Merge pull request #262 from umccr/feat/crypt4gh-storage

feat: Crypt4GH support using LocalStorage

Author: brainstorm

Cargo.lock

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+# Crypt4GH example file
+
+This is just a customised summary for htsget-rs. Please refer to the official [`crypt4gh-rust` documentation](https://ega-archive.github.io/crypt4gh-rust) for further information.
+
+## Keygen
+
+```sh
+cargo install crypt4gh
+crypt4gh keygen --sk keys/alice.sec --pk keys/alice.pub
+crypt4gh keygen --sk keys/bob.sec --pk keys/bob.pub
+```
+
+## Encrypt
+```
+crypt4gh encrypt --sk keys/alice.sec --recipient_pk keys/bob.pub < htsnexus_test_NA12878.bam > htsnexus_test_NA12878.bam.c4gh
+```
+
+## Decrypt
+
+```sh
+crypt4gh decryptor --range 0-65535 --sk data/crypt4gh/keys/bob.sec \
+                                 --sender-pk data/crypt4gh/keys/alice.pub \
+                                 < data/crypt4gh/htsnexus_test_NA12878.bam.c4gh \
+                                 > out.bam
+
+samtools view out.bam
+(...)
+SRR098401.61822403	83	11	5009470	60	76M	=	5009376	-169	TCTTCTTGCCCTGGTGTTTCGCCGTTCCAGTGCCCCCTGCTGCAGACCATAAAGGATGGGACTTTGTTGAGGTAGG	?B6BDCD@I?JFI?FHHFEAIIAHHDIJHHFIIIIIJEIIFIJGHCIJDDEEHHHDEHHHCIGGEGFDGFGFBEDC	X0:i:1	X1:i:0	MD:Z:76	RG:Z:SRR098401	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+
+samtools view: error reading file "out.bam"
+samtools view: error closing "out.bam": -1
+```
+
+The last samtools view error suggests that the returned bytes do not include BAM file termination.

data/c4gh/README.md

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+-----BEGIN CRYPT4GH PUBLIC KEY-----
+ToQrpj4UfuLgxZRe1wSGIZtXC19fOEHUHe3RQy63qwM=
+-----END CRYPT4GH PUBLIC KEY-----

data/c4gh/htsnexus_test_NA12878.bam.bai

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+-----BEGIN CRYPT4GH PRIVATE KEY-----
+YzRnaC12MQAEbm9uZQAEbm9uZQAgxi4tNmUO++HAApv9ryZB9S8QfqrWKKe5CunJuChH5vU=
+-----END CRYPT4GH PRIVATE KEY-----

data/c4gh/htsnexus_test_NA12878.bam.c4gh

@@ -0,0 +1,3 @@
+-----BEGIN CRYPT4GH PUBLIC KEY-----
+TyKEXZPnfon6dj1kRXl6HumfZDzo/h60RIc8Wd0Ig2s=
+-----END CRYPT4GH PUBLIC KEY-----

data/c4gh/htsnexus_test_NA12878.cram.c4gh

@@ -0,0 +1,3 @@
+-----BEGIN CRYPT4GH PRIVATE KEY-----
+YzRnaC12MQAEbm9uZQAEbm9uZQAg6uLXNqcXAi6FRKzRBk2KBKF4BnmueySZv5MGzKjIPcI=
+-----END CRYPT4GH PRIVATE KEY-----