Just trying to keep line wraps consistent

Author: andrewdavidsmith

README.md

@@ -9,13 +9,13 @@ SYSTEM REQUIREMENTS:
 ========================================================================
 The preseq software will only run on 64-bit UNIX-like operating
 systems and was developed on both Linux and Mac. The preseq software
-requires a C++ compiler that supports C++11. 
+requires a C++ compiler that supports C++11.
 
 INSTALLATION:
 ========================================================================
 ### Installing from a release
 
-1. Download preseq-x.tar.gz from the releases tab of this repository.
+1. Download `preseq-x.tar.gz` from the releases tab of this repository.
 2. Unpack the archive:
 ```
 $ tar -zxvf preseq-x.tar.gz
@@ -89,23 +89,23 @@ USAGE EXAMPLES:
 Each program included in this software package will print a list of
 options if executed without any command line arguments. Many of the
 programs use similar options (for example, output files are specified
-with '-o'). 
+with '-o').
 
 We have provided a data directory to test each of our programs.
-Change to the `data` directory and try some of our commands. 
+Change to the `data` directory and try some of our commands.
 To predict the yield of a future experiment, use `lc_extrap`.
-For the most basic usage of `lc_extrap` to compute the expected yield, 
+For the most basic usage of `lc_extrap` to compute the expected yield,
 use the command on the following data:
 ```
-preseq lc_extrap -o yield_estimates.txt SRR1003759_5M_subset.mr 
+preseq lc_extrap -o yield_estimates.txt SRR1003759_5M_subset.mr
 ```
 If the input file is in `.bam` format, use the `-B` flag:
 ```
 preseq lc_extrap -B -o yield_estimates.txt SRR1106616_5M_subset.bam
 ```
 For the counts histogram format, use the `-H` flag:
 ```
-preseq lc_extrap -H -o yield_estimates.txt SRR1301329_1M_read.txt 
+preseq lc_extrap -H -o yield_estimates.txt SRR1301329_1M_read.txt
 ```
 
 The yield estimates will appear in yield_estimates.txt, and will be a
@@ -115,33 +115,33 @@ by two columns giving the corresponding confidence intervals.
 
 To investigate the past yield of an experiment, use `c_curve`.
 `c_curve` can take in the same file formats as `lc_extrap` by using
-the same flags. The estimates will appear in estimates.txt with two 
-columns.  The first column gives the total number of reads in a 
-theoretically smaller experiment and the second gives the corresponding 
-number of distinct reads.
+the same flags. The estimates will appear in estimates.txt with two
+columns.  The first column gives the total number of reads in a
+theoretically smaller experiment and the second gives the
+corresponding number of distinct reads.
 
-`bound_pop` provides an estimate for the species richness
-of the sampled population. The input file formats and corresponding flags
-are identical to `c_curve` and `lc_extrap`. The output provides the median 
-species richness in the first column and the confidence intervals
-in the next two columns.
-
-Finally, `gc_extrap` predicts the expected genomic coverage for a future experiment.
-It produces the coverage in an output format identical to `lc_extrap`. `gc_extrap` 
-can only take in files in BED and mapped reads format (using the `-B` flag for BED):
+`bound_pop` provides an estimate for the species richness of the
+sampled population. The input file formats and corresponding flags are
+identical to `c_curve` and `lc_extrap`. The output provides the median
+species richness in the first column and the confidence intervals in
+the next two columns.
 
+Finally, `gc_extrap` predicts the expected genomic coverage for a
+future experiment.  It produces the coverage in an output format
+identical to `lc_extrap`. `gc_extrap` can only take in files in BED
+and mapped reads format (using the `-B` flag for BED):
 ```
-preseq gc_extrap -B -o coverage_estimates.txt SRR1003759_5M_subset.mr 
+preseq gc_extrap -B -o coverage_estimates.txt SRR1003759_5M_subset.mr
 ```
 
-More data is available in the `additional_data.txt` file in the `data` directory.
-For an extended write-up on our programs, please read the manual in the `docs`
-directory. 
+More data is available in the `additional_data.txt` file in the `data`
+directory.  For an extended write-up on our programs, please read the
+manual in the `docs` directory.
 
 UPDATES TO VERSION 3.0.2
 ========================================================================
-GSL has been completely removed, and a data directory has been added for
-users to test our programs. 
+GSL has been completely removed, and a data directory has been added
+for users to test our programs.
 
 UPDATES TO VERSION 3.0.1
 ========================================================================