diff --git a/README.textile b/README.textile index a6a42fa..26c7386 100644 --- a/README.textile +++ b/README.textile @@ -81,7 +81,9 @@ h3. Per Library Output Beginning with version 0.5.0, bam-readcount can now output counts per each library within a single BAM file. Libraries are reported with the same metrics as in normal counting, but each library is listed by name and its metrics denoted by curly braces as follows: -bc. chr position reference_base depth libname { base:count:avg_mapping_quality:avg_basequality:avg_se_mapping_quality:num_plus_strand:num_minus_strand:avg_pos_as_fraction:avg_num_mismatches_as_fraction:avg_sum_mismatch_qualities:num_q2_containing_reads:avg_distance_to_q2_start_in_q2_reads:avg_clipped_length:avg_distance_to_effective_3p_end } ... +bc. chr position reference_base depth library_1_name { base:count:avg_mapping_quality:avg_basequality:avg_se_mapping_quality:num_plus_strand:num_minus_strand:avg_pos_as_fraction:avg_num_mismatches_as_fraction:avg_sum_mismatch_qualities:num_q2_containing_reads:avg_distance_to_q2_start_in_q2_reads:avg_clipped_length:avg_distance_to_effective_3p_end } ... library_N_name { base:count:avg_mapping_quality:avg_basequality:avg_se_mapping_quality:num_plus_strand:num_minus_strand:avg_pos_as_fraction:avg_num_mismatches_as_fraction:avg_sum_mismatch_qualities:num_q2_containing_reads:avg_distance_to_q2_start_in_q2_reads:avg_clipped_length:avg_distance_to_effective_3p_end } + +In the output, after the chromosome, position, reference base, and depth fields the of per library output is formated as lib_name[TAB]{bam readcount metrics}[TAB]lib_name[TAB]{bam readcount metrics}. The libraries are repeated in this format from library 1 to library N. h2. Build Dependencies