gkno build : some programs of Tangram were not built

[okbys]

Hello,

I have downloaded gkno file sets and builded them. "gkno build" seemed ok, however tangram_merge and tangram_scan were not built.

• stdout/stderr of gkno build.

$ gkno build
Initialized empty Git repository in /path/to/gkno_launcher/src/configurationClass/.git/
remote: Reusing existing pack: 1051, done.
remote: Counting objects: 7, done.
remote: Compressing objects: 100% (7/7), done.
remote: Total 1058 (delta 1), reused 0 (delta 0)
Receiving objects: 100% (1058/1058), 712.06 KiB | 491 KiB/s, done.
Resolving deltas: 100% (512/512), done.

======================================================
  Boston College gkno package

  version:    1.0.4
  date:       May 2014
  git commit: 6f52694cea6048617aa31afb4bc201aa302c8510
======================================================

Checking dependencies...done.
Initializing component data...done.
Building tools:
  bamtools...done.
  blast...done.
  freebayes...done.
  gatk...done.
  glia...done.
  jellyfish...done.
  libStatGen...done.
  bamUtil...done.
  fastQValidator...done.
  qplot...done.
  verifyBamID...done.
  mosaik...done.
  musket...done.
  mutatrix...done.
  ogap...done.
  picard...done.
  premo...done.
  Rufus...done.
  samtools...done.
  scissors...done.
  seqan...done.
  snpEff...done.
  tabix...done.
  tangram...done.
  vcflib...done.
Fetching default resources:
  tutorial:
    Downloading files... 100%
    Unpacking files...done.

• Builded programs of Tangram.

$ ls -1 tools/Tangram/bin/
tangram_bam
tangram_detect
tangram_filter.pl
tangram_index
tangram_view_scan_file.py

• Rebuilding Tangram.

$ pushd tools/Tangram/src/
$ make clean
$ make
Building Tangram
=========================================================
- Building in OutSources
  * compiling ssw_cpp.cpp
  * compiling ssw.c
  * compiling Fasta.cpp
  * compiling split.cpp
  * compiling md5.c
  * compiling TGM_BamHeader.c
  * compiling TGM_Error.c

- Building in TangramBam
  * compiling hashes_collection.cpp
  * compiling special_hasher.cpp
  * compiling tangram_bam.cpp
  * compiling ConvertHashTableOutToIn.c
  * compiling seq_converter.c
  * compiling SR_BamHeader.c
  * compiling SR_BamInStream.c
  * compiling SR_BamMemPool.c
  * compiling SR_Error.c
  * compiling SR_HashRegionTable.c
  * compiling SR_InHashTable.c
  * compiling SR_OutHashTable.c
  * compiling SR_QueryRegion.c
  * compiling SR_Reference.c
  * linking /path/to/gkno_launcher/tools/Tangram/bin/tangram_bam

- Building in TangramScan
  * compiling TGM_ReadPairScan.c
  * compiling TGM_ReadPairScanGetOpt.c
  * compiling TGM_ReadPairScanMain.c
  * compiling TGM_LibInfo.c
  * compiling TGM_FragLenHist.c
  * compiling TGM_GetOpt.c
  * compiling TGM_Utilities.c
  * compiling TGM_BamInStream.c
  * compiling TGM_BamPairAux.c
  * compiling TGM_BamMemPool.c
  * linking /path/to/gkno_launcher/tools/Tangram/bin/tangram_scan

- Building in TangramMerge
  * compiling TGM_MergeLibGetOpt.c
  * compiling TGM_MergeLibMain.c
  * compiling TGM_LibInfo.c
  * compiling TGM_FragLenHist.c
  * compiling TGM_GetOpt.c
  * compiling TGM_Utilities.c
  * linking /path/to/gkno_launcher/tools/Tangram/bin/tangram_merge

- Building in TangramDetect
  * compiling TGM_Aligner.cpp
  * compiling TGM_BamPair.cpp
  * compiling TGM_Cluster.cpp
  * compiling TGM_Detector.cpp
  * compiling TGM_FirstMapThread.cpp
  * compiling TGM_FragLenTable.cpp
  * compiling TGM_Genotype.cpp
  * compiling TGM_LibTable.cpp
  * compiling TGM_PairAttrbt.cpp
  * compiling TGM_Parameters.cpp
  * compiling TGM_Printer.cpp
  * compiling TGM_Reference.cpp
TGM_Reference.cpp: In function ‘int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)’:
TGM_Reference.cpp:28: warning: comparison between signed and unsigned integer expressions
  * compiling TGM_RescuePartial.cpp
  * compiling TGM_SecondMapThread.cpp
TGM_SecondMapThread.cpp: In member function ‘bool Tangram::SecondMapThread::SecondFilterSpecial(bool&, Tangram::RescuePartial&, uint8_t&, const s_align*, uint8_t, const Tangram::PrtlAlgnmnt&, const Tangram::RefRegion&, const int8_t*, int)’:
TGM_SecondMapThread.cpp:457: warning: comparison between signed and unsigned integer expressions
TGM_SecondMapThread.cpp:458: warning: comparison between signed and unsigned integer expressions
  * compiling TGM_Tangram.cpp
  * compiling TGM_GetOpt.c
  * compiling TGM_Utilities.c
  * linking /path/to/gkno_launcher/tools/Tangram/bin/tangram_detect

- Building in TangramIndex
  * compiling TGM_IndexRef.cpp
  * compiling TGM_RefParameters.cpp
  * linking /path/to/gkno_launcher/tools/Tangram/bin/tangram_index

- Building in TangramTools
  * copying /path/to/gkno_launcher/tools/Tangram/bin/tangram_filter.pl /path/to/gkno_launcher/tools/Tangram/bin/tangram_view_scan_file.py

$ popd

• After rebuilding: Builded programs of Tangram.

$ ls -1 tools/Tangram/bin/
tangram_bam
tangram_detect
tangram_filter.pl
tangram_index
tangram_merge
tangram_scan
tangram_view_scan_file.py
$

• Version of Tangram.

$ pushd tools/Tangram
$ git log | head -6
commit 1fb2e76028eaffe4894a9fab00a71bf5e8c91011
Author: Jiantao Wu <jiantaowu.xining@gmail.com>
Date:   Sun Feb 9 00:39:29 2014 -0800

    Update the readme file

$

[AlistairNWard]

Thanks for this report. I am able to recreate the error and am looking into a resolution. Should have this fixed later today.

[AlistairNWard]

Problem has been fixed in Version 1.7.1.

[okbys]

I confirmed it. Thank you for your very quick fix.

[AlistairNWard]

Thanks for the independent test! It's definitely helpful to us to know that fixes work on systems other than our own.