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Improve per library documentation #38
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| -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{bam readcount metrics}. The libraries are repeated in this format from library 1 to library N. |
ernfrid
Mar 8, 2017
Contributor
This should be:
lib_name[TAB]{bam readcount metrics}[TAB]lib_name[TAB]{bam readcount metrics} I think.
bainscou
Mar 9, 2017
Contributor
Good catch! I missed that. For some reason I am having trouble committing the fix to this pull request. It is not updating from my fork.
jasonwalker80
merged commit 1b9c52c
into genome:master
Mar 9, 2017
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bainscou commentedMar 8, 2017
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