Hi!
I was installing BAFextract, which seemed to work until I got these warning messages during the install
g++ -c -Wall -O3 src/main.cpp -o src/main.o
src/main.cpp: In function 'void dump_nucleotide_pileup_per_SAM_file(char*, std::vector<char*>, std::vector, char*, int, int, int&)':
src/main.cpp:595:144: warning: format '%d' expects a matching 'int' argument [-Wformat=]
fprintf(stderr, "Loaded pileup is not the same length as the chromosome info: %s: %d, %d\n", chr_ids->at(i_chr), chr_lengths->at(i_chr));
^
src/main.cpp: In function 'int main(int, char**)':
src/main.cpp:1062:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i_chr = 0; i_chr < chr_ids->size(); i_chr++)
^
src/main.cpp:1098:64: warning: array subscript has type 'char' [-Wchar-subscripts]
bool is_alternate_allele = (nuc_2_num_array[cur_chr_seq[i]] != i_all);
^
g++ -c -Wall -O3 src/utils.cpp -o src/utils.o
g++ -c -Wall -O3 src/ansi_string.cpp -o src/ansi_string.o
src/ansi_string.cpp: In static member function 'static std::vector<char*>* t_string::copy_tokens_2_strs(t_string_tokens*)':
src/ansi_string.cpp:1367:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i_t = 0; i_t < toks->size(); i_t++)
^
g++ -c -Wall -O3 src/genomics_coords.cpp -o src/genomics_coords.o
g++ -O3 -o bin/BAFExtract src/main.o src/utils.o src/ansi_string.o src/genomics_coords.
When I run this code, on a sorted 10X cellranger generated BAMfile
samtools view ./bam_input/possorted_genome_bam.bam | ./BAFExtract -generate_compressed_pileup_per_SAM stdin hg38.list ./bam_input/ 50 0; ./BAFExtract -get_SNVs_per_pileup hg38.list ./bam_input/ ./genome_fasta_pileup_dir/ 20 4 0.1 FB016.snps
I do get a *.snps output but it is empty and very small. I also tried tweaking the filter option such as the 20 reads per SNP position and the 4 reads supporting the SNP. However, this did not change the output
I would be really gratefull if you could help me out!
kind regards,
Jeroen van den Berg
Hi!
I was installing BAFextract, which seemed to work until I got these warning messages during the install
g++ -c -Wall -O3 src/main.cpp -o src/main.o
src/main.cpp: In function 'void dump_nucleotide_pileup_per_SAM_file(char*, std::vector<char*>, std::vector, char*, int, int, int&)':
src/main.cpp:595:144: warning: format '%d' expects a matching 'int' argument [-Wformat=]
fprintf(stderr, "Loaded pileup is not the same length as the chromosome info: %s: %d, %d\n", chr_ids->at(i_chr), chr_lengths->at(i_chr));
^
src/main.cpp: In function 'int main(int, char**)':
src/main.cpp:1062:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i_chr = 0; i_chr < chr_ids->size(); i_chr++)
^
src/main.cpp:1098:64: warning: array subscript has type 'char' [-Wchar-subscripts]
bool is_alternate_allele = (nuc_2_num_array[cur_chr_seq[i]] != i_all);
^
g++ -c -Wall -O3 src/utils.cpp -o src/utils.o
g++ -c -Wall -O3 src/ansi_string.cpp -o src/ansi_string.o
src/ansi_string.cpp: In static member function 'static std::vector<char*>* t_string::copy_tokens_2_strs(t_string_tokens*)':
src/ansi_string.cpp:1367:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i_t = 0; i_t < toks->size(); i_t++)
^
g++ -c -Wall -O3 src/genomics_coords.cpp -o src/genomics_coords.o
g++ -O3 -o bin/BAFExtract src/main.o src/utils.o src/ansi_string.o src/genomics_coords.
When I run this code, on a sorted 10X cellranger generated BAMfile
samtools view ./bam_input/possorted_genome_bam.bam | ./BAFExtract -generate_compressed_pileup_per_SAM stdin hg38.list ./bam_input/ 50 0; ./BAFExtract -get_SNVs_per_pileup hg38.list ./bam_input/ ./genome_fasta_pileup_dir/ 20 4 0.1 FB016.snps
I do get a *.snps output but it is empty and very small. I also tried tweaking the filter option such as the 20 reads per SNP position and the 4 reads supporting the SNP. However, this did not change the output
I would be really gratefull if you could help me out!
kind regards,
Jeroen van den Berg