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

Name		Name	Last commit message	Last commit date
Latest commit History 82 Commits
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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