Improve per library documentation #38

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merged 4 commits into from Mar 9, 2017
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@@ -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