Commits for kent

v351_preview to v351_preview2 (2017-06-12 to 2017-06-19) v351

24e1ec0d7f5e51ab76208bda3a15a74e24d82e42 Fri Jun 9 20:22:14 2017 -0700

• We don't seem to need this utility. I didn't realize the protocols were actually in the idf.txt file.
  • src/hca/oneShot/arrayExpressFetchProtocols/arrayExpressFetchProtocols.c - lines changed 84, context: html, text, full: html, text
  • src/hca/oneShot/arrayExpressFetchProtocols/makefile - lines changed 3, context: html, text, full: html, text

c4b5aa62f38a281c0f78cd90f0e7444b9c9c0a72 Sat Jun 10 09:08:50 2017 -0700

• Adding logic to deal with paired end sets having two lines per read.
  • src/hca/fromArrayExpress/arrayExpressToTagStorm/arrayExpressToTagStorm.c - lines changed 71, context: html, text, full: html, text

e3829b31e46f467d1efed0717d212866dff860d8 Sun Jun 11 13:30:56 2017 -0700

• Adding in sample.donor.id from one place it could appear. Adding in project.uuid.
  • src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/arrayExpressStormToHcaStorm.c - lines changed 5, context: html, text, full: html, text

648839701eb8ba10b71f5d456f53a500e7803a2e Sun Jun 11 13:34:25 2017 -0700

• Generating uuids on sample.donor.id
  • src/hca/fromGeo/geoStormToHcaStorm/geoStormToHcaStorm.c - lines changed 46, context: html, text, full: html, text
  • src/hca/fromGeo/geoStormToHcaStorm/in.tags - lines changed 5, context: html, text, full: html, text

3250ccef57e0a9c28c586d67fc5facec46cb4449 Sun Jun 11 16:36:22 2017 -0700

• Making it so that lineFileUdcMayOpen will work with stdin in a pipe.
  • src/lib/linefile.c - lines changed 6, context: html, text, full: html, text

82f2f54a85ec37827f6dbf2a1b4a863db5260288 Sun Jun 11 23:52:46 2017 -0700

• A quick table maker.
  • src/tabFile/tabToHtml/makefile - lines changed 3, context: html, text, full: html, text
  • src/tabFile/tabToHtml/tabToHtml.c - lines changed 108, context: html, text, full: html, text
  • src/tabFile/tabToHtml/test.in - lines changed 5, context: html, text, full: html, text

076d54726c175d8fab099e10b8e83e3e89ef4eea Mon Jun 12 10:02:30 2017 -0700

• Adding title option
  • src/tabFile/tabToHtml/tabToHtml.c - lines changed 17, context: html, text, full: html, text

d156dc9e9c0f2cf8971bfa4d8ab777d43f743e7a Mon Jun 12 10:03:01 2017 -0700

• Adding tabToHtml to build.
  • src/tabFile/makefile - lines changed 2, context: html, text, full: html, text

2d15d70daa7bd690dc653169391f269bcb118f9b Mon Jun 12 10:04:33 2017 -0700

• Tolerating soft lines with nothing after symbol as they are common.
  • src/hca/fromGeo/geoToTagStorm/geoToTagStorm.c - lines changed 4, context: html, text, full: html, text

35cd53e650da0fb23cf7ade0b78dc06d75f4d7b7 Mon Jun 12 10:06:32 2017 -0700

• Adding barcode info even if it is not on root stanza since have some submissions that are only partly barcoded.
  • src/hca/fromGeo/hcaAddSrrFiles/hcaAddSrrFiles.c - lines changed 55, context: html, text, full: html, text

12dd2c658e0f18bc1060f644ae67acfe3f45d5af Mon Jun 12 10:07:43 2017 -0700

• Adding a manifest with file directory info instead of symbolically linking fastq files into submission dir.
  • src/hca/toHca/hcaStormToBundles/hcaStormToBundles.c - lines changed 151, context: html, text, full: html, text
  • src/hca/toHca/hcaStormToBundles/testIt - lines changed 1, context: html, text, full: html, text

66d8efb12fa1ec4d72a160c1ac3221ef42bbe1ee Mon Jun 12 13:27:38 2017 -0700

• Adding lane to assay.files.
  • src/hca/toHca/hcaStormToBundles/hcaStormToBundles.c - lines changed 49, context: html, text, full: html, text

9c9eab2cfea930f9a1a2e6ca74bac93345457ee1 Tue Jun 13 16:49:04 2017 -0700

• Moving the job of assigning uuids to this new program. It will avoid regenerating them if possible.
  • src/hca/toHca/hcaAddUuidToStorm/hcaAddUuidToStorm.c - lines changed 145, context: html, text, full: html, text
  • src/hca/toHca/hcaAddUuidToStorm/makefile - lines changed 4, context: html, text, full: html, text
  • src/inc/tagStorm.h - lines changed 8, context: html, text, full: html, text
  • src/lib/tagStorm.c - lines changed 13, context: html, text, full: html, text

5a74a4b4a4da39cb0b03cef3d6ad0561d20ee8c4 Tue Jun 13 16:50:19 2017 -0700

• Moving uuid generation to dedicated new program.
  • src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/arrayExpressStormToHcaStorm.c - lines changed 5, context: html, text, full: html, text
  • src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/makefile - lines changed 1, context: html, text, full: html, text
  • src/hca/fromGeo/geoStormToHcaStorm/geoStormToHcaStorm.c - lines changed 28, context: html, text, full: html, text
  • src/hca/fromGeo/geoStormToHcaStorm/makefile - lines changed 1, context: html, text, full: html, text

7fc011d226f55f9ad88f3b455b5b9a26aeb67567 Wed Jun 14 09:42:49 2017 -0700

• Respecting limit clause.
  • src/tagStorm/tagStormQuery/tagStormQuery.c - lines changed 3, context: html, text, full: html, text

2462760a02e47839b89ec632d331f78b894deef2 Wed Jun 14 09:47:00 2017 -0700

• Respecting limit clause.
  • src/tabFile/tabQuery/tabQuery.c - lines changed 5, context: html, text, full: html, text

f796875d8c3fd7460f3837f7151962a6f92bf324 Wed Jun 14 09:50:54 2017 -0700

• Respecting limit clause.
  • src/tabFile/tabQuery/tabQuery.c - lines changed 1, context: html, text, full: html, text

2ce283d49f98288b99b087b91936f2b548b78726 Wed Jun 14 09:54:26 2017 -0700

• Respecting limit clause.
  • src/tagStorm/tagStormQuery/tagStormQuery.c - lines changed 2, context: html, text, full: html, text

d07c9499caaab327d4104756436b37c021d8e7c4 Sun Jun 18 09:27:40 2017 -0700

• Changing '-' to '_' in field names.
  • src/hca/fromGeo/geoToTagStorm/geoToTagStorm.c - lines changed 2, context: html, text, full: html, text

0b149d763e8c04f7f84e321c4f7fe2f4f0b00370 Sun Jun 18 09:28:54 2017 -0700

• Moving uuid generation to a separate program.
  • src/hca/toHca/hcaStormToBundles/hcaStormToBundles.c - lines changed 7, context: html, text, full: html, text