Commits for krish

v245_preview to v245_preview2 (2010-12-14 to 2010-12-21) v245

• added SOFT file for hg19.wgEncodeCshlShortRnaSeq
  • src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeCshlShortRnaSeq.hg19.soft - lines changed 407, context: html, text, full: html, text
• change RR path for C' and D sections as per #2100
  • src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes - lines changed 2, context: html, text, full: html, text
• fixed makefile
  • src/hg/encode/encodeMkGeoPkg/makefile - lines changed 2, context: html, text, full: html, text
• added vars for wgEncodeHudsonalphaMethylSeq
  • src/hg/encode/encodeValidate/config/expVars.ra - lines changed 3, context: html, text, full: html, text
• added support DGF (treated as DNase) and made provider optional (gives warning)
  • src/hg/encode/encodeMkGeoPkg/encodeMkGeoPkg - lines changed 17, context: html, text, full: html, text
• first draft of FASTA pair alignment to PSL converter
  • src/hg/fastaToPsl/fastaToPsl.c - lines changed 86, context: html, text, full: html, text
  • src/hg/fastaToPsl/makefile - lines changed 24, context: html, text, full: html, text
• test file for fastaToPsl
  • src/hg/fastaToPsl/tests/input/fa_seq_align.fa - lines changed 4, context: html, text, full: html, text
• fixed size bugs and makefile bug
  • src/hg/fastaToPsl/fastaToPsl.c - lines changed 86, context: html, text, full: html, text
  • src/hg/fastaToPsl/makefile - lines changed 24, context: html, text, full: html, text
  • src/hg/fastaToPsl/tests/input/fa_seq_align.fa - lines changed 4, context: html, text, full: html, text
  • src/utils/fastaToPsl/fastaToPsl.c - lines changed 95, context: html, text, full: html, text
  • src/utils/fastaToPsl/makefile - lines changed 24, context: html, text, full: html, text
  • src/utils/fastaToPsl/tests/input/fa_seq_align.fa - lines changed 4, context: html, text, full: html, text
• better logging and now iterates over targets
  • src/utils/fastaToPsl/fastaToPsl.c - lines changed 36, context: html, text, full: html, text