Commits for markd

v467_preview to v467_preview2 (2024-06-10 to 2024-06-17) v467

4ac9486a77f0ed4e87de2e946f29e203b354398b Thu Jun 13 13:56:46 2024 -0700

• added chainToBigChain command
  • src/hg/inc/bigChain.h - lines changed 3, context: html, text, full: html, text
  • src/hg/inc/bigLink.h - lines changed 70, context: html, text, full: html, text
  • src/hg/lib/bigChain.c - lines changed 12, context: html, text, full: html, text
  • src/hg/lib/bigLink.c - lines changed 152, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/pslToChain/pslToChain.c - lines changed 8, context: html, text, full: html, text
  • src/hg/pslToChain/tests/expected/error - lines changed 1, context: html, text, full: html, text
  • src/hg/pslToChain/tests/makefile - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/chainToBigChain/chainToBigChain.c - lines changed 128, context: html, text, full: html, text
  • src/hg/utils/chainToBigChain/makefile - lines changed 54, context: html, text, full: html, text
  • src/hg/utils/chainToBigChain/tests/expected/simpleTest.bigChain - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/chainToBigChain/tests/expected/simpleTest.bigChainLink - lines changed 11, context: html, text, full: html, text
  • src/hg/utils/chainToBigChain/tests/input/hg38.chrom.sizes - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/chainToBigChain/tests/input/hg38.mm10.test.chain - lines changed 19, context: html, text, full: html, text
  • src/hg/utils/chainToBigChain/tests/makefile - lines changed 26, context: html, text, full: html, text
  • src/hg/utils/makefile - lines changed 1, context: html, text, full: html, text

bfad6170abfeb8f1e3c38200acc6acb50ae70a5a Thu Jun 13 14:01:04 2024 -0700

• added pslToChain -fixStrand option to correct negative target strands rather than abort or ignore psl
  • src/hg/pslToChain/tests/expected/example3.chain - lines changed 114, context: html, text, full: html, text
  • src/hg/pslToChain/tests/input/mtor.psl - lines changed 2, context: html, text, full: html, text
  • src/hg/pslToChain/tests/input/mtor.psl.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

14f06e520a97d5e7d68df145edd88b642200e007 Thu Jun 13 22:56:52 2024 -0700

• fixed decoding of chain scores, which is a double in the data structures; it still displays as an int in hgc
  • src/hg/lib/chainNetDbLoad.c - lines changed 1, context: html, text, full: html, text