1 files changed, 0 insertions, 96 deletions
diff --git a/sci-biology/goby-cpp/files/Reads.proto b/sci-biology/goby-cpp/files/Reads.proto
deleted file mode 100644
index 32c1244a3eb3..000000000000
--- a/sci-biology/goby-cpp/files/Reads.proto
+++ /dev/null
@@ -1,96 +0,0 @@
-package goby;
-
-option java_package = "edu.cornell.med.icb.goby.reads";
-option optimize_for = SPEED;
-
-message ReadCollection {
-     repeated ReadEntry reads = 1;
-}
-
-message ReadEntry {
-  /*
-    Index of a read.
-  */
-  required uint32 read_index = 1;
-   /*
-    Index of the barcode, if any.
-  */
-  optional uint32 barcode_index = 10;
-  /*
-     Read identifier/name may be present.
-  */
-  optional string read_identifier = 23;
-  /*
-     Additional description about the read (from Fasta/Q format).
-   */
-  optional string description = 22;
-  /*
-    Length of the sequence.
-   */
-  required uint32 read_length = 2;
-  /*
-    Sequence, encoded as ascii characters stored in single bytes.
-   */
-  optional bytes sequence = 3;
-  /*
-   The second sequence in a pair. Stored the same way as the sequence attribute.
-  */
-  optional bytes sequence_pair = 5;
-  /*
-    Length of the second sequence in a pair.
-  */
-  optional uint32 read_length_pair = 6;
-  /*
-    Quality scores in Phred units, stored as single bytes (0-255).
-  */
-  optional bytes quality_scores = 4;
-  /*
-    Quality scores for the second sequence in a pair. Stored as the 'qualityScores' attribute.
-   */
-  optional bytes quality_scores_pair = 7;
-  /*
-    Compressed stream of data. The first byte indicates the compression/decompression method (codec). The remaining bytes are
-    content compressed with the codec.
-  */
-  optional bytes compressed_data = 8;
-  /*
-     Stores meta-data about the reads. Typically meta-data is stored in the very first read of a
-     read collection, with the understanding that the meta-data applies to all the reads in the
-     collection. Meta-data can be used to store information about when the sample was sequenced,
-     or other information of interest. The key-value pair format is sufficiently flexible to
-     accomodate a variety of needs. The following keys are pre-defined. Please use pre-defined
-     keys so that automated tools can use metadata in relatively standard way. Please note that
-     some keys provide a format for the value. This format should also be followed to garantee
-     that meta data can be used computationally in fully automatic manner.
-
-     key="sequencing-run-start-date" value="MM/DD/YYYY" Used to record when the sequencing run
-     was initiated on the instrument. Can be used to detect batch effect in a large set of samples.
-     key="platform" value="<free-text>". Value is free text, but the following terms are pre-defined.
-      Illumina GaIIx
-      Illumina HiSeq 1000
-      Illumina HiSeq 2000
-      Helicos Heliscope
-      LifeTech 5500 SOLiD
-      LifeTech 5500xl SOLiD
-      Roche 454 GS FLX Ti
-
-      key="organism" value="species name"
-      Since Goby 1.9.1
-  */
-  repeated MetaData meta_data = 25;
-
-}
-/*
- A message to store a key/value pair and represent metadata about reads.
- Since Goby 1.9.1
- */
-message MetaData {
- /*
-   Provides the key. See examples in the documentation of meta_data for ReadEntry.
- */
- required string key=1;
- /*
-   Describes the value associated with the key. See examples in the documentation of meta_data for ReadEntry.
- */
- required string value=2;
-}