adding
adding ..
updating
Update blessed build - changes due to bam-readcount version bump
Always make file_path and file_content_hash match
Fix warning about software_result->get
Revert lumpy commits until we figure it out
Revert "changed the paths so that it will run on any machine"

This reverts commit eea9994d91c3fa4d39c56063130c5406df5e0f0d.

Revert "adds extra output for when the test fails"

This reverts commit 02eba26aeffdd0b102f14263b9da9ed5d9121069.

Revert "Removed the params hash and renamed variables"

This reverts commit f8705fb24e72926dc46a8c95b0e79764adb3e4cf.

Revert "removed temporary variables"

This reverts commit 472716e3fcdf4f314d8ac97edc83d18edb4548c3.

Revert "more changes ugh!"

This reverts commit 7122c39cfe9f8b48b819cbd884c8fe86c45af171.

Revert "Rempved a bit of excess code"

This reverts commit ab5cdc1bc86e7e80837a2bdad49f1bffbcc4a44c.

Revert "Removed the extra debug and print statments"

This reverts commit 09b89260e199ddc3cda3c4450985505f17be42d0.

Revert "removed the extra print statments"

This reverts commit cdc666c9cf573ac2a0376f417ba1fbe0867b9c2c.

Revert "Fixed the version test error"

This reverts commit 6bc926253bfbde18ffee2776658e5c131538faeb.

Revert "Added a test to make sure the version exists"

This reverts commit 8cf7eb5dc739014f69b91aa3db339658f2a7e0cc.

Revert "added a test to make sure the version exists"

This reverts commit 8f28018a75202a689cd5027787478ccc47a46eec.

Revert "Incororated versioning into the program"

This reverts commit f495327276d8e1e7efa7f8755e72bfd85c05d654.

Revert "incorporated versioning into the program"

This reverts commit f8dd7869ba1ded3d652eda35440fc9f6c4777545.

Revert "DB2 lumpy wrote tests to check lumpy script methods"

This reverts commit e79cfc78522b2e1f146af63a81cec804a058342f.

Revert "DB2 lumpy made methods to find lumpy scripts"

This reverts commit 21df0bd263e2ed8a63aaf62b0f654e2739b6e59c.

Revert "DV2 lumpy: mean and stdev temp file storage"

This reverts commit d1861ab07e5681b49320ccf86b7e221941088487.

Revert "Changed some of the print statements to debug"

This reverts commit f9d163bcf9e9c0409d18802dc827d2d6cb6fd6f3.

Revert "added a Matched samples test"

This reverts commit af53ea4f3e576d4cce42d80b81babf2d6ab05d76.

Revert "Parameters and the histo files were put in a hash"

This reverts commit 959f5d1d46c4679d6363f5b523c7526a06badc40.

Revert "rearranged the sr parameters to see if they would work"

This reverts commit 32a7df2d67c2799ec0ed3df6e79d9534719c43a8.

Revert "updated and improved pe_cmd_arrangement & its test"

This reverts commit cc03d83f5fee7781f66af028722cb869a239ae92.

Revert "changed mean and stdv to a hash"

This reverts commit c25caa31694ae716da057a317c4b41dc92bc2f32.

Revert "added a subtest to test the absence of split reads in the bam_file"

This reverts commit f110094edefd2641913d15a760b2d9599f39117f.

Revert "Lumpy fixed mean and stdev subroutine"

This reverts commit acec6fdf7283ed59858e174af8e212c0da7f9e76.

Revert "Changed the sam-bam converter to picard tools"

This reverts commit 9afe92a57e79a651b8a67244cbb0fabcc6e5dd2c.

Revert "PE & SR command subroutines and tests added"

This reverts commit 84304734796acb317bc0688459236799b444b76d.

Revert "Lumpy wrapper - removed read_params command"

This reverts commit 6ec2145b9288d4862a09a450be69e8f7e4ff749a.

Revert "lumpy stage2 - runs with multiple libraries"

This reverts commit b8b757456ba022a563f81e05eb2406bda60be2db.

Revert "Lumpy test1"

This reverts commit f7d6eb2cf5ca270672ce92bd0e78d40d160f019a.

Revert "initial commit"

This reverts commit 889b0615a5526b9e0f6f897e0ea9e386db2a71e2.
Merge branch 'copy' into gb_master