From 909f953f8d6fe57ad3e36d28ff3af0cd5f697105 Mon Sep 17 00:00:00 2001 From: Ben Ainscough Date: Wed, 8 Mar 2017 12:55:31 -0600 Subject: [PATCH 1/4] Improve per library documentation --- README.textile | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.textile b/README.textile index a6a42fa..9468402 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 per library output is formated as lib_name{bam readcount metrics}lib_name{bam readcount metrics}. The libraries are repeated in this format from library 1 to library N. h2. Build Dependencies From a0afe49311cc1bbb1a36bd589170305c7bd0a365 Mon Sep 17 00:00:00 2001 From: Ben Ainscough Date: Wed, 8 Mar 2017 13:00:11 -0600 Subject: [PATCH 2/4] Fixed formatting --- README.textile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.textile b/README.textile index 9468402..b6f0bd1 100644 --- a/README.textile +++ b/README.textile @@ -83,7 +83,7 @@ normal counting, but each library is listed by name and its metrics denoted by c 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 per library output is formated as lib_name{bam readcount metrics}lib_name{bam readcount metrics}. The libraries are repeated in this format from library 1 to library N. +In the output, after the chromosome, position, reference base, and depth fields the 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. h2. Build Dependencies From 2cfbcf10aeaa513c4396d44d8f1bc28169ded099 Mon Sep 17 00:00:00 2001 From: Ben Ainscough Date: Wed, 8 Mar 2017 13:01:05 -0600 Subject: [PATCH 3/4] typo --- README.textile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.textile b/README.textile index b6f0bd1..7882fa2 100644 --- a/README.textile +++ b/README.textile @@ -83,7 +83,7 @@ normal counting, but each library is listed by name and its metrics denoted by c 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 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. +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. h2. Build Dependencies From fc3d5a03a080c0b7755ac4ff2e5f0050a6aa8675 Mon Sep 17 00:00:00 2001 From: Ben Ainscough Date: Thu, 9 Mar 2017 11:07:55 -0600 Subject: [PATCH 4/4] Included missing [tab] --- README.textile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.textile b/README.textile index 7882fa2..26c7386 100644 --- a/README.textile +++ b/README.textile @@ -83,7 +83,7 @@ normal counting, but each library is listed by name and its metrics denoted by c 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. +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