Update with JOSS review suggestions #82

README.md

@@ -37,6 +37,8 @@ For details see [docker/README.md](docker/README.md).
 Requires a C++ toolchain and `cmake`. For details see
 [BUILD.md](BUILD.md). 
 
+    git clone https://github.com/genome/bam-readcount 
+    cd bam-readcount
     mkdir build
     cd build
     cmake ..
@@ -132,4 +134,4 @@ avg_distance_to_effective_3p_end | Average distance to the 3’ prime end of the
 With the `-p` option, each output line will have a set of `{}`-delimited
 results, one for each library:
 
-    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	}
+    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	}