applicativesystem

Finished writing the code for this and this is specific for the specific range. Final and binary release.
sciencegenome · Dec 4, 2024 · e03b78a · e03b78a
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diff --git a/.gitignore b/.gitignore
@@ -0,0 +1 @@
+/target
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
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+[package]
+name = "rust-samtools-generateid-range"
+version = "0.1.0"
+edition = "2021"
+
+[dependencies]
+clap = { version = "4.5.22", features = ["derive"] }
diff --git a/README.md b/README.md
@@ -1,2 +1,18 @@
 # rust-samtools-generateid-range
-rust-samtools generateid range
+
+ - rust-samtools generateid range
+ - rust samtools generateid range will only generate the fastidx for the specified range for the use with the other rust-samtools. 
+ - The difference between this and the rust-samtools-generateid is that rust-samtools-generateid for all the identifiers whereas in this you can specify a start and stop coordinate and it will generate only the fastidx for those range and not for the whole sam file. 
+ - general note: Incase of Golang and RUST, please see the last commit message and if it says compiled binary then it is completed or else still in development version.
+
+ ```
+ cargo build 
+ 
+ ```
+
+ ```
+  ./target/debug/rust-samtools-generateid-range 
+         ./sample-files/alignreads-metagenomics.sam  540849 613960
+ ```
+
+ Gaurav Sablok
diff --git a/rust-samtools-generateid-range b/rust-samtools-generateid-range
diff --git a/rust-samtools-generateid-range.tar b/rust-samtools-generateid-range.tar
diff --git a/sample-files/alignreads-metagenomics.sam b/sample-files/alignreads-metagenomics.sam
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+@HD    VN:1.3    SO:coordinate
+@SQ    SN:conticA    LN:443
+@SQ    SN:contigB    LN:1493
+@SQ    SN:contigC    LN:328
+
+readID43GYAX15:7:1:1202:19894/1    256    contig43    613960    1    65M    *    0    0    CCAGCGCGAACGAAATCCGCATGCGTCTGGTCGTTGCACGGAACGGCGGCGGTGTGATGCACGGC    EDDEEDEE=EE?DE??DDDBADEBEFFFDBEFFEBCBC=?BEEEE@=:?::?7?:8-6?7?@??#    AS:i:0    XS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:65  YT:Z:UU
+readID43GYAX15:7:1:1202:19894/1    272    contig32    21001    1    65M    *    0    0    GCCGGACGTCACACGGCCGCCGGGCCGGTCTACGACCAGACGCATGCGGATTTCGTTAGAGCCGG    #??@?7?6-8:?7?::?:=@EEEEB?=CBCBEFFEBDFFFEBEDABDDD??ED?EE=EEDEEDDE    AS:i:-5    XS:i:0   XN:i:0  XM:i:1   XO:i:0   XG:i:0   NM:i:1   MD:Z:42T22   YT:Z:UU
+readID43GYAX15:7:1:1202:19894/1    256    contig87    540849    1    65M    *    0    0    CCTGCACGAACGAAATCCGCATGCGTCTGGTCGTTGTACGGAACGGCGGTTGTGTGACGAACGGC    EDDEEDEE=EE?DE??DDDBADEBEFFFDBEFFEBCBC=?BEEEE@=:?::?7?:8-6?7?@??# AS:i:0  XS:i:0 XN:i:0  XM:i:0 XO:i:0  XG:i:0  NM:i:0    MD:Z:65    YT:Z:UU