Update SAM.md

documentation/SAM.md

@@ -1,3 +1,46 @@
 # Bonito Draft SAM specification
 
-
+Bonito v0.5.0 added support for outputing aligned and unaligned SAM, BAM or CRAM. 
+
+```
+$ bonito basecaller $model $data > unaligned.sam
+$ bonito basecaller $model $data > unaligned.bam
+$ bonito basecaller $model $data > unaligned.cram
+
+$ bonito basecaller $model $data --reference ref.mmi   > aligned.sam
+$ bonito basecaller $model $data --reference ref.mmi   > aligned.bam
+$ bonito basecaller $model $data --reference ref.fasta > aligned.cram
+```
+
+#### Header
+
+```
+@HD     VN:1.5  SO:unknown      ob:0.0.1
+@PG     ID:basecaller   PN:bonito       VN:0.4.0        CL:bonito basecaller [email protected] reads
+@PG     ID:aligner      PN:minimap2     VN:2.20 DS:mappy
+```
+
+#### Read Group Header
+
+|    |    |                                                       |
+| -- | -- | ----------------------------------------------------- |            
+| RG | ID | `<runid>_<basecalling_model>`  	                      |
+|    | PU | `<flow_cell_id>`                                      |	    
+|    | PM | `<device_id>`                                         |
+|    | DT | `<exp_start_time>`                                    |
+|    | PL | `ONT`                                                 |
+|    | DS | `basecall_model=<basecall_model_name> runid=<run_id>` |
+|    | LB | `<sample_id>`                                         |    
+|    | SM | `<sample_id>`                                         |
+
+#### Read Tags
+
+|       |                                                     |
+| ----- | --------------------------------------------------- |
+| RG:Z: | `<runid>_<basecalling_model>`                        |
+| qs:i: | mean basecall qscore rounded to the nearest integer |
+| mx:i:	| read mux                                            | 
+| ch:i: | read channel                                        |
+| rn:i:	| read number                                         |
+| st:Z:	| read start time                                     |
+| f5:Z:	| fast5 file name                                     |