Merge branch 'main' of github.com:michaeljon/fasterqc.net

michaeljon · May 20, 2022 · deb97b8 · deb97b8
2 parents b311874 + eb1a733
commit deb97b8
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Showing 3 changed files with 103 additions and 5 deletions.
diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -12,18 +12,17 @@
       // If you have changed target frameworks, make sure to update the program path.
       "program": "${workspaceFolder}/bin/Debug/net6.0/Ovation.FasterQC.Net.dll",
       "args": [
-        "-v",
         "-d",
         "-l",
-        "1000000",
+        "10",
         "-f",
-        "sam",
+        "bam",
         "-i",
-        "./tmp/in3257_2_S1.sorted.sam",
+        "./tmp/in3257_2_S1.sorted.bam",
         "-o",
         "./tmp/bob.json",
         "-m",
-        "MeanQualityDistribution"
+        "BasicStatistics"
       ],
       "cwd": "${workspaceFolder}",
       // For more information about the 'console' field, see https://aka.ms/VSCode-CS-LaunchJson-Console

diff --git a/Models/BamAlignment.cs b/Models/BamAlignment.cs
@@ -1,4 +1,7 @@
+using System;
+using System.ComponentModel;
 using System.Diagnostics.CodeAnalysis;
+using System.Text;
 
 namespace Ovation.FasterQC.Net
 {
@@ -37,4 +40,94 @@ public class BamAlignment
 
         public byte[] qual { get; set; } = null!;
     }
+
+    [SuppressMessage("Code style", "IDE1006", Justification = "Names correspond to BAM structure field names")]
+    public class BamOptionalElement
+    {
+        public char[] tag { get; set; }
+
+        public char val_type { get; set; }
+
+        public object value { get; set; } = null!;
+
+        public BamOptionalElement(byte[] block, ref int offset)
+        {
+            tag = Encoding.ASCII.GetChars(block, offset, 2); offset += 2;
+            val_type = Encoding.ASCII.GetChars(block, offset, 1)[0]; offset += 1;
+
+            // consume the rest
+            switch (val_type)
+            {
+                case 'A': offset += 1; break;
+
+                // byte
+                case 'c': offset += 1; break;
+                case 'C': offset += 1; break;
+
+                // short
+                case 's': offset += 2; break;
+                case 'S': offset += 2; break;
+
+                // int
+                case 'i': offset += 4; break;
+                case 'I': offset += 4; break;
+
+                // float
+                case 'f': offset += 4; break;
+
+                // null-terminated string
+                case 'Z':
+                    while (block[offset++] != 0) ;
+                    break;
+
+                // null-terminated hex digit pairs
+                case 'H':
+                    while (block[offset++] != 0) ;
+                    break;
+
+                // array of stuff
+                case 'B':
+                    var subtype = Encoding.ASCII.GetChars(block, offset, 1)[0]; offset += 1;
+                    var length = BitConverter.ToUInt32(new Span<byte>(block, offset, 4)); offset += 4;
+
+                    // consume the stuff
+                    for (var element = 0; element < length; element++)
+                    {
+                        switch (subtype)
+                        {
+                            // byte
+                            case 'c': offset += 1; break;
+                            case 'C': offset += 1; break;
+
+                            // short
+                            case 's': offset += 2; break;
+                            case 'S': offset += 2; break;
+
+                            // int
+                            case 'i': offset += 4; break;
+                            case 'I': offset += 4; break;
+
+                            // float
+                            case 'f': offset += 4; break;
+                        }
+                    }
+
+                    break;
+            }
+        }
+
+        public override string ToString()
+        {
+            var sb = new StringBuilder();
+
+            sb.Append("tag: ");
+            sb.Append(tag[0]);
+            sb.Append(tag[1]);
+
+            sb.Append(", type: ");
+            sb.Append(val_type);
+
+            return sb.ToString();
+        }
+    }
 }
diff --git a/Readers/BamReader.cs b/Readers/BamReader.cs
@@ -164,6 +164,12 @@ private BamAlignment ReadSequence()
             {
                 bamAlignment.qual = Array.Empty<byte>();
             }
+            offset += (int)bamAlignment.l_seq;
+
+            while (offset < block_size)
+            {
+                _ = new BamOptionalElement(block, ref offset);
+            }
 
             return bamAlignment;
         }