* more README work

Author: iontorrent-dev

README.md

@@ -1,20 +1,21 @@
-This is *NOT* the official repository of SAMtools.  The official SAMtools repository can be found at: http://samtools.sourceforge.net/ 
+## This is *NOT* the official repository of SAMtools.  
+The official SAMtools repository can be found at: http://samtools.sourceforge.net/ 
 
-Major fixes:
-- added "samtools sample" command, to sample reads from a SAM/BAM file at a given frequency.
-- added "samtools qa" command, to compute the mean and median coverage, as well a histogram from 1 to N (defined by param) containing the number of bases covered a maximum of 1X, 2X...NX. Furthermore, "other" information is also available in the output file, namely:
-    1. Total number of reads
-    2. Total number of duplicates found and ignored (duplicates are "found" based on the sam flag and are ignored in the counting of coverage)
-    3. Percentage of unmapped reads
-    4. Percentage of zero quality mappings
-    5. Number of proper paired reads (based on sam flag of proper pairs)
-    6. Percentage of proper pairs.e
+## Major fixes:
+    - added "samtools sample" command, to sample reads from a SAM/BAM file at a given frequency.
+    - added "samtools qa" command, to compute the mean and median coverage, as well a histogram from 1 to N (defined by param) containing the number of bases covered a maximum of 1X, 2X...NX. Furthermore, "other" information is also available in the output file, namely:
+        - Total number of reads
+        - Total number of duplicates found and ignored (duplicates are "found" based on the sam flag and are ignored in the counting of coverage)
+        - Percentage of unmapped reads
+        - Percentage of zero quality mappings
+        - Number of proper paired reads (based on sam flag of proper pairs)
+        - Percentage of proper pairs.e
 
-Minor fixes:
-- Check the write filehandle after opening for write.
-- allow for user defined [lowercase] tags in header elements.
-- allow the maximum memory for "samtools sort" to be specified with units.
-- adjust for leading hard clip on colorspace reads.
-- catches and reports an invalid BAM header, instead of segfaulting later on.
-- fixes a small underflow/overflow bug in integer parsing.
-- checks for a lowerbound in text entry box to avoid segfault in tview.
+## Minor fixes:
+    - Check the write filehandle after opening for write.
+    - allow for user defined [lowercase] tags in header elements.
+    - allow the maximum memory for "samtools sort" to be specified with units.
+    - adjust for leading hard clip on colorspace reads.
+    - catches and reports an invalid BAM header, instead of segfaulting later on.
+    - fixes a small underflow/overflow bug in integer parsing.
+    - checks for a lowerbound in text entry box to avoid segfault in tview.