cleanup repo and documentation

Remove old build code to avoid confusion.

Update license to reflect ongoing work and authorship.

Always cite original authors--- they are listed in the README. MashMap
is public domain.

Upda readme to talk a little about -N.

LICENSE

@@ -0,0 +1,20 @@
+The MIT License (MIT)
+
+Copyright (c) 2020 Erik Garrison
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

@@ -28,10 +28,11 @@ Suitable default settings are provided for this purpose.
 
 Four parameters shape the length, number, and identity of the resulting mappings:
 
-* `-s[N], --segment-length=[N]` is the length of the mapped and aligned segment
+* `-s[N], --segment-length=[N]` is the length of the mapped and aligned segment (when `-N` is not set)
+* `-N, --no-split` avoids splitting queries into segments, and instead maps them in their full length
 * `-p[%], --map-pct-id=[%]` is the percentage identity minimum in the _mapping_ step
-* `-n[N], --n-secondary=[N]` is the maximum number of mappings (and alignments) to report for each segment
-* `-a[%], --align-pct-id=[%]` defines the minimum percentage identity allowed in the _alignment_ step
+* `-n[N], --n-secondary=[N]` is the maximum number of mappings (and alignments) to report for each segment above `segment-length` (the number of mappings for sequences shorter than the segment length is defined by `-S[N], --n-short-secondary=[N]`, and defaults to 1)
+* `-a[%], --align-pct-id=[%]` defines the minimum percentage identity alignment to report from the _alignment_step
 
 Together, these settings allow us to precisely define an alignment space to consider.
 During all-to-all mapping, `-X` can additionally help us by removing self mappings from the reported set.