Summary

A server implementation of htsget protocol.

FAQ

• Dependencies
  • Asio
  • Catch
  • nlohmann/json
  • OpenSSL
  • CMake
  • Samtools
• C++17
  • flags -std=c++1z -stdlib=libc++
  • compiled with clang-802.0.42 on macOS
• Build

  cmake -H. -Bbuild -Wno-dev
  cmake --build build -- -j5

• Run
  • on localhost

    ./bin/htsgetserver

  • check in browser

Example

• Routes

  GET
      \       
      1|-/ 
          2|-data/    
              3|-<filename>     
          2|-reads/  
              3|-<id>   

  • /reads/<id>
    • handles incoming request, dispatch tickets in json
  • /data/<filename>
    • handles data transfer, according to byte range
• Test with samtools

  samtools view "http://127.0.0.1:8888/reads/bamtest?format=BAM&referenceName=1&start=10145&end=10150"

  SOLEXA-1GA-2_2_FC20EMB:5:251:979:328    0       chr1    10145   25      36M     *       0       0       AACCCCTAACCCTAACCCTAACCCTAACCCTAAACT    hhhhHcWhhHTghcKA_ONhAAEEBZE?H?CBC?DA       NM:i:1  X1:i:1  MD:Z:33A2
  SOLEXA-1GA-2_2_FC20EMB:5:102:214:278    0       chr1    10148   25      36M     *       0       0       CCCTAACCCTAACCCTAACCCTAACCCTAACCTAAC    hbfhhhXUYhT_ULZdLRTKNIMIKGLJCHFFJQJN       NM:i:0  X0:i:1  MD:Z:36
  SOLEXA-1GA-2_2_FC20EMB:5:195:284:685    16      chr1    10149   25      36M     *       0       0       CCAAACACTAACCCTAACCCTAACCCTAACCTAACC    ><>B@>?>?D>>?B?D>DBC?E@BDHAKCEKERLOO       NM:i:1  X1:i:1  MD:Z:29A3A2
  SOLEXA-1GA-2_2_FC20EMB:5:35:583:827     0       chr1    10150   25      36M     *       0       0       CTAACCCTAAACCTAACCCTAACCCTAACCTAACCA    hhW_X]MXNOHQQWMILHGIFMJGJLCFGGJAKIEH       NM:i:1  X1:i:1  MD:Z:10A24A0