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A collection of C++ tools to manipulate SAM/BAM/CRAM and BCF/VCF files in various contexts of sequence analysis.

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Eigen
Eigen
 
 
experimental
experimental
 
 
.gitignore
.gitignore
 
 
AUTHORS
AUTHORS
 
 
CMakeLists.txt
CMakeLists.txt
 
 
Constant.h
Constant.h
 
 
Error.cpp
Error.cpp
 
 
Error.h
Error.h
 
 
IO.cpp
IO.cpp
 
 
IO.h
IO.h
 
 
LICENSE
LICENSE
 
 
MathConstant.h
MathConstant.h
 
 
MathGenMin.cpp
MathGenMin.cpp
 
 
MathGenMin.h
MathGenMin.h
 
 
MathGold.cpp
MathGold.cpp
 
 
MathGold.h
MathGold.h
 
 
MathMatrix.cpp
MathMatrix.cpp
 
 
MathMatrix.h
MathMatrix.h
 
 
MathVector.cpp
MathVector.cpp
 
 
MathVector.h
MathVector.h
 
 
PhredHelper.cpp
PhredHelper.cpp
 
 
PhredHelper.h
PhredHelper.h
 
 
README
README
 
 
README.md
README.md
 
 
Random.cpp
Random.cpp
 
 
Random.h
Random.h
 
 
Sort.cpp
Sort.cpp
 
 
Sort.h
Sort.h
 
 
allele.cpp
allele.cpp
 
 
allele.h
allele.h
 
 
ancestry_estimator.cpp
ancestry_estimator.cpp
 
 
ancestry_estimator.h
ancestry_estimator.h
 
 
augmented_bam_record.cpp
augmented_bam_record.cpp
 
 
augmented_bam_record.h
augmented_bam_record.h
 
 
bam_ordered_reader.cpp
bam_ordered_reader.cpp
 
 
bam_ordered_reader.h
bam_ordered_reader.h
 
 
bam_pool.h
bam_pool.h
 
 
bcf_chunked_reader.cpp
bcf_chunked_reader.cpp
 
 
bcf_chunked_reader.h
bcf_chunked_reader.h
 
 
bcf_filter_arg.h
bcf_filter_arg.h
 
 
bcf_filtered_reader.cpp
bcf_filtered_reader.cpp
 
 
bcf_filtered_reader.h
bcf_filtered_reader.h
 
 
bcf_ordered_reader.cpp
bcf_ordered_reader.cpp
 
 
bcf_ordered_reader.h
bcf_ordered_reader.h
 
 
bcf_ordered_writer.cpp
bcf_ordered_writer.cpp
 
 
bcf_ordered_writer.h
bcf_ordered_writer.h
 
 
bcf_variant_key.h
bcf_variant_key.h
 
 
bcftools.h
bcftools.h
 
 
bgzf.h
bgzf.h
 
 
boolParser.h
boolParser.h
 
 
cmd_bed_delta_svm_train.cpp
cmd_bed_delta_svm_train.cpp
 
 
cmd_bed_matched_shuffle.cpp
cmd_bed_matched_shuffle.cpp
 
 
cmd_bed_shuffle.cpp
cmd_bed_shuffle.cpp
 
 
cmd_bgen_to_vcf.cpp
cmd_bgen_to_vcf.cpp
 
 
cmd_cram_context_indel_analysis.cpp
cmd_cram_context_indel_analysis.cpp
 
 
cmd_cram_demuxlet.cpp
cmd_cram_demuxlet.cpp
 
 
cmd_cram_dense_genotype.cpp
cmd_cram_dense_genotype.cpp
 
 
cmd_cram_digital_pileup.cpp
cmd_cram_digital_pileup.cpp
 
 
cmd_cram_dsc_dump.cpp
cmd_cram_dsc_dump.cpp
 
 
cmd_cram_dsc_dump2pileup.cpp
cmd_cram_dsc_dump2pileup.cpp
 
 
cmd_cram_dsc_pileup.cpp
cmd_cram_dsc_pileup.cpp
 
 
cmd_cram_flagstat.cpp
cmd_cram_flagstat.cpp
 
 
cmd_cram_freemux2.cpp
cmd_cram_freemux2.cpp
 
 
cmd_cram_freemuxlet.cpp
cmd_cram_freemuxlet.cpp
 
 
cmd_cram_gtf_util.cpp
cmd_cram_gtf_util.cpp
 
 
cmd_cram_mux_pileup.cpp
cmd_cram_mux_pileup.cpp
 
 
cmd_cram_procap_detect.cpp
cmd_cram_procap_detect.cpp
 
 
cmd_cram_simul_contam.cpp
cmd_cram_simul_contam.cpp
 
 
cmd_cram_simuxlet.cpp
cmd_cram_simuxlet.cpp
 
 
cmd_cram_sparse_genotype.cpp
cmd_cram_sparse_genotype.cpp
 
 
cmd_cram_update_rg.cpp
cmd_cram_update_rg.cpp
 
 
cmd_cram_verify_bam.cpp
cmd_cram_verify_bam.cpp
 
 
cmd_cram_verify_pair_id.cpp
cmd_cram_verify_pair_id.cpp
 
 
cmd_dge_barcode_summary.cpp
cmd_dge_barcode_summary.cpp
 
 
cmd_dge_randomize.cpp
cmd_dge_randomize.cpp
 
 
cmd_dge_shuffle.cpp
cmd_dge_shuffle.cpp
 
 
cmd_fasta_gc_content.cpp
cmd_fasta_gc_content.cpp
 
 
cmd_m3vcf_subsample.cpp
cmd_m3vcf_subsample.cpp
 
 
cmd_plp_find_mux_clust.cpp
cmd_plp_find_mux_clust.cpp
 
 
cmd_plp_make_dge_matrix.cpp
cmd_plp_make_dge_matrix.cpp
 
 
cmd_run_test.cpp
cmd_run_test.cpp
 
 
cmd_sc_kallisto_count.cpp
cmd_sc_kallisto_count.cpp
 
 
cmd_sc_map_stamps.cpp
cmd_sc_map_stamps.cpp
 
 
cmd_sc_multinom_em.cpp
cmd_sc_multinom_em.cpp
 
 
cmd_sc_multinom_gibbs.cpp
cmd_sc_multinom_gibbs.cpp
 
 
cmd_tsv_util.cpp
cmd_tsv_util.cpp
 
 
cmd_vcf_delta_svm.cpp
cmd_vcf_delta_svm.cpp
 
 
cmd_vcf_extract.cpp
cmd_vcf_extract.cpp
 
 
cmd_vcf_fill_plink2.cpp
cmd_vcf_fill_plink2.cpp
 
 
cmd_vcf_ibs0_phase.cpp
cmd_vcf_ibs0_phase.cpp
 
 
cmd_vcf_ibs0_summary.cpp
cmd_vcf_ibs0_summary.cpp
 
 
cmd_vcf_ibs_matrix.cpp
cmd_vcf_ibs_matrix.cpp
 
 
cmd_vcf_infer_ancestry.cpp
cmd_vcf_infer_ancestry.cpp
 
 
cmd_vcf_infer_isaf.cpp
cmd_vcf_infer_isaf.cpp
 
 
cmd_vcf_mendel_dup_conc.cpp
cmd_vcf_mendel_dup_conc.cpp
 
 
cmd_vcf_merge_candidate_variants.cpp
cmd_vcf_merge_candidate_variants.cpp
 
 
cmd_vcf_normalize_depth.cpp
cmd_vcf_normalize_depth.cpp
 
 
cmd_vcf_paste_calls.cpp
cmd_vcf_paste_calls.cpp
 
 
cmd_vcf_ref_phase.cpp
cmd_vcf_ref_phase.cpp
 
 
cmd_vcf_sample_summary.cpp
cmd_vcf_sample_summary.cpp
 
 

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cramore

cramore is a collection of C++ tools to manipulate SAM/BAM/CRAM and BCF/VCF files in various contexts of sequence analysis.

Installing cramore

Before installing cramore, you need to install htslib in the same directory you want to install cramore (i.e. cramore and htslib should be siblings). You also need cmake installed in your system.

After installing htslib, you can clone the current snapshot of this repository to install as well

$ mkdir build

$ cd build

$ cmake ..

In case any required libraries is missing, you may specify customized installing path by replacing "cmake .." with:

For libhts:
  - $ cmake -DHTS_INCLUDE_DIRS=/hts_absolute_path/include/  -DHTS_LIBRARIES=/hts_absolute_path/lib/libhts.a ..

For bzip2:
  - $ cmake -DBZIP2_INCLUDE_DIRS=/bzip2_absolute_path/include/ -DBZIP2_LIBRARIES=/bzip2_absolute_path/lib/libbz2.a ..

For lzma:
  - $ cmake -DLZMA_INCLUDE_DIRS=/lzma_absolute_path/include/ -DLZMA_LIBRARIES=/lzma_absolute_path/lib/liblzma.a ..

Finally, to build the binary, run

$ make

List of tools contained in cramore

cramore contains many in-house C++ tools that are currently under the hood development phase. To list the available commands of tools, type:

cramore --help

To see the usage of individual commands, type:

cramore [command] --help

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A collection of C++ tools to manipulate SAM/BAM/CRAM and BCF/VCF files in various contexts of sequence analysis.

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