def extract_and_assemble(bam_files, genome_file, white_list_file, output_dir, assembly_function_list,
subsample_nb_read=None,rg_ids=[], adapter_file=None, force_merge=False):
logging.info('processing %s'%output_dir)
logging.info("--------------------------")
logging.info("Extract the reads from bam")
logging.info("--------------------------")
list_consensus=RAD_bam_to_fastq.read_white_list(white_list_file)
RAD_bam_to_fastq.extract_reads_from_all_bam_files_set_of_consensus(bam_files, list_consensus=list_consensus,
output_dir=output_dir, all_read1_consensus_file=genome_file )
logging.info("--------------")
logging.info("Assemble read2")
logging.info("--------------")
RAD_assemble_read2.run_all_fastq_files(output_dir, assembly_function_list, 600, force_merge=force_merge,
subsample_nb_read=subsample_nb_read, rg_ids=rg_ids, adapter_file=adapter_file)
logging.info("----------------------------")
logging.info("Extract read groups from bam")
logging.info("----------------------------")
all_read_groups=get_readgroup_from_bam(bam_files)
logging.info("-------------------------------------")
logging.info("Align both reads back to the assembly")
logging.info("-------------------------------------")
RAD_smalt_align_reads_back_to_consensus.run_all_fastq_files(output_dir, all_read_groups=all_read_groups, snp_call=True)
logging.info("---------------------")
logging.info("Merge all the results")
logging.info("---------------------")
RAD_merge_results.merge_results(output_dir)
logging.info("------------------------------")
logging.info("Get the summary of the results")
logging.info("------------------------------")
RAD_summarize_assembly.run_all_summaries(output_dir)
