal and no format arguments [-Wformat-security] fprintf(vfile,filter_strings[varfilters[i]]); if (i < variant->varalleles-1) fprintf(vfile,","); ^~~ crisp/newcrispprint.c:386:7: warning: unused variable ‘FILTER’ [-Wunused-variable] char FILTER[1024]; int filters = 0; //strcpy(FILTER,"\0"); ^~ In file included from crisp/newcrispcaller.c:27:0: crisp/pooledFET.c: In function ‘FETpvalue_variant’: crisp/pooledFET.c:58:4: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (k=0;k<R;k++) table_index[j][offset+k] =i; offset += R; ^~~ crisp/pooledFET.c:58:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ for (k=0;k<R;k++) table_index[j][offset+k] =i; offset += R; ^~ crisp/pooledFET.c:95:2: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (i=0;i<12;i++) free(table_index[i]); free(table_index); ^~~ crisp/pooledFET.c:95:43: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ for (i=0;i<12;i++) free(table_index[i]); free(table_index); ^~~~ crisp/pooledFET.c:96:2: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (i=0;isamples;i++) free(newtable[i]); free(newtable); ^~~ crisp/pooledFET.c:96:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ for (i=0;isamples;i++) free(newtable[i]); free(newtable); ^~~~ crisp/pooledFET.c: In function ‘FETpvalue_indels’: crisp/pooledFET.c:136:17: warning: assignment makes integer from pointer without a cast [-Wint-conversion] if (j ==0) R = variant->indcounts[i][allele1] + variant->indcounts[i][allele2] + variant->indcounts_binned[i][allele3]; ^ crisp/pooledFET.c:138:4: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (k=0;k<R;k++) table_index[j][offset+k] =i; offset += R; ^~~ crisp/pooledFET.c:138:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ for (k=0;k<R;k++) table_index[j][offset+k] =i; offset += R; ^~ crisp/pooledFET.c:161:2: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (i=0;i<2;i++) free(table_index[i]); free(table_index); ^~~ crisp/pooledFET.c:161:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ for (i=0;i<2;i++) free(table_index[i]); free(table_index); ^~~~ crisp/pooledFET.c:162:2: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (i=0;isamples;i++) free(newtable[i]); free(newtable); ^~~ crisp/pooledFET.c:162:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ for (i=0;isamples;i++) free(newtable[i]); free(newtable); ^~~~ In file included from crisp/newcrispcaller.c:28:0: crisp/poolstats.c: In function ‘calculate_pool_statistics’: crisp/poolstats.c:8:55: warning: unused variable ‘i’ [-Wunused-variable] int spools =0; int variantpools =0; int a=0; int r=0,i=0; int varpool =0; int uniquess =0; int middle = 0; ^ crisp/poolstats.c:8:51: warning: unused variable ‘r’ [-Wunused-variable] int spools =0; int variantpools =0; int a=0; int r=0,i=0; int varpool =0; int uniquess =0; int middle = 0; ^ crisp/poolstats.c:7:9: warning: unused variable ‘p’ [-Wunused-variable] double p=0; double pvstrand[variant->samples]; double pvallow[4] = {0.0,0.0,0.0,0.0}; ^ In file included from crisp/newcrispcaller.c:29:0: crisp/oldcrispmethod.c: In function ‘call_genotypes’: crisp/oldcrispmethod.c:17:20: warning: unused variable ‘Er’ [-Wunused-variable] double Ef =0.001, Er=0.001; ^~ crisp/oldcrispmethod.c:14:9: warning: variable ‘sum’ set but not used [-Wunused-but-set-variable] double sum =0; ^~~ crisp/oldcrispmethod.c:9:32: warning: unused variable ‘r’ [-Wunused-variable] int variants =0; int a=0; int r=0,i=0; ^ In file included from crisp/newcrispcaller.c:29:0: crisp/oldcrispmethod.c: In function ‘pooled_variantcaller’: crisp/oldcrispmethod.c:192:4: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else variant->alleles[variant->varalleles] = allele1; variant->nvariants[variant->varalleles] = variants; ^~~~ crisp/oldcrispmethod.c:192:58: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ else variant->alleles[variant->varalleles] = allele1; variant->nvariants[variant->varalleles] = variants; ^~~ crisp/oldcrispmethod.c:157:25: warning: unused variable ‘pvaluelog’ [-Wunused-variable] int variants=0; double pvaluelog = variant->ctpval[variant->varalleles]; ^~~~~ crisp/oldcrispmethod.c:134:33: warning: unused variable ‘potentialvar’ [-Wunused-variable] int i=0,j=0,al=0,pv=0,sample=0,potentialvar=0; ^~~~ crisp/oldcrispmethod.c:134:24: warning: unused variable ‘sample’ [-Wunused-variable] int i=0,j=0,al=0,pv=0,sample=0,potentialvar=0; ^~ crisp/oldcrispmethod.c:134:19: warning: unused variable ‘pv’ [-Wunused-variable] int i=0,j=0,al=0,pv=0,sample=0,potentialvar=0; ^~ crisp/oldcrispmethod.c:134:14: warning: unused variable ‘al’ [-Wunused-variable] int i=0,j=0,al=0,pv=0,sample=0,potentialvar=0; ^~ crisp/oldcrispmethod.c:134:10: warning: unused variable ‘j’ [-Wunused-variable] int i=0,j=0,al=0,pv=0,sample=0,potentialvar=0; ^ crisp/newcrispcaller.c: In function ‘evaluate_variant’: crisp/newcrispcaller.c:113:25: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] else if (FAST_FILTER ==1 & variant->ctpval[variant->varalleles] >= -3 && variant->ploidy[0] > 2 && hplength >= 8 && (p[0]/K) <= 0.1) return 0;


crisp/newcrispcaller.c:40:45: warning: unused variable ‘N’ [-Wunused-variable]
  double p1=0,p2=0,ep; double C1=0,C2=0,C3=0,N=0;
                                             ^
crisp/newcrispcaller.c:40:19: warning: unused variable ‘ep’ [-Wunused-variable]
  double p1=0,p2=0,ep; double C1=0,C2=0,C3=0,N=0;
                   ^~
crisp/newcrispcaller.c: In function ‘output_allele_counts’:
crisp/newcrispcaller.c:137:87: warning: unused variable ‘allele4’ [-Wunused-variable]
  int allele=0,allele1 = maxvec[0].al, allele2 = maxvec[1].al, allele3 = maxvec[2].al, allele4=maxvec[3].al;
                                                                                       ^~~~~~~
crisp/newcrispcaller.c:137:63: warning: unused variable ‘allele3’ [-Wunused-variable]
  int allele=0,allele1 = maxvec[0].al, allele2 = maxvec[1].al, allele3 = maxvec[2].al, allele4=maxvec[3].al;
                                                               ^~~~~~~
crisp/newcrispcaller.c:137:39: warning: unused variable ‘allele2’ [-Wunused-variable]
  int allele=0,allele1 = maxvec[0].al, allele2 = maxvec[1].al, allele3 = maxvec[2].al, allele4=maxvec[3].al;
                                       ^~~~~~~
crisp/newcrispcaller.c:137:15: warning: unused variable ‘allele1’ [-Wunused-variable]
  int allele=0,allele1 = maxvec[0].al, allele2 = maxvec[1].al, allele3 = maxvec[2].al, allele4=maxvec[3].al;
               ^~~~~~~
crisp/newcrispcaller.c: In function ‘newCRISPcaller’:
crisp/newcrispcaller.c:184:88: warning: unused variable ‘allele4’ [-Wunused-variable]
  int allele=0, allele1 = maxvec[0].al, allele2 = maxvec[1].al, allele3 = maxvec[2].al, allele4=-1;
                                                                                        ^~~~~~~
crisp/newcrispcaller.c:183:10: warning: unused variable ‘j’ [-Wunused-variable]
  int i=0,j=0,al=0,potentialvar=0,is_variant =0,variantpools=0;
          ^
In file included from crisp/newcrispcaller.c:27:0:
crisp/pooledFET.c: In function ‘chi2pvalue_variant’:
crisp/pooledFET.c:259:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
In file included from crisp/newcrispcaller.c:29:0:
crisp/oldcrispmethod.c: In function ‘calculate_chernoff_stats’:
crisp/oldcrispmethod.c:217:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
gcc -Wall -D_GNU_SOURCE -Isamtools -c parsebam/bamread.c -o include/bamread.o
In file included from parsebam/bamread.c:6:0:
parsebam/../indels/left_align_indels.c: In function ‘left_align_indels’:
parsebam/../indels/left_align_indels.c:8:10: warning: unused variable ‘j’ [-Wunused-variable]
  int i=0,j=0,op=0,l=0,l1=0,l2=0,j1=0,j2=0,op_prev = 0,l_prev =0;
          ^
parsebam/bamread.c: In function ‘parse_cigar’:
parsebam/bamread.c:12:34: warning: unused variable ‘j’ [-Wunused-variable]
  int i=0,t=0, l1=0,l2=0; int l=0,j=0;
                                  ^
parsebam/bamread.c: In function ‘get_read_bamfile’:
parsebam/bamread.c:111:2: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  for (i=0;i<c->l_qname;i++) read->readid[i] = b->data[i]; read->readid[i]= '\0';
  ^~~
parsebam/bamread.c:111:59: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  for (i=0;i<c->l_qname;i++) read->readid[i] = b->data[i]; read->readid[i]= '\0';
                                                           ^~~~
parsebam/bamread.c:123:2: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  for (i=0;i<b->core.l_qseq;i++) read->sequence[i] = bam_nt16_rev_table[bam1_seqi(sequence,i)]; read->sequence[i] = '\0';
  ^~~
parsebam/bamread.c:123:96: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  for (i=0;i<b->core.l_qseq;i++) read->sequence[i] = bam_nt16_rev_table[bam1_seqi(sequence,i)]; read->sequence[i] = '\0';
                                                                                                ^~~~
parsebam/bamread.c:124:2: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  for (i=0;i<b->core.l_qseq;i++) read->quality[i] = (char)(quality[i]+33); read->quality[i] = '\0';
  ^~~
parsebam/bamread.c:124:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  for (i=0;i<b->core.l_qseq;i++) read->quality[i] = (char)(quality[i]+33); read->quality[i] = '\0';
                                                                           ^~~~
In file included from parsebam/bamread.c:6:0:
parsebam/../indels/left_align_indels.c: In function ‘left_align_indels’:
parsebam/../indels/left_align_indels.c:55:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
gcc -Wall -D_GNU_SOURCE -DPICALL=3 -Iparsebam -Isamtools -g -O2 include/readfasta.o include/variant.o include/allelecounts.o include/bamsreader.o include/newcrispcaller.o include/chisquare.o include/contables.o include/bamread.o -lm readmultiplebams.c -o bin/CRISP.binary -Lsamtools -lbam -lz
In file included from readmultiplebams.c:11:0:
indels/generate_candidate_indels.c: In function ‘extract_indel_reads’:
indels/generate_candidate_indels.c:143:17: warning: unused variable ‘j’ [-Wunused-variable]
         int i=0,j=0,op=0,l=0,flag=0, l1=0,l2=0;
                 ^
In file included from readmultiplebams.c:12:0:
indels/realignment.c: In function ‘realign_read’:
indels/realignment.c:415:87: warning: unused variable ‘ss’ [-Wunused-variable]
  int alignments =0; int rlflag =0; int best = -1; int bestscore[2] = {-100,100};  int ss=0;
                                                                                       ^~
In file included from readmultiplebams.c:56:0:
optionparser.c: In function ‘parse_bamfilenames’:
optionparser.c:158:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   for (k=s;k<j;k++) options->bamfilelist[i][k-s] = buffer[k]; options->bamfilelist[i][k-s] ='\0';
   ^~~
optionparser.c:158:63: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   for (k=s;k<j;k++) options->bamfilelist[i][k-s] = buffer[k]; options->bamfilelist[i][k-s] ='\0';
                                                               ^~~~~~~
optionparser.c:162:3: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation]
   while (buffer[j] == ' ' || buffer[j] == '\t') j++; s = j; // empty spaces
   ^~~~~
optionparser.c:162:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’
   while (buffer[j] == ' ' || buffer[j] == '\t') j++; s = j; // empty spaces
                                                      ^
optionparser.c:181:3: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation]
   while (buffer[j]  != '\t' && buffer[j] != '\n' && buffer[j] !=' ') j++; e = j;
   ^~~~~
optionparser.c:181:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’
   while (buffer[j]  != '\t' && buffer[j] != '\n' && buffer[j] !=' ') j++; e = j;
                                                                           ^
optionparser.c:183:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   for (k=s;k<e;k++) options->sampleids[i][k-s] = buffer[k]; options->sampleids[i][k-s] ='\0';
   ^~~
optionparser.c:183:61: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   for (k=s;k<e;k++) options->sampleids[i][k-s] = buffer[k]; options->sampleids[i][k-s] ='\0';
                                                             ^~~~~~~
In file included from readmultiplebams.c:61:0:
variantcalls.c: In function ‘callvariants’:
variantcalls.c:137:6: warning: unused variable ‘i’ [-Wunused-variable]
  int i=0, k=0,reads=0;
      ^
readmultiplebams.c: In function ‘multisampleVC’:
readmultiplebams.c:133:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
      if (INDEL_REALIGNMENT >=1) clean_indel_lists(bamfiles_data,bamfiles,-1); current_position = 0;
      ^~
readmultiplebams.c:133:79: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
      if (INDEL_REALIGNMENT >=1) clean_indel_lists(bamfiles_data,bamfiles,-1); current_position = 0;
                                                                               ^~~~~~~~~~~~~~~~
readmultiplebams.c:134:6: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
      for(j=0;j<bamfiles;j++) bamfiles_data[j].last=NULL; last =0;
      ^~~
readmultiplebams.c:134:58: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
      for(j=0;j<bamfiles;j++) bamfiles_data[j].last=NULL; last =0;
                                                          ^~~~
readmultiplebams.c: In function ‘main’:
readmultiplebams.c:258:2: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  if (read_fastaheader(options->fastafile,&reflist) == -1)  return -1;  strcpy(reflist.fastafile,options->fastafile);
  ^~
readmultiplebams.c:258:72: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  if (read_fastaheader(options->fastafile,&reflist) == -1)  return -1;  strcpy(reflist.fastafile,options->fastafile);
                                                                        ^~~~~~
In file included from readmultiplebams.c:56:0:
optionparser.c: In function ‘parse_bamfilenames’:
optionparser.c:154:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
   fgets(buffer,4096,fp);
   ^~~~~~~~~~~~~~~~~~~~~
optionparser.c: In function ‘optparser’:
optionparser.c:274:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%d\n",&options->phenotypes[i]);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from readmultiplebams.c:61:0:
variantcalls.c: In function ‘update_error_table’:
variantcalls.c:41:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
make[1]: Leaving directory '/home/administrator/Documents/Software/crisp/crisp'
#make -C . crisp
#make -C . indel
tvdwbar commented 2 years ago

Ah the executable Crisp is a binary in the bin folder. Nevermind!