fc825ca18eeb99e3807a73d23fd26b614807fa0f
markd
  Tue Oct 11 19:26:06 2022 -0700
add row number of output psl to pslMap mapInfo file to make it easy to sync up the two files

diff --git src/utils/pslMap/usage.txt src/utils/pslMap/usage.txt
index 84c4224..b70742f 100644
--- src/utils/pslMap/usage.txt
+++ src/utils/pslMap/usage.txt
@@ -39,26 +39,28 @@
      o mappingTName, mappingTStart, mappingTEnd - tName, etc of
        mapping psl
      o mappingStrand - strand of mapping psl
      o mappingId - chain id, or psl file row
      o mappedQName mappedQStart, mappedQEnd - qName, etc of
        mapped psl
      o mappedTName, mappedTStart, mappedTEnd - tName, etc of
        mapped psl
      o mappedStrand - strand of mapped psl
      o mappedAligned - number of aligned bases that were mapped
      o qStartTrunc - aligned bases at qStart not mapped due to
        mapping psl/chain not covering the entire soruce psl.
        This is from the start of the query in the positive
        direction.
      o qEndTrunc - similary for qEnd
+     o mappedPslLine - zero-based line number of the corresponding PSL line number
+       in outPsl.
    If the psl count not be mapped, the mapping* and mapped* columns are empty.
   -mappingPsls=pslFile - write mapping alignments that were used in
    PSL format to this file.  Transformations that were done, such as
    -swapMap, will be reflected in this file.  There will be a one-to-one
    correspondence of rows of this file to rows of the outPsl file.
   -simplifyMappingIds - simplifying mapping ids (inPsl target
    name and mapFile query name) before matching them. This
    first drops everything after the last `-', and then drops
    everything after the last remaining `.'.
   -verbose=n  - verbose output
      2 - show each overlap and the mapping